{"took": 8, "timed_out": false, "_shards": {"total": 5, "successful": 5, "skipped": 0, "failed": 0}, "hits": {"total": 492, "max_score": 15.110872, "hits": [{"_index": "study", "_type": "docs", "_id": "Jyx4KYoBQNpn7gUYhULS", "_score": 15.110872, "_source": {"Authoritative Source URL": "OSD-554/", "Flight Program": "International Space Station (ISS)", "Mission": {"End Date": "2020-03-17", "Start Date": "2019-11-02", "Name": "NG-12"}, "Material Type": "Cells", "Project Identifier": "Space Biofilms", "Accession": "OSD-554", "Identifiers": "GLDS-554", "Study Identifier": "OSD-554", "Study Protocol Name": "Treatment protocol     sample collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Analysis Data Transformation     GeneLab raw data processing protocol     GeneLab RNAseq data processing protocol", "Study Assay Technology Type": "RNA Sequencing (RNA-Seq)", "Acknowledgments": "", "Study Assay Technology Platform": "Illumina", "Study Person": {"Last Name": "Flores Zea", "Middle Initials": "", "First Name": "Pamela Luis"}, "Study Protocol Type": "treatment protocol     samle collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Analysis Data Transformation     data transformation     data transformation", "Space Program": "NASA", "Study Title": "Characterization of Biofilm Formation, Growth, and Gene Expression on Different Materials and Environmental Conditions in Microgravity (Gene expression of Pseudomonas aeruginosa biofilms)", "Study Factor Type": "growth environment     time     Space Flight", "Study Public Release Date": 1692835200.0, "Parameter Value": "", "thumbnail": "/geode-py/ws/studies/OSD-554/image", "Study Factor Name": "Growth Environment     Time     Spaceflight", "Study Assay Measurement Type": "transcription profiling", "Project Type": "Spaceflight Study", "Factor Value": "", "Data Source Accession": "", "Project Title": "", "Study Funding Agency": "This project was supported by the National Aeronautics and Space Administration under Grants No. 80NSSC17K0036 and 80NSSC21K1950.", "Study Protocol Description": "Bacterial strain and Inoculum: All the biofilm experiments were performed using Pseudomonas aeruginosa UCBPP-PA14 strain, which was kindly provided by Dr. George O\u2019Toole. This strain was selected for the project to replicate the column-and-canopy biofilm structure previously observed in microgravity by Kim et. al (2013) when growing PA14 biofilms over cellulose membrane. The results of the biofilms grown over cellulose membrane are reported in a separate publication (currently under revision). The bacterial inoculum was prepared with 6 ml of LBK media inoculated with PA14 and incubated at 37 C for 16 hours (final OD595 0.706). The overnight inoculum was diluted 1:100 with PBS (final OD595 0.001) to maintain cells in stasis. The diluted inoculum was used to load the second chamber of FPAs. Test surface preparation: Biofilms were grown on 1 cm2 material coupons of SS316 (MPPR-311-6), pSS316, and LIS. SS316 coupons were cleaned with 1% Liquinox (Alconox Cat. 1201-1). For the pSS316, clean SS316 coupons were passivated with citric acid (Sigma-Aldrich, Cat. C-8385). Preparation of LIS coupons (silicon wafer impregnated with silicone oil) has been described in detail previously. LIS coupons were not cleaned, to avoid removing the silicone oil, but they were prepared in sterile conditions. LIS\u2019s silicone oil layer (0.5-1.5 um in thickness) has no bactericidal nor growth boost effect on P. aeruginosa PA14. Sample Preparation: A total of 144 samples were prepared, 72 for flight and 72 for corresponding ground controls. All coupons were prepared in the same fashion. Each gravitational condition tested three material surfaces (SS316, pSS316, and LIS), three biofilm incubation times (1, 2, or 3 days), and two termination reagents (PFA for morphology analysis and RNAlater for transcriptomics) with four replicates per condition. Flight samples were sent to the ISS on the Cygnus NG-12 spacecraft. Double-sided tape (3M, Cat. 9731) was placed on the backside of the coupons to adhere them onto the inserts. Adhered coupons on inserts were installed in the FPAs and autoclaved. FPAs were loaded with 2.75 ml of sterile 1.18X LBK and the first chamber was closed with a second insert. The use of solid inserts prevents gas exchange and forces anaerobic growth of P. aeruginosa. The first chamber was incubated at 37 C for 24 hours as a contamination check. Afterwards, the second chamber was loaded with 0.5ml of the PA14 inoculum in stasis and closed with a rubber septum. The third and last chamber was filled with 1.75 ml of PFA or RNAlater and closed with a rubber septum. Eight FPAs with the three-chamber configuration were assembled into each GAP and transferred to 4 C. Spaceflight samples were launched in stasis (in PBS and at 4 C) to the ISS to avoid bacterial growth before microgravity conditions were achieved. Once in microgravity, astronauts Jessica Meir and Christina Koch activated the spaceflight samples by combining the first and second chambers of the FPAs, which introduced the inoculum into the culture media. Samples were incubated at 37 C inside BioServe\u2019s Space Automated Bioproduct Lab (SABL) for the designated incubation times (1, 2, or 3 days) in anaerobic conditions. At the end of incubation, the third chamber was introduced to fix (PFA) or preserve (RNAlater) the samples in microgravity, and samples were transferred to 4 C or -80 C, respectively, until unberthing. Fixed and preserved samples then returned to Earth at 4 C and -20 C, respectively. Once on Earth, samples were stored at 4 C (fixed) and -80 C (preserved) until sample processing. Ground samples were performed asynchronously, activating and terminating two hours later to replicate the order of flight procedures. The temperature profile of spaceflight samples was also reproduced for the ground samples. When spaceflight samples returned to Earth, all coupons (both flight and ground) were recovered from the FPAs and processed for morphology analysis (PFA) or transcriptomic analysis (RNAlater).     Samples preserved in RNAlater were thawed at room temperature and washed 3 times with 1ml PBS to get rid of any planktonic cells. PBS was removed and 1ml of fresh RNAlater was added. The samples were ultrasonicated for 15 min at 40 kHz, followed by 5 min of vortexing to detach biofilm bacterial cells from the surface materials.     RNA extraction was performed by University of Colorado Boulder BioFrontiers Sequencing Core and the sequencing by the Anschutz Genomics Shared Resource. The RNAlater with the suspended biofilm cells was centrifuged, and the pellet was used to extract total RNA using the Quick-RNA Fungal/Bacterial microprep Kit (Zymo Research Cat. R2010). RIN values were measured for the RNA extracted     RNA sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v3 (Takara Cat. 634485).     Paired-end sequencing was performed on Illumina NovaSeq 6000 with 40 million reads per sample.     Transcriptomic analysis was performed on CU Boulder\u2019s RMACC Summit supercomputing cluster. Raw sequencing files were checked for quality control using FastQC (version 0.11.9) and multiQC (version 1.0.dev0). Then Illumina adapter contamination was eliminated using Trimgalore (version 0.6.6) with cutadapt (version 2.6), after which quality control was performed again. Trimmed reads were mapped to PA14 rRNA sequences to remove the\ncontamination, the resulting unmapped reads were then mapped to the Ensembl Bacteria reference genome of Pseudomonas aeruginosa UCBPP-PA14 (accession number GCA_000014625), both mapping steps were performed using Bowtie2 (version 2.4.4). The mapping results were sorted, indexed, and converted from .sam files to .bam files using SAMtools (version 1.11). The reads per gene were counted with Feature Counts (Rsubread package version 2.8.2), and differential gene expression analyses were done in an R (version 4.1.1) with DESeq2 (version 1.34.0). Pathways enrichment analyses were performed online using ESKAPE Act PLUS and the whole list of DEG (including \u22642-fold change genes) per condition as input.     Fastq format was checked with fastq_utils v0.25.1. Quality assessment of reads was performed with FastQC v0.12.1 and reports were combined with MultiQC v1.26. rRNA percentages of reads were estimated with the 'hts_SeqScreener' program of htstream v1.4.1 screened against a fasta file of Pseudomonas rRNA sequences retrieved from NCBI on 08-Jan-2026.     Data were processed as described in GL-DPPD-7115 (https://github.com/nasa/GeneLab_Data_Processing/blob/master/RNAseq/Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md), using NF_RCP version 2.1.0 (https://github.com/nasa/GeneLab_RNASeq_Workflow/tree/NF_RCP_2.1.0). In short, raw fastq files were filtered using Trim Galore! (version 0.6.10) powered by Cutadapt (version 4.2). Trimmed fastq file quality was evaluated with FastQC (version 0.12.1), and MultiQC (version 1.26) was used to generate MultiQC reports. Pseudomonas Aeruginosa Bowtie 2 reference was built using Bowtie 2 (version 2.5.4), NCBI genome assembly ASM1462v1 (GCF_000014625.1_ASM1462v1_genomic.fna) and the following gtf annotation file: GCF_000014625.1_ASM1462v1_genomic.gtf. Trimmed reads were aligned to the Pseudomonas Aeruginosa Bowtie 2 reference with Bowtie 2 (version 2.5.4) and alignment log files were compiled with MultiQC (version 1.26). Aligned reads were assessed for strandedness using RSeQC infer_experiment.py (version 5.0.4), gene body coverage using RSeQC geneBody_coverage.py (version 5.0.4), inner distance was assessed using RSeQC inner_distance.py (version 5.0.4), and distribution of RNA features using RSeQC read_distribution.py (version 5.0.4). Aligned reads from all samples were quantified using featureCounts from the Subread package (version 2.0.8), with isStrandSpecific set to 2 and featureCounts log files were compiled with MultiQC (version 1.26). To create a set of rRNA-removed quantification data, gene IDs mapping to ribosomal RNA (rRNA) were removed from the featureCounts gene count data. Both the original set of featureCounts quantification data and the rRNA-removed data were subject to differential gene expression analysis as follows. A runsheet was generated with dp_tools (version 1.3.8) and the runsheet and quantification data were imported to R (version 4.4.2) and normalized with DESeq2 (version 1.46.0) median of ratios method. Normalized gene counts were subject to differential expression analysis. Differential expression analysis was performed in R (version 4.4.2) using DESeq2 (version 1.46.0); all groups were compared pairwise using the Wald test and the likelihood ratio test was used to generate the F statistic p-value. Gene annotations were assigned using the custom annotation tables generated in-house as detailed in GL-DPPD-7110-A (https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable-A_1.1.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A.md), with STRINGdb (version 2.16.4), and PANTHER.db (version 1.0.12).", "Experiment Platform": "BioServe Space Technologies' Fluid Processing Apparatus (FPA)", "Characteristics": "", "Study Grant Number": "", "Study Publication Author List": "Zea Luis  McLean Robert J.C.  Rook Tony A.  Angle Geoffrey  Carter D. Layne  Delegard Angela  Denvir Adrian  Gerlach Robin  Gorti Sridhar  McIlwaine Doug  Nur Mononita  Peyton Brent M.  Stewart Philip S.  Sturman Paul  Velez Justiniano Yo Ann     Zea Luis  Nisar Zeena  Rubin Phil  Cortes\u00e3o Marta  Luo Jiaqi  McBride Samantha A.  Moeller Ralf  Klaus David  M\u00fcller Daniel  Varanasi Kripa K.  Muecklich Frank  Stodieck Louis     Flores  P.  Zea  L.     Hupka Megan  Kedia Raj  Schauer Rylee  Shepard Brooke  Granados-Presa Mar\u00eda  Vande Hei Mark  Flores Pamela  Zea Luis     Flores Pamela  Schauer Rylee  McBride Samantha A.  Luo Jiaqi  Hoehn Carla  Doraisingam Shankini  Widhalm Dean  Chadha Jasmin  Selman Leah  Mueller Daniel Wyn  Floyd Shannon  Rupert Mark  Gorti Sridahr  Reagan Shawn  Varanasi Kripa K.  Koch Christina  Meir Jessica U.  Muecklich Frank  Moeller Ralf  Stodieck Louis  Countryman Stefanie  Zea Luis     Flores  P     Hupka  Megan     Flores  P.  McBride  S. A.  Galazka  J.  Varanasi  K.  and Zea  L     Flores Pamela  McBride Samantha A.  Galazka Jonathan M.  Varanasi Kripa K.  Zea Luis", "Project Link": "", "Study Publication Title": "Potential biofilm control strategies for extended spaceflight missions     Design of a spaceflight biofilm experiment     SPACE BIOFILMS \u2013 AN OVERVIEW OF THE MORPHOLOGY AND GENE EXPRESSION OF PSEUDOMONAS AERUGINOSA BIOFILMS GROWN ON BOARD THE INTERNATIONAL SPACE STATION     Morphology of Penicillium rubens Biofilms Formed in Space     Preparation for and performance of a Pseudomonas aeruginosa biofilm experiment on board the International Space Station     Effects of Spaceflight on Morphology and Gene Expression of Biofilms of Pseudomonas aeruginosa Grown over Different Spaceflight- and Medically-Relevant Materials     Penicillium rubens Biofilms Formed in Space on Seven Different Materials \u2013 Biomass, Surface Area, and Thickness Comparisons With Respect to Earth Controls     Lubricant-impregnated surface minimizes biofilm formation of Pseudomonas aeruginosa in spaceflight     Biofilm formation of Pseudomonas aeruginosa in spaceflight is minimized on lubricant impregnated surfaces", "Managing NASA Center": "", "Study Description": "Microorganisms' natural ability to live as organized multicellular communities \u2013 also known as biofilms \u2013 provides them with unique survival advantages. For instance, biofilms are protected against environmental stresses thanks to their extracellular matrix, which could contribute to persistent infections after treatment. Biofilms are also capable of strongly attaching to surfaces, where their metabolism byproducts could lead to surface material degradation. Furthermore, microgravity can alter biofilm behavior in unexpected ways, making the presence of biofilms in space a risk for both astronauts and spaceflight hardware. Despite the efforts to eliminate microorganism contamination from spacecrafts surfaces, it is impossible to prevent human-associated bacteria or fungus from eventually establishing biofilm surface colonization. Nevertheless, by understanding the changes that biofilms undergo in microgravity, it is possible to identify key differences and pathways that could be targeted to significantly reduce biofilm formation. The Space Biofilms project, performed at the International Space Station, contributes to such understanding by characterizing the morphology and gene expression of bacterial and fungal biofilms formed in microgravity with respect to ground controls. Pseudomonas aeruginosa was used as model organism for the bacterial morphology and transcriptomic studies, while Penicillium rubens was used for the fungal morphology study. Bacterial biofilm formation was characterized at one, two, and three days of incubation (37C) over six different materials: stainless steel 316, passivated stainless steel 316, a lubricant impregnated surface (LIS), catheter grade silicone with and without a linear microtopography, and cellulose membrane.", "organism": "Pseudomonas aeruginosa", "Data Source Type": "cgene", "ESA Acronym": ""}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>Space</em> Biofilms", "growth environment     time     <em>Space</em> Flight", "The <em>Space</em> Biofilms project, performed at the International <em>Space</em> Station, contributes to such understanding", "<em>cgene</em>"]}}, {"_index": "study", "_type": "docs", "_id": "D9_6g4QB28eYt3lGL7b9", "_score": 12.2163925, "_source": {"Space Program": "NASA", "Flight Program": "Internation Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "During the course of the Veggie project (a vegetable production system flown onboard the International Space Station [ISS] to study the effects of the space environment on plant growth and function), Zinnia hybrida plants became afflicted with a foliar, stem, and root rot disease caused by the fungus Fusarium oxysporum. Isolates were cultured from the leaf (VEG-01C1) and the root (VEG-01C2) of these infected plants.     The whole-genome sequences were paired-end sequenced (2 x 100 bp) on the Illumina HiSeq platform with a 350-bp insert size.     Postprocessed reads were de novo assembled with ABySS version 2.0.2 using k-mer sizes of 80 (VEG-01C1) and 88 (VEG-01C2).", "Material Type": "Cells", "Study Identifier": "OSD-177", "Study Person": {"First Name": "Kasthuri Camilla", "Middle Initials": "", "Last Name": "Venkateswaran Urbaniak"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Ames Research Center (ARC)", "Data Source Type": "cgene", "Mission": {"Start Date": "18-Apr-2014", "End Date": "18-May-2014", "Name": "SpaceX-3"}, "Study Grant Number": "19-12829-26", "Experiment Platform": "Vegetable Production System (VEGGIE)", "Study Factor Name": "Spaceflight", "Study Publication Author List": "Urbaniak C  Massa G  Hummerick M  Khodadad C  Schuerger A  Venkateswaran K", "Study Assay Technology Platform": "Illumina", "Authoritative Source URL": "OSD-177/", "Project Identifier": "VEGGIE", "thumbnail": "/geode-py/ws/studies/OSD-177/image", "Project Title": "'Veggie' Vegetable Production System Proof of Concept Flight", "Study Public Release Date": 1522368000.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13890", "Study Publication Title": "Draft Genome Sequences of Two Fusarium oxysporum Isolates Cultured from Infected Zinnia hybrida Plants Grown on the International Space Station.", "organism": "Fusarium oxysporum", "Accession": "OSD-177", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Draft Genome Sequences of Two Fusarium oxysporum Isolates Cultured from Infected Zinnia hybrida Plants Grown on the International Space Station", "Study Protocol Type": "sample collection     nucleic acid sequencing     sequence assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "This research was funded by a 2012 Space Biology NNH12ZTT001N grant number 19-12829-26 under Task Order NNN13D111T", "Study Factor Type": "Space Flight", "Factor Value": "", "Study Description": "Draft genome sequences of two Fusarium oxysporum isolates cultured from infected Zinnia hybrida plants grown on the International Space Station", "Study Protocol Name": "sample collection     nucleic acid sequencing     sequence assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-177", "Data Source Accession": "PRJNA437451"}, "highlight": {"all": ["Internation <em>Space</em> Station (ISS)", "During the course of the Veggie project (a vegetable production system flown onboard the International <em>Space</em>", "Station [ISS] to study the effects of the <em>space</em> environment on plant growth and function), Zinnia hybrida", "<em>cgene</em>", "<em>Space</em> Flight"]}}, {"_index": "study", "_type": "docs", "_id": "4d_6g4QB28eYt3lGLLV-", "_score": 11.73589, "_source": {"Space Program": "NASA", "Flight Program": "Internation Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Purified culture were subjected to DNA extraction By Zymo using ZymoBIOMICS DNA Magbead Kit according to the manufacturer's instructions.     The Shotgun library was prepared by use of illuminq Nextera Flex Protocol (Singh et al, 2018).     A pair-end sequencing was performed on the DNA fragments with a NovaSeq 6000 s4 flowcell PE 2x150 platform. The sequenced data was saved in a FASTQ format.     The FASTQ files were cleaned and assembled by SPAdes (v3.11.1) (Bankevich et al, 2012), and the contigs generated were scaffolded in a FASTA format.     During the microbial tracking-1 (MT-1) investigation to characterize airborne and surface-associated microbial population aboard the International Space Station (ISS), Samples were collected from 8 locations across the ISS across 2 flights, and ground samples were collected from Space-X on the ground. A sterile polyester wipe premoistened with Phosphate buffer saline (PBS) was used to collect the samples from various areas across those 8 locations, and the details and description of the sample collection and cultivation have already been reported in Checinska et al, 2019 and Singh et al, 2018.", "Material Type": "Cells", "Study Identifier": "OSD-293", "Study Person": {"First Name": "Kasthuri Robert", "Middle Initials": "", "Last Name": "Venkateswaran Daudu"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Jet Propulsion Laboratory (JPL)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "OSD-293/", "Project Identifier": "ISS-MO", "thumbnail": "/geode-py/ws/studies/OSD-293/image", "Project Title": "Microbial Tracking-1A", "Study Public Release Date": 1589500800.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13629#data", "Study Publication Title": "", "organism": "Rhodotorula mucilaginosa", "Accession": "OSD-293", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Draft Genome sequences of Rhodotorula mucilaginosa isolated from the International space station", "Study Protocol Type": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "Draft Genome sequences of Rhodotorula mucilaginosa isolated from the International space station.", "Study Protocol Name": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-293", "Data Source Accession": "PRJNA625575  PRJNA628952"}, "highlight": {"all": ["Internation <em>Space</em> Station (ISS)", "<em>cgene</em>", "Draft Genome sequences of Rhodotorula mucilaginosa isolated from the International <em>space</em> station", "<em>Space</em> Flight     strain", "Draft Genome sequences of Rhodotorula mucilaginosa isolated from the International <em>space</em> station."]}}, {"_index": "study", "_type": "docs", "_id": "Jt_6g4QB28eYt3lGTrdM", "_score": 11.5688305, "_source": {"Space Program": "NASA", "Flight Program": "Internation Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Samples were obtained from one location across the ISS which which is the Cupola. A sterile polyester wipe pre-moistened with Phosphate buffer saline (PBS) was used to collect the samples from various areas across these 5 locations. The description of the sample collection and cultivation have already been reported in Checinska et al, 2019 and Singh et al, 2018.     Purified culture were subjected to DNA extraction By Zymo using ZymoBIOMICS DNA Magbead Kit according to the manufacturer's instructions.     The Shotgun library was prepared by use of Illumina Nextera Flex Protocol (Singh et al, 2018).     A pair-end sequencing was performed on the DNA fragments with a NovaSeq 6000 s4 flowcell PE 2x150 platform. The sequenced data was saved in a FASTQ format.     Sequence Assembly: The FASTQ files were cleaned and assembled by SPAdes (v3.11.1) (Bankevich et al, 2012), and the contigs generated were scaffolded in a FASTA format.", "Material Type": "Cells", "Study Identifier": "GLDS-306", "Study Person": {"First Name": "Kasthuri Achintya", "Middle Initials": "", "Last Name": "Venkateswaran Bharadwaj"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Jet Propulsion Laboratory (JPL)", "Data Source Type": "cgene", "Study Grant Number": "19-12829-26", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Experiment Platform": "", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "Singh Nitin K.  Lavire C\u00e9line  Nesme Joseph  Vial Ludovic  Nesme Xavier  Mason Christopher E.  Lassalle Florent  Venkateswaran Kasthuri", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "GLDS-306/", "Project Identifier": "ISS-MO (MT-1B)", "thumbnail": "/genelab/img/GLDS306__study_image.png", "Project Title": "ISS Microbial Observatory (Microbial Tracking-1B)", "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13630", "Study Public Release Date": 1663200000.0, "Study Publication Title": "Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.", "organism": "Agrobacterium genomosp. 3", "Accession": "OSD-306", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Draft Genome Sequences of novel Agrobacterium genomospecies 3 Associated from the International Space Station", "Study Protocol Type": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "This research was funded by a 2012 Space Biology NNH12ZTT001N grant nos. 19-12829-26 under Task Order NNN13D111T award to Dr. Kasthuri Venkateswaran.", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "The whole-genome sequences (WGS) of three pathogenic bacterial strains collected from the International Space Station (ISS) were generated and identified as being part of Class Alphaproteobacteria. The WGS studies would enable further genomic/biochemical characterization of taxa for these bacteria that have been subjected to the microgravity conditions of space.", "Study Protocol Name": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-306", "Data Source Accession": "PRJNA641116"}, "highlight": {"all": ["Internation <em>Space</em> Station (ISS)", "<em>cgene</em>", "Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International <em>Space</em> Station", "Draft Genome Sequences of novel Agrobacterium genomospecies 3 Associated from the International <em>Space</em>", "<em>Space</em> Flight     strain"]}}, {"_index": "study", "_type": "docs", "_id": "Ld_6g4QB28eYt3lGMrZC", "_score": 11.225164, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "          The whole-genome sequences of these eight fungal strains were obtained by shotgun sequencing performed on an Illumina HiSeq2500 platform with a paired-end module.     The NGS QC toolkit version 2.3 was used to filter the data for high-quality vector- and adaptor-free reads for genome assembly (cutoff read length for high quality: 80%; cutoff quality score: 20). High-quality vector-filtered reads were used for assembly with the MaSuRCA genome assembler (k-mer size=70).     We thank the implementation team of the Center for Advanced Study in Space and Duane\nPierson, Johnson Space Center for providing the A. niger\nstrain. The other fungal strains are maintained at Lawrence Berkeley National Laboratory.", "Material Type": "Soil     Wipes", "Study Identifier": "OSD-132", "Study Person": {"First Name": "Nitin Adriana Jillian Clay Tamas Kasthuri", "Middle Initials": "K", "Last Name": "Singh Blachowicz Romsdahl Wang Torok Venkateswaran"}, "ESA Acronym": "", "Acknowledgments": "We thank the implementation team of the Center for Advanced Study in Space and Duane Pierson, Johnson Space Center for providing the A. niger strain. The other fungal strains are maintained at Lawrence Berkeley National Laboratory.", "Managing NASA Center": "JPL", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "radiation", "Study Publication Author List": "Singh NK  Blachowicz A  Romsdahl J  Wang C  Torok T  Venkateswaran K.", "Study Assay Technology Platform": "Illumina", "Authoritative Source URL": "OSD-132/", "Project Identifier": "", "thumbnail": "/geode-py/ws/studies/OSD-132/image", "Project Title": "", "Study Public Release Date": 1492041600.0, "Project Link": "", "Study Publication Title": "Draft Genome Sequences of Several Fungal Strains Selected for Exposure to Microgravity at the International Space Station.", "organism": "Beauveria bassiana     Aspergillus niger     Aspergillus terreus     Aureobasidium pullulans     Cladosporium cladosporioides     Fusarium solani     Trichoderma virens     Cladosporium sphaerospermum", "Accession": "OSD-132", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Whole genome sequencing and assembly of Eukaryotic microbes isolated from ISS environmental surface, Kirovograd region soil, Chernobyl Nuclear Power Plant and Chernobyl Exclusion Zone", "Study Protocol Type": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "Part of the research described in this publication was carried out at the Jet Propulsion Laboratory (JPL), California Institute of Technology, under a contract with NASA. This research was supported by the JPL Advanced Concept Development fund awarded to K.V. that funded a student fellowship to A.B. Part of the research described in this publication was carried out at Lawrence Berkeley National Laboratory (T.T.) and the University of Southern California (C.W.), which funded a student fellowship to J.R.", "Study Factor Type": "Radiation", "Factor Value": "", "Study Description": "The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.", "Study Protocol Name": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-132", "Data Source Accession": "PRJNA355122"}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "We thank the implementation team of the Center for Advanced Study in <em>Space</em> and Duane\nPierson, Johnson", "<em>Space</em> Center for providing the A. niger\nstrain.", "<em>Space</em> Center for providing the A. niger strain.", "<em>cgene</em>"]}}, {"_index": "study", "_type": "docs", "_id": "7d_6g4QB28eYt3lGRrYg", "_score": 11.163609, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Genomic DNA from isolated colonies was extracted using the ZymoBIOMICS DNA MagBead kit according to the manufacturer's instructions.     Libraries for whole-genome shotgun sequencing were prepared using the Illumina Nextera DNA Flex Library Prep as in Be et al. 2017.     Libraries were sequenced using the NovaSeq 6000 S4 flow cell paired-end 2x150-bp platform.     Sequencing reads were quality-filtered and trimmed, and adapter sequences removed, using fastQC v0.11.7 and fastp v02.20.0, reads were assembled into scaffolds using SPAdes v3.11.1 and assembly quality was determined using Quast v5.0.2.     Samples were collected using pre-moistened polyester from 8 surfaces on the ISS: cupola, Waste and Hygiene Compartment (WHC), crew quarters, Advanced Resistive Exercise Device (ARED), Overhead 4, dining table, Permanent Multipurpose Module (PMM) 1, and Lab 3 Overhead. Wipes were stored at 4 degrees C until return to Earth. Upon return to Earth, wipes were shaken in PBS (Phosphate-buffered saline). PBS was concentrated and plated onto R2A and PDA (25 degrees C, 7 days) and blood agar (37 degrees C, 3 days). Details of sampling locations and methods have been reported in Checinska et al, 2019 and Singh et al, 2018.", "Material Type": "Cells", "Study Identifier": "OSD-400", "Study Person": {"First Name": "Anna Camilla Nitin John Jason Marilyne Niamh Jos Chris Kasthuri", "Middle Initials": " K M B E", "Last Name": "Simpson Urbaniak Singh Bateh Wood Debieu O'Hara Houbraken Mason Venkateswaran"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Ames Research Center (ARC)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "International Space Station (ISS)", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "", "Study Assay Technology Platform": "Illumina", "Authoritative Source URL": "OSD-400/", "Project Identifier": "MT-2 (ISS-MOP)", "thumbnail": "/geode-py/ws/studies/OSD-400/image", "Project Title": "International Space Station Microbial Observatory of Pathogenic Virus Bacteria and Fungi Project (ISS_MOP)", "Study Public Release Date": 1627344000.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13751", "Study Publication Title": "", "organism": "Aspergillus unguis     Cladosporium sphaerospermum     Rhodotorula mucilaginosa     Penicillium palitans     Aureobasidium pullulans     Penicillium rubens     Penicillium corylophilum     Cladosporium cladosporioides     Penicillium citrinum     Fusarium annulatum     Fusarium veterinarium", "Accession": "OSD-400", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Draft Genomes of Fungi Isolated from the International Space Station during the Microbial Tracking-2 Experiment", "Study Protocol Type": "Nucleic acid extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly     sample collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "2014 Space Biology Flight (ILSRA) NNH14ZTT002N", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "Draft genomes of fungi isolated from different surfaces on the International Space Station, as part of the Microbial Tracking 2 mission (ISS-MOP).", "Study Protocol Name": "Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly     sample collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-400", "Data Source Accession": "PRJNA723004"}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>cgene</em>", "International <em>Space</em> Station (ISS)", "2014 <em>Space</em> Biology Flight (ILSRA) NNH14ZTT002N", "<em>Space</em> Flight     strain"]}}, {"_index": "study", "_type": "docs", "_id": "Kt_6g4QB28eYt3lGMrYS", "_score": 11.102325, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Genomic DNA from isolated colonies was extracted using the ZymoBIOMICS DNA MagBead kit according to the manufacturer's instructions.     Libraries for whole-genome shotgun sequencing were prepared using the Illumina Nextera DNA Flex Library Prep as in Be et al. 2017.     Libraries were sequenced using the NovaSeq 6000 S4 flow cell paired-end 2x150-bp platform.     Sequencing reads were quality-filtered and trimmed, and adapter sequences removed, using fastQC v0.11.7 and fastp v02.20.0, reads were assembled into scaffolds using SPAdes v3.11.1 and assembly quality was determined using Quast v5.0.2.     Samples were collected using pre-moistened polyester from 8 surfaces on the ISS: cupola, Waste and Hygiene Compartment (WHC), crew quarters, Advanced Resistive Exercise Device (ARED), Overhead 4, dining table, Permanent Multipurpose Module (PMM) 1, and Lab 3 Overhead. Upon return to Earth, wipes were shaken in PBS. PBS was concentrated and plated onto R2A and PDA (25 degrees C, 7 days) and blood agar (37 degrees C, 3 days). Details of sampling locations and methods have been reported in Checinska et al, 2019 and Singh et al, 2018.", "Material Type": "Cells", "Study Identifier": "OSD-361", "Study Person": {"First Name": "Anna Kasthuri Camilla Nitin Jason Marilyne Niamh Christopher", "Middle Initials": " J K M B E", "Last Name": "Simpson Venkateswaran Urbaniak Urbaniak Wood Debieu O\u2019Hara Mason"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Ames Research Center (ARC)", "Data Source Type": "cgene", "Mission": {"Start Date": "06/03/2017", "End Date": "07/03/2017", "Name": "SpaceX-11"}, "Study Grant Number": "80NSSC18K0113", "Experiment Platform": "International Space Station (ISS)", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "", "Study Assay Technology Platform": "Illumina", "Authoritative Source URL": "OSD-361/", "Project Identifier": "Microbial Tracking-2, ISS-MOP", "thumbnail": "/geode-py/ws/studies/OSD-361/image", "Project Title": "International Space Station Microbial Observatory of Pathogenic Virus Bacteria and Fungi Project", "Study Public Release Date": 1618358400.0, "Project Link": "https://nlsp.nasa.gov/view/lsdapub/lsda_experiment/2df8e010-cb73-5553-ac25-53b2de12c5ed", "Study Publication Title": "", "organism": "Micrococcus luteus     Acinetobacter pittii     Bacillus horneckiae     Staphylococcus warneri     Methylobacterium organophilum     Staphylococcus caprae     Kocuria palustris     Pseudoclavibacter alba     Pseudomonas granadensis     Staphylococcus epidermidis     Staphylococcus saprophyticus     Pseudomonas fulva     Kocuria indica     Staphylococcus capitis", "Accession": "OSD-361", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "ISS Surfaces Bacterial Genomes from MT-2 (ISS-MOP)", "Study Protocol Type": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "2014 Space Biology Flight (ILSRA) NNH14ZTT002N", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "Draft genomes of various bacterial phyla isolated from different locations on the International Space Station as part of the Microbial Tracking 2 mission (ISS-MOP).", "Study Protocol Name": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-361", "Data Source Accession": "PRJNA690512"}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>cgene</em>", "International <em>Space</em> Station (ISS)", "2014 <em>Space</em> Biology Flight (ILSRA) NNH14ZTT002N", "<em>Space</em> Flight     strain"]}}, {"_index": "study", "_type": "docs", "_id": "iIle7ZUBT6_JreR4ljfq", "_score": 10.889875, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "The genomic DNA was extracted by Zymo using ZymoBIOMICS DNA Magbead Kit according to the manufacturer's instructions.     The shotgun libraries were prepared using the Illumina Nextera Flex protocol. Amplified genomic DNA fragments were indexed and pooled in a 384 plex configuration.     Paired-end sequencing was performed on a NovaSeq 6000 S4 flowcell PE 2X150 platform.     Quality analysis was performed with the software FastQC (v0.11.7) to validate the quality of the raw sequencing data. For quality control, adapter trimming and quality filtering were performed using the software fastp (v0.20.0), and then the cleaned sequences were assembled using SPAdes (v3.11.1).     The strains used for this whole-genome sequencing (WGS) project were collected from 5 predefined locations in the ISS across one flight, and then transported to NASA Jet Propulsion Laboratory for further analysis. Each sample was aseptically transferred to a 500mL bottle containing 200mL of phosphate-buffered saline, vigorously shaken, and concentrated using an InnovaPrep (Drexel, MO) CP-150 concentrated pipette. A 100 ul aliquot from each sample was plated on R2A/Blood Agar with 100 ug/ml chloramphenicol. The plates were incubated at 37C for 7 days. A colony obtained was re-streaked on R2A/Blood Agar plates, incubated at 37C for 3 days, and a single colony was collected for DNA extraction.", "Material Type": "Cells", "Study Identifier": "OSD-309", "Study Person": {"First Name": "Kasthuri Samuel", "Middle Initials": "", "Last Name": "Venkateswaran Solomon"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "OSD-309/", "Project Identifier": "ISS-MO (MT-1C)", "thumbnail": "/geode-py/ws/studies/OSD-309/image", "Project Title": "ISS Microbial Observatory (Microbial Tracking-1C)", "Study Public Release Date": 1597190400.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13671", "Study Publication Title": "", "organism": "Klebsiella quasipneumoniae     Klebsiella pneumoniae     Klebsiella aerogenes", "Accession": "OSD-309", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Comparative Genomic Analysis of Klebsiella Exposed to Various Space Conditions at the International Space Station", "Study Protocol Type": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "Due to the bacteria's evolved resistance to radiation, Klebsiella poses a great threat to not only planetary protection, but also to the integrity of future biological experiments in outer space. While previous literature has shown varying degrees of sensitivity in klebsiella to a high radiation environment, not much is known about the genetic component that yields this microbial advantage. Our research objective is to pinpoint the genetic advantage some Klebsiella species acquire as they are exposed to a space-like environment through a comparison of whole genomes sequences to better control microbial contamination onboard the ISS.", "Study Protocol Name": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-309", "Data Source Accession": ""}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>cgene</em>", "Comparative Genomic Analysis of Klebsiella Exposed to Various <em>Space</em> Conditions at the International <em>Space</em>", "<em>Space</em> Flight     strain", "not only planetary protection, but also to the integrity of future biological experiments in outer <em>space</em>"]}}, {"_index": "study", "_type": "docs", "_id": "-9_6g4QB28eYt3lGLrVI", "_score": 10.835321, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "A biomass of approximately 1 ug wet weight was collected for each strain and pooled for DNA extraction. Total nucleic acid extraction was carried out by lysing the cells using Bertin Precelys bead-beater followed by DNA extraction using ZymoBIOMICS 96 MagBead DNA kit (Lysis tubes) (Zymo Research, USA).     DNA library was prepared using Illumina Nextera Flex Protocol as per Illumina document number 1000000025416 v07. The initial amount of DNA for library preparation was quantified and depending on the input DNA concentration, 5-12 cycles of PCR were carried out to normalize the output. The amplified genomic DNA fragments were indexed and pooled in 384 plex configuration.     Whole-genome shotgun sequencing was performed on a NovaSeq 6000 S4 flowcell PE 2x150 platform with a paired-end module.     The data was filtered with NGS QC Toolkit v2.3 for high-quality (HQ) vector- and adaptor free reads for genome assembly (cutoff read length for HQ, 80%; cutoff quality score, 20). The number of filtered reads obtained were used for assembly with SPAdes 3.14.0 genome assembler (k-mer size- 32-72 bases). Default parameters were used for all the software except where otherwise noted.     Briefly, samples collected from the ISS were processed, 100 ul of each dilution was plated on Reasoner's 2A agar (R2A) and incubated at 25C for 7 days. The single colony obtained was re-streaked on R2A plates and incubated at 25C for 3 days.", "Material Type": "Cells", "Study Identifier": "OSD-300", "Study Person": {"First Name": "Kasthuri Swati", "Middle Initials": "", "Last Name": "Venkateswaran Bijlani"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Ames Research Center (ARC)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "International Space Station (ISS)", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "Bijlani S  Singh NK  Wood JM  Debieu MM  O'Hara NB  Mason CE  Wang CCC  and Venkateswaran K", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "OSD-300/", "Project Identifier": "ISS-MO (MT-1A)", "thumbnail": "/geode-py/ws/studies/OSD-300/image", "Project Title": "ISS Microbial Observatory (Microbial Tracking-1A)", "Study Public Release Date": 1609459200.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13629", "Study Publication Title": "Draft Genome Sequences of Members of the family Methylobacteriaceae Associated with the International Space Station", "organism": "Methylobacterium sp.     Methylorubrum rhodesianum", "Accession": "OSD-300", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Draft Genome Sequences of Members of the family Methylobacteriaceae Associated with the International Space Station", "Study Protocol Type": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "This research was funded by a 2012 Space Biology NNH12ZTT001N grant nos. 19-12829-26 under Task Order NNN13D111T award to KV, which was also subcontracted to CCCW, and funded post-doctoral fellowship for SB.", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "Draft Genome Sequences of isolates belonging to family Methylobacteriaceae Isolated from the International Space Station", "Study Protocol Name": "nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly     sample collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-300", "Data Source Accession": "PRJNA634337"}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>cgene</em>", "International <em>Space</em> Station (ISS)", "This research was funded by a 2012 <em>Space</em> Biology NNH12ZTT001N grant nos. 19-12829-26 under Task Order", "<em>Space</em> Flight     strain"]}}, {"_index": "study", "_type": "docs", "_id": "8d_6g4QB28eYt3lGRrZ9", "_score": 10.821463, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Isolates were collected from surfaces of the ISS using the Surface Sampler Kit (https://lsda.jsc.nasa.gov/Hardware/hardw/670), isolated on tryptic soy agar (TSA) plates, and stored at -80C in 15% glycerol. Isolates from the ISS potable water dispenser were obtained by filtering sample from both the ambient and hot water outlets of the potable water system through a microbial capture device. The device filter was then placed on R2A agar and then stored at -80C in 15% glycerol.     DNA was extracted from isolates using a phenol/chloroform protocol and quantified using a nanodrop and run on a gel to inspect quality.     Microbial-isolate DNA library preparation was performed with the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer\u2019s instructions, but using half the standard reaction volumes.      Sequencing was performed on Illumina's NextSeq 500 platform with 2x150 paired-end reads.     Adapters were searched and removed with bcl2fastq2 Conversion Software v2.17 (Illumina). Quality trimming and filtering was performed with Trimmomatic v0.39 (Bolger et al., 2014) using a sliding window setting of 5:20 and filtering out reads shorter than 100 bp after trimming. Assemblies were performed using SPAdes v3.12.0 (Bankevich et al., 2012) with default settings.", "Material Type": "Cells", "Study Identifier": "GLDS-372", "Study Person": {"First Name": "Michael Aubrie", "Middle Initials": "D", "Last Name": "Lee O'Rourke"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "Data Source Type": "cgene", "Study Grant Number": "NNH16ZTT001N-MOBE  80NSSC17K0035", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Experiment Platform": "International Space Station (ISS)", "Study Factor Name": "Spaceflight     Collection Date     Sample Location", "Study Publication Author List": "Lee Michael D.  O'Rourke Aubrie  Lorenzi Hernan  Bebout Brad M.  Dupont Chris L.  Everroad R. Craig     O'Rourke Aubrie  Lee Michael D.  Nierman William C.  Everroad R. Craig  Dupont Chris L.", "Study Assay Technology Platform": "Illumina", "Authoritative Source URL": "GLDS-372/", "Project Identifier": "", "thumbnail": "/genelab/img/GLDS372__study_image.png", "Project Title": "Microbial Analysis of International Space Station (ISS) Air  Surfaces and Water (ISS_Micro_Analysis)", "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13823", "Study Public Release Date": 1636934400.0, "Study Publication Title": "Reference-guided metagenomics reveals genome-level evidence of potential microbial transmission from the ISS environment to an astronaut's microbiome     Genomic and phenotypic characterization of Burkholderia isolates from the potable water system of the International Space Station", "organism": "Staphylococcus auricularis     Staphylococcus epidermidis     Burkholderia cepacia     Burkholderia contaminans     Ralstonia pickettii     Ralstonia insidiosa     Staphylococcus saprophyticus     Staphylococcus lugdunensis     Staphylococcus aureus", "Accession": "OSD-372", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Genome sequencing of Staphylococcus, Burkholderia, and Ralstonia bacterial isolates isolated from the ISS", "Study Protocol Type": "sample collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "NASA Space Biology, NNH16ZTT001N-MOBE and 80NSSC17K0035", "Study Factor Type": "Space Flight     Collection Date     Sample Location", "Factor Value": "", "Study Description": "This repository holds genome assemblies for Staphylococcus, Burkholderia, and Ralstonia bacterial isolates isolated from the ISS between the years of 2006-2015. Information on the overall microbial isolation effort is stored under NASA's Life Science Data Archive experiment 13823 (https://lsda.jsc.nasa.gov/Experiment/exper/13823). For the genomes presented here, isolates were received from NASA's Johnson Space Center and their genomes were sequenced and assembled thanks to NASA Space Biology awards to Michael D. Lee (NNH16ZTT001N-MOBE) and Aubrie O'Rourke (80NSSC17K0035).", "Study Protocol Name": "sample collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-372", "Data Source Accession": "PRJNA486830  PRJNA493516"}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>cgene</em>", "International <em>Space</em> Station (ISS)", "NASA <em>Space</em> Biology, NNH16ZTT001N-MOBE and 80NSSC17K0035", "<em>Space</em> Flight     Collection Date     Sample Location"]}}, {"_index": "study", "_type": "docs", "_id": "ht_6g4QB28eYt3lGOLbo", "_score": 10.779473, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Briefly, samples collected from the ISS were processed and 100 ul of each dilution was plated on Reasoner's 2A agar (R2A). The plates were incubated at 25C for 7 days. The single colony obtained was re-streaked on R2A plates, incubated at 25C for 3 days. A biomass of approximately 1 ug wet weight was collected for each strain and pooled for DNA extraction.     Total nucleic acid extraction was carried out using ZymoBIOMICS 96 MagBead DNA kit (Lysis tubes) (Zymo Research, USA) after bead beating using Bertin Precelys. This was followed by library preparation using the Illumina Nextera Flex Protocol as per Illumina document number 1000000025416 v07.     The initial amount of DNA for library preparation was quantified and depending on the input DNA concentration, 5-12 cycles of PCR were carried out to normalize the output. The amplified genomic DNA fragments were indexed and pooled in 384 plex configuration.     Whole-genome shotgun sequencing was performed on a NovaSeq 6000 S4 flowcell PE 2x150 platform with a paired-end module.     The data was filtered with NGS QC Toolkit v2.3 (12) for high-quality (HQ) vector- and adaptor free reads for genome assembly (cutoff read length for HQ, 80%; cutoff quality score, 20). The number of filtered reads obtained were used for assembly with SPAdes 3.14.0 genome assembler (k-mer size- 32-72 bases).", "Material Type": "Cells", "Study Identifier": "OSD-298", "Study Person": {"First Name": "Kasthuri Swati", "Middle Initials": "", "Last Name": "Venkateswaran Bijlani"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Jet Propulsion Laboratory (JPL)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "19-12829-26", "Experiment Platform": "", "Study Factor Name": "Strain     Spaceflight", "Study Publication Author List": "Bijlani S  Singh NK  Mason CE  Wang CCC  and Venkateswaran K", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "OSD-298/", "Project Identifier": "", "thumbnail": "/geode-py/ws/studies/OSD-298/image", "Project Title": "", "Study Public Release Date": 1588982400.0, "Project Link": "", "Study Publication Title": "Draft Genome Sequences of Sphingomonas species Associated with the International Space Station", "organism": "Sphingomonas sanguinis     Sphingobacterium paucimobilis", "Accession": "OSD-298", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Draft Genome Sequences of Sphingomonas sp. Isolated from the International Space Station Genome sequencing and assembly", "Study Protocol Type": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "This research was funded by a 2012 Space Biology NNH12ZTT001N grant nos. 19-12829-26.", "Study Factor Type": "strain     Space Flight", "Factor Value": "", "Study Description": "Draft Genome Sequences of Sphingomonas sp. Isolated from the International Space Station", "Study Protocol Name": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-298", "Data Source Accession": "PRJNA629834"}, "highlight": {"all": ["<em>cgene</em>", "Isolated from the International <em>Space</em> Station Genome sequencing and assembly", "This research was funded by a 2012 <em>Space</em> Biology NNH12ZTT001N grant nos. 19-12829-26.", "strain     <em>Space</em> Flight", "Isolated from the International <em>Space</em> Station"]}}, {"_index": "study", "_type": "docs", "_id": "kd_6g4QB28eYt3lGObag", "_score": 10.7245, "_source": {"Space Program": "NASA", "Flight Program": "Internation Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "During the microbial tracking investigation to characterize airborne and surface-associated microbial population aboard the International Space Station (ISS), samples were collected from 6 locations across the ISS, and ground samples were collected from Crew resupply vehicle (CRV). A sterile polyester wipe premoistened with Phosphate buffered saline (PBS) was used to collect the samples from various areas across those 6 locations, and the details and description of the sample collection and cultivation have already been reported in Checinska et al, 2019 and Singh et al, 2018.\n\n\nabbreviations. ARED: Advanced Resistive exercise device, WHC: Waste and Hygience Compartment, CRV: Crew Resupply Vehicle     Purified culture were subjected to DNA extraction By Zymo using ZymoBIOMICS DNA Magbead Kit according to the manufacturer's instructions.     The Shotgun libraries were prepared by use of illuminq Nextera Flex Protocol (Singh et al, 2018).     A pair-end sequencing was performed on the DNA fragments with a NovaSeq 6000 s4 flowcell PE 2x150 platform. The sequenced data was saved in a FASTQ format.     The FASTQ files were cleaned and assembled by SPAdes (v3.11.1) (Bankevich et al, 2012), and the contigs generated were scaffolded in a FASTA format.", "Material Type": "Cells", "Study Identifier": "OSD-303", "Study Person": {"First Name": "Kasthuri Robert", "Middle Initials": "", "Last Name": "Venkateswaran Daudu"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Jet Propulsion Laboratory (JPL)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "19-12829-26", "Experiment Platform": "", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "Daudu R  Singh NK  Wood JM  Debieu M  O'Hara NB  Mason C  and Venkateswaran K", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "OSD-303/", "Project Identifier": "ISS-MO (MT-1B)", "thumbnail": "/geode-py/ws/studies/OSD-303/image", "Project Title": "ISS Microbial Observatory (Microbial Tracking-1B)", "Study Public Release Date": 1592179200.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13630", "Study Publication Title": "Draft Genome Sequences of Bacillaceae strains isolated from International Space Station", "organism": "Bacillus cereus thuringiensis     Bacillus amyloliquefaciens     Paenibacillus polymyxa     Thermus amyloliquefaciens     Bacillus firmus", "Accession": "OSD-303", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "ISS Bacillus Genomes", "Study Protocol Type": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "This research was funded by a 2012 Space Biology NNH12ZTT001N grant nos. 19-12829-26 under Task Order NNN13D111T award to KV.", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "SRA of spore forming Bacillus strains isolated from various areas of the ISS during Microbial tracking investigation", "Study Protocol Name": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-303", "Data Source Accession": "PRJNA637984"}, "highlight": {"all": ["Internation <em>Space</em> Station (ISS)", "investigation to characterize airborne and surface-associated microbial population aboard the International <em>Space</em>", "<em>cgene</em>", "Draft Genome Sequences of Bacillaceae strains isolated from International <em>Space</em> Station", "<em>Space</em> Flight     strain"]}}, {"_index": "study", "_type": "docs", "_id": "4N_6g4QB28eYt3lGLLVr", "_score": 10.629288, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Sampling wipes were prepared at the Jet Propulsion Laboratory (JPL; Pasadena, CA). Briefly, each polyester wipe (9 x 9 inch; ITW Texwipe, Mahwah, NJ) was folded two times and soaked in 15 mL of sterile molecular grade water (Sigma-Aldrich, St. Louis, MO) for 30 min followed by the transfer to a sterile zip lock bag. The sampling kit was assembled at NASA Ames Research Center (ARC, Moffett Field, CA). The implementation team at NASA ARC delivered the kit to the Cargo Mission Contract at Johnson Space Center (Texas) which was then transferred to Kennedy Space Center (Florida) in order to be loaded into the Space Exploration Technologies (SpaceX) Dragon spacecraft prior to launch. The samples were stored at room temperature in orbit. The kits were delivered to JPL immediately after arrival to Earth at 4C with processing at JPL commencing within 2 h of receipt.     Total nucleic acid extraction was carried out using ZymoBIOMICS 96 MagBead DNA kit (Lysis tubes) (Zymo Research, USA) after bead beating using Bertin Precelys.     This was followed by library preparation using the Illumina Nextera Flex Protocol. The initial amount of DNA for library preparation was quantified and depending on the input DNA concentration, 5-12 cycles of PCR were carried out to normalize the output. The amplified genomic DNA fragments were indexed and pooled in 384 plex configuration.     Whole-genome shotgun sequencing was performed on a NovaSeq 6000 S4 flowcell PE 2x150 platform with a paired-end module.     The data was filtered with NGS QC Toolkit v2.3 for high-quality (HQ) vector- and adaptor free reads for genome assembly(cutoff read length for HQ, 80%; cutoff quality score, 20). The number of filtered reads obtained were used for assembly with SPAdes genome assembler (k-mer size- 32-72 bases).", "Material Type": "Cells", "Study Identifier": "OSD-290", "Study Person": {"First Name": "Kasthuri Swati Nitin", "Middle Initials": " K", "Last Name": "Venkateswaran Bijlani Singh"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Jet Propulsion Laboratory (JPL)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "NNH12ZTT001N grant nos. 19-12829-26", "Experiment Platform": "", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "Bijlani S  Singh NK  Mason CE  Wang CCC  and Venkateswaran K", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "OSD-290/", "Project Identifier": "ISS-MO", "thumbnail": "/geode-py/ws/studies/OSD-290/image", "Project Title": "Microbial Tracking-1A", "Study Public Release Date": 1586131200.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13629#data", "Study Publication Title": "Draft Genome Sequences of Tremellomycetes strains Isolated from the International Space Station", "organism": "Naganishia sp.     Naganishia adeliensis     Papiliotrema laurentii     Naganishia albida", "Accession": "OSD-290", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Lower eukaryotic isolates belonging to class Tremellomycetes isolated from International Space Station Genome sequencing and assembly", "Study Protocol Type": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "This research 92 was funded by a 2012 Space Biology NNH12ZTT001N grant nos. 19-12829-26 under Task 93 Order NNN13D111T award to KV, which also subcontracted to CCCW, and funded post- 94 doctoral fellowship for SB.", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "Genome sequencing and assembly of lower Eukaryotic isolates belonging to class Tremellomycetes isolated from International Space Station", "Study Protocol Name": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-290", "Data Source Accession": "PRJNA623412"}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "the <em>Space</em> Exploration Technologies (SpaceX) Dragon spacecraft prior to launch.", "<em>cgene</em>", "Draft Genome Sequences of Tremellomycetes strains Isolated from the International <em>Space</em> Station", "<em>Space</em> Flight     strain"]}}, {"_index": "study", "_type": "docs", "_id": "nd_6g4QB28eYt3lGOrbh", "_score": 10.5661, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Total nucleic acid extraction was carried out using ZymoBIOMICS 96 MagBead DNA kit (Lysis tubes) (Zymo Research, USA) after bead beating using Bertin Precelys.     This was followed by library preparation using the Illumina Nextera Flex Protocol. The initial amount of DNA for library preparation was quantified and depending on the input DNA concentration, 5-12 cycles of PCR were carried out to normalize the output. The amplified genomic DNA fragments were indexed and pooled in 384 plex configuration.     Whole-genome shotgun sequencing was performed on a NovaSeq 6000 S4 flowcell PE 2x150 platform with a paired-end module.     The data was filtered with NGS QC Toolkit v2.3 for high-quality (HQ) vector- and adaptor free reads for genome assembly(cutoff read length for HQ, 80%; cutoff quality score, 20). The number of filtered reads obtained were used for assembly with SPAdes genome assembler (k-mer size- 32-72 bases).     Sampling wipes were prepared at the Jet Propulsion Laboratory (JPL; Pasadena, CA). Briefly, each polyester wipe (9 x 9 inch; ITW Texwipe, Mahwah, NJ) was folded two times and soaked in 15 mL of sterile molecular grade water (Sigma-Aldrich, St. Louis, MO) for 30 min followed by the transfer to a sterile zip lock bag. The sampling kit was assembled at NASA Ames Research Center (ARC, Moffett Field, CA). The implementation team at NASA ARC delivered the kit to the Cargo Mission Contract at Johnson Space Center (Texas) which was then transferred to Kennedy Space Center (Florida) in order to be loaded into the Space Exploration Technologies (SpaceX) Dragon spacecraft prior to launch. The samples were stored at room temperature in orbit. The kits were delivered to JPL immediately after arrival to Earth at 4C with processing at JPL commencing within 2 h of receipt.", "Material Type": "Cells", "Study Identifier": "OSD-350", "Study Person": {"First Name": "Adriana Kasthuri Nitin Kumar Jason Marilyne Niamh Christopher", "Middle Initials": " M B E", "Last Name": "Blachowicz Venkateswaran Singh Wood Debieu O\u2019Hara Mason"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Ames Research Center (ARC)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "International Space Station (ISS)", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "Adriana Blachowicz  Nitin Kumar Singh  Jason M. Wood  Marilyne Debieu  Niamh B. O\u2019Hara  Christopher E. Mason  Kasthuri Venkateswarana", "Study Assay Technology Platform": "Illumina", "Authoritative Source URL": "OSD-350/", "Project Identifier": "ISS-MO", "thumbnail": "/geode-py/ws/studies/OSD-350/image", "Project Title": "", "Study Public Release Date": 1616457600.0, "Project Link": "", "Study Publication Title": "Draft Genome Sequences of Aspergillus and Penicillium Species Isolated from the International Space Station and Crew Resupply Vehicle Capsule", "organism": "Aspergillus niger     Penicillium griseoroseum     Penicillium camemberti     Penicillium polonicum     Penicillium dipodomyicola     Aspergillus unguis     Penicillium chrysogenum", "Accession": "OSD-350", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Draft genome sequences of Aspergillus and Penicillium species isolated from the International Space Station and Crew Resupply Vehicle Capsule", "Study Protocol Type": "Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly     Sample Collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "This research was funded by 2012 Space Biology NNH12ZTT001N grant number 19-12829-26 under task order NNN13D111T awarded to K.V., also funded a postdoctoral fellowship for A.B.", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "Genome sequencing and assembly of fungal isolates belonging to Penicilliium and Aspergillus genera isolated from International Space Station", "Study Protocol Name": "Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly     Sample Collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-350", "Data Source Accession": "PRJNA659567  PRJNA667181"}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "the <em>Space</em> Exploration Technologies (SpaceX) Dragon spacecraft prior to launch.", "<em>cgene</em>", "International <em>Space</em> Station (ISS)", "<em>Space</em> Flight     strain"]}}, {"_index": "study", "_type": "docs", "_id": "Bt_6g4QB28eYt3lGSrf0", "_score": 10.518446, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "K. quasipneumoniae subsp. similipneumoniae strain IF3SW-P1 was isolated from a surface sample collected from the foot panel of the Advanced Resistive Exercise Device (ARED) on the ISS on 4 March 2015. Briefly, wipes containing the surface sample were returned to Earth and transported to the Jet Propulsion Laboratory (JPL), where they were then centrifuged followed by culturing using the spread plate method for isolation on R2A medium and then stored as freezer stocks at -80\u00b0C. Strain IF3SW-P1 was subcultured to late log phase in TSB at 37\u00b0C prior to DNA extraction.     Genomic DNA was extracted using the DOE Joint Genome Institute 'Bacterial genomic isolation using CTAB' protocol.     The sequencing library was constructed using Q20+EA early access ligation reagents (SQK-LSK112-XL).     Oxford Nanopore sequencing with Q20+ chemistry was performed using GridION MK1 sequencer on a FLO-MIN112 R10.4 flow cell. Raw reads were base-called using MinKNOW v29.10.8, with a mean quality score of 16.3 and mode of 18.03.     The genome was assembled and polished using Flye v2.9.", "Material Type": "Bacteria", "Study Identifier": "GLDS-470", "Study Person": {"First Name": "Natasha Nitin Daniel Scott Brian Kasthuri Duane", "Middle Initials": "S K L W P P", "Last Name": "Sushenko Singh Vellone Tighe Hedlund Venkateswaran Moser"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Jet Propulsion Laboratory (JPL)", "Data Source Type": "cgene", "Study Grant Number": "", "Mission": {"Start Date": "10-Nov-2014", "End Date": "11-Mar-2015", "Name": "Expedition 42"}, "Experiment Platform": "", "Study Factor Name": "Spaceflight", "Study Publication Author List": "Natasha S Sushenko  Nitin K Singh  Daniel L Vellone  Scott W Tighe  Brian P Hedlund  Kasthuri Venkateswaran  Duane P Moser", "Study Assay Technology Platform": "Oxford Nanopore Technologies", "Authoritative Source URL": "GLDS-470/", "Project Identifier": "19_12829_26_1A", "thumbnail": "/genelab/img/GLDS470__study_image.png", "Project Title": "ISS Microbial Observatory (Microbial Tracking-1A)", "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13629?", "Study Public Release Date": 1647475200.0, "Study Publication Title": "Draft genome sequence of Klebsiella quasipneumoniae subsp. similipneumoniae strain IF3SW-P1 isolated from the International Space Station", "organism": "Klebsiella quasipneumoniae subsp. similipneumoniae", "Accession": "OSD-470", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Draft genome sequence of Klebsiella quasipneumoniae subsp. similipneumoniae strain IF3SW-P1 isolated from the International Space Station", "Study Protocol Type": "sample collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "2012 Space Biology NNH12ZTT001N grant no. 19-12829-26 under Task Order NNN13D111T; Project MANGO, a 2018 Space Biology NNH16ZTT001N grant under Task Order 80NM0018F0589", "Study Factor Type": "Space Flight", "Factor Value": "", "Study Description": "In 2015, the Advanced Resistive Exercise Device (ARED) foot panel on the International Space Station (ISS) was sampled to identify culturable microorganisms. The whole-genome of the strain IF3SW-P1 was sequenced using the Oxford Nanopore Technologies platform and identified as Klebsiella quasipneumoniae subsp. quasipneuomoniae, a Biosafety Level-2 (BSL-2) human pathogen. This whole-genome sequence will aid in comparative genomic analyses with Earth-origin pathogens for differences in virulence and antimicrobial resistance in microorganisms exposed to spaceflight conditions.", "Study Protocol Name": "sample collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-470", "Data Source Accession": ""}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>cgene</em>", "<em>Space</em> Biology NNH16ZTT001N grant under Task Order 80NM0018F0589", "<em>Space</em> Flight", "In 2015, the Advanced Resistive Exercise Device (ARED) foot panel on the International <em>Space</em> Station"]}}, {"_index": "study", "_type": "docs", "_id": "kN_6g4QB28eYt3lGObaP", "_score": 10.488773, "_source": {"Space Program": "NASA", "Flight Program": "Internation Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Samples were obtained from 5 locations across the ISS which includes: Control, Overhead 4, Cupola, Waste and Hygiene Compartment (WHC), and Advanced Resistive Exercise Device (ARED). A sterile polyester wipe pre-moistened with Phosphate buffer saline (PBS) was used to collect the samples from various areas across these 5 locations. The description of the sample collection and cultivation have already been reported in Checinska et al, 2019 and Singh et al, 2018.     Purified culture were subjected to DNA extraction By Zymo using ZymoBIOMICS DNA Magbead Kit according to the manufacturer's instructions.     The Shotgun library was prepared by use of Illumina Nextera Flex Protocol (Singh et al, 2018).     A pair-end sequencing was performed on the DNA fragments with a NovaSeq 6000 s4 flowcell PE 2x150 platform. The sequenced data was saved in a FASTQ format.     The FASTQ files were cleaned and assembled by SPAdes (v3.11.1) (Bankevich et al, 2012), and the contigs generated were scaffolded in a FASTA format.", "Material Type": "Cells", "Study Identifier": "OSD-302", "Study Person": {"First Name": "Kasthuri Achintya", "Middle Initials": "", "Last Name": "Venkateswaran Bharadwaj"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Jet Propulsion Laboratory (JPL)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "OSD-302/", "Project Identifier": "ISS-MO", "thumbnail": "/geode-py/ws/studies/OSD-302/image", "Project Title": "ISS Microbial Observatory", "Study Public Release Date": 1590883200.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13629  https://lsda.jsc.nasa.gov/Experiment/exper/13630", "Study Publication Title": "", "organism": "Enterobacter bugandensis     Pantoea brenneri     Klebsiella quasipneumoniae", "Accession": "OSD-302", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "ISS Enterobacteriales Genomes", "Study Protocol Type": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "The microbial tracking-1 (MT-1) investigation allowed the characterization of the microbial population aboard the International Space Station (ISS).", "Study Protocol Name": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-302", "Data Source Accession": "PRJNA635942"}, "highlight": {"all": ["Internation <em>Space</em> Station (ISS)", "<em>cgene</em>", "<em>Space</em> Flight     strain", "-1) investigation allowed the characterization of the microbial population aboard the International <em>Space</em>"]}}, {"_index": "study", "_type": "docs", "_id": "T9_6g4QB28eYt3lGNLaB", "_score": 10.4843445, "_source": {"Space Program": "NASA", "Flight Program": "Internation Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Samples were obtained from 5 locations across the ISS which includes: Control, Overhead 4, Waste and Hygiene Compartment (WHC), Permanent multipurpose module (PMM), and Location 5. A sterile polyester wipe pre-moistened with Phosphate buffer saline (PBS) was used to collect the samples from various areas across these 5 locations. The description of the sample collection and cultivation have already been reported in Checinska et al, 2019 and Singh et al, 2018.     Purified culture were subjected to DNA extraction By Zymo using ZymoBIOMICS DNA Magbead Kit according to the manufacturer's instructions.     The Shotgun library was prepared by use of Illumina Nextera Flex Protocol (Singh et al, 2018).     A pair-end sequencing was performed on the DNA fragments with a NovaSeq 6000 s4 flowcell PE 2x150 platform. The sequenced data was saved in a FASTQ format.     The FASTQ files were cleaned and assembled by SPAdes (v3.11.1) (Bankevich et al, 2012), and the contigs generated were scaffolded in a FASTA format.", "Material Type": "Cells", "Study Identifier": "OSD-311", "Study Person": {"First Name": "Kasthuri Achintya", "Middle Initials": "", "Last Name": "Venkateswaran Bharadwaj"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Jet Propulsion Laboratory (JPL)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "Spaceflight     Strain", "Study Publication Author List": "", "Study Assay Technology Platform": "Illumina NovaSeq 6000", "Authoritative Source URL": "OSD-311/", "Project Identifier": "ISS-MO", "thumbnail": "/geode-py/ws/studies/OSD-311/image", "Project Title": "ISS Microbial Observatory", "Study Public Release Date": 1596153600.0, "Project Link": "https://lsda.jsc.nasa.gov/Experiment/exper/13629  https://lsda.jsc.nasa.gov/Experiment/exper/13630  https://lsda.jsc.nasa.gov/Experiment/exper/13671", "Study Publication Title": "", "organism": "Enterobacter bugandensis     Kalamiella piersonii     Pantoea brenneri     Pantoea agglomerans", "Accession": "OSD-311", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Part two: ISS Enterobacteriales", "Study Protocol Type": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "", "Study Factor Type": "Space Flight     strain", "Factor Value": "", "Study Description": "The microbial tracking-1 (MT-1) investigation allowed the characterization of the microbial population aboard the International Space Station (ISS).", "Study Protocol Name": "sample collection     nucleic acid extraction     library construction     nucleic acid sequencing     sequence assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-311", "Data Source Accession": "PRJNA635942"}, "highlight": {"all": ["Internation <em>Space</em> Station (ISS)", "<em>cgene</em>", "<em>Space</em> Flight     strain", "-1) investigation allowed the characterization of the microbial population aboard the International <em>Space</em>"]}}, {"_index": "study", "_type": "docs", "_id": "pzSylIYBUmOM_59H6xmz", "_score": 9.967646, "_source": {"Space Program": "NASA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "genome sequencing", "Study Protocol Description": "Microbial isolates in agar stabs were provided by the Microbial Tracking 2 PI at NASA JPL and stored at 5C. A 10 microliter aliquot of the stab was diluted into 100 microliters of trypic soy broth and spread onto the surface of a tryptic soy agar petri dish. After 72 hours of growth, the plate was gently scrapped to remove the biomass and placed in a 2 mL microcentrifuge tube for genomic DNA extraction.     Cell pellets resuspended in 400 microliters of 100 mM Tris, 50 mM EDTA, 100 mM NaCl buffer at pH 7.0 were mixed with 15 microliters RNAase A and 20 microliters of lysozyme (20 mg/mL) and incubated at 58 C for 1 hour with gentle mixing by inversion every 15 minutes.\n\nTo this mixture, 10 microliters of proteinase K (20 mg/mL) and 20% SDS to a final concentration of 2%, were added, gently mixed by inversion and incubated at 58C for 1 hour.\n\nThe mixture was then cooled on ice for 5 minutes and cell debris pelleted by centrifugation (10k x g for 10 minutes).\n\nThe supernatant was treated with 2x chloroform extractions and the genomic DNA was isolated from the aqueous phase via ethanol precipitation.\n\nDNA quality was assessed by fluorometric quantification (Qubit, Invitrogen, Waltham, MA, USA) and UV-Vis microvolume spectrophotometry (Nanodrop, Thermo Fischer Scientific, Waltham, MA, USA). All gDNA manipulation was performed using wide-bore pipet tips to prevent gDNA shearing.     Native genomic DNA (gDNA) was sequenced on a MinION R9.4 flowcell (Oxford Nanopore Technologies (ONT), Oxford, UK). The sequencing library was prepared using the ONT Rapid Barcoding Sequencing kit (SQK-RBK004) according to the manufacturer\u2019s protocol.     Native genomic DNA was sequenced on a MinION Mk1.B sequencing device with an R9.4.1 Flowcell using standard configuration settings. Data were output as raw fast5 files.     Sequencing Fast5 files were base-called using the ONT Guppy base-caller (v6.21) using the super high accuracy model. Genomes were assembled using Flye (v2.9.1) and polished with the ONT tool Medaka (v1.7.0, https://github.com/nanoporetech/medaka) using default parameters for both.", "Material Type": "Cells", "Study Identifier": "OSD-582", "Study Person": {"First Name": "Jared", "Middle Initials": "", "Last Name": "Broddrick"}, "ESA Acronym": "", "Acknowledgments": "Anna Simpson and Kasthuri Venkateswaran, NASA JPL for providing the isolates.", "Managing NASA Center": "Ames Research Center (ARC)", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "Surfaces", "Study Factor Name": "Spaceflight", "Study Publication Author List": "Iris Irby and Jared T. Broddrick", "Study Assay Technology Platform": "Oxford Nanopore Technologies", "Authoritative Source URL": "OSD-582/", "Project Identifier": "", "thumbnail": "/geode-py/ws/studies/OSD-582/image", "Project Title": "International Space Station Microbial Observatory of Pathogenic Virus Bacteria and Fungi Project", "Study Public Release Date": 1677456000.0, "Project Link": "https://nlsp.nasa.gov/view/lsdapub/lsda_experiment/2df8e010-cb73-5553-ac25-53b2de12c5ed", "Study Publication Title": "Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions", "organism": "Staphylococcus saprophyticus     Pseudomonas fulva", "Accession": "OSD-582", "Study Assay Technology Type": "nucleotide sequencing", "Study Title": "Resequencing of select microbial isolates from the International Space Station with the Nanopore MinION", "Study Protocol Type": "sample collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly", "Project Type": "Spaceflight Study", "Study Funding Agency": "Space Biology", "Study Factor Type": "Space Flight", "Factor Value": "", "Study Description": "Microbial isolates from the NASA Space Biology-funded microbial tracking experiments were re-sequenced using the Oxford Nanopore MinION.", "Study Protocol Name": "sample collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     Sequence Assembly", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-575", "Data Source Accession": ""}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>cgene</em>", "International <em>Space</em> Station Microbial Observatory of Pathogenic Virus Bacteria and Fungi Project", "<em>Space</em> Biology", "<em>Space</em> Flight"]}}, {"_index": "study", "_type": "docs", "_id": "1t_6g4QB28eYt3lGK7WC", "_score": 9.764195, "_source": {"Authoritative Source URL": "OSD-41/", "Flight Program": "International Space Station (ISS)", "Mission": {"End Date": "11/27/09", "Start Date": "11/16/09", "Name": "STS-129"}, "Material Type": "Whole Organism", "Project Identifier": "CERISE", "Accession": "OSD-41", "Identifiers": "GLDS-41", "Study Identifier": "OSD-41", "Study Protocol Name": "Growth Protocol     Sample Collection     RNA Extraction     Labeling     Nucleic Acid Hybridization     Data Collection", "Study Assay Technology Type": "DNA microarray", "Acknowledgments": "", "Study Assay Technology Platform": "Agilent", "Study Person": {"Last Name": "Higashibata Hashizume", "Middle Initials": "", "First Name": "Akira Toko"}, "Study Protocol Type": "growth protocol     sample collection protocol     RNA Extraction     labeling     hybridization     Data Collection", "Space Program": "JAXA", "Study Title": "Microgravity effect on C. elegans N2/VC (CERISE, 8days)", "Study Factor Type": "Space Flight     Gravity, Altered", "Study Public Release Date": 0, "Parameter Value": "", "thumbnail": "/geode-py/ws/studies/OSD-41/image", "Study Factor Name": "Spaceflight     Altered Gravity", "Study Assay Measurement Type": "transcription profiling", "Project Type": "Spaceflight Study", "Factor Value": "", "Data Source Accession": "E-GEOD-27338", "Project Title": "C. elegans RNAi space experiment: CERISE", "Study Funding Agency": "This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan, the Japan Society for the Promotion of Science, and \u201cGround-Based Research Announcement for Space Utilization\u201d promoted by the Japan Space Forum. TE was supported by the Medical Research Council UK (G0801271). NJS was supported by the National Institutes of Health (NIH NIAMS ARO54342).", "Study Protocol Description": "We tested three experimental conditions in each culture: ground control, 1G (control) centrifuge onboard the International Space Station (ISS) and micro-gravity samples onboard ISS. Briefly, for the microarray gene expression experiment N2 wild type L1 larvae were used. All larvae were maintained in stasis within S basal medium until initiation of the experiment. The experiment was activated once onboard the ISS by reintroducing animals to food. All experiments were carried out under temperature controlled conditions in the Cell Biology Experiment Facility (CBEF) within the KIBO module. Cultures for microarray analysis were grown for 8 d.     Experiments were stopped by first observing the animals by light microscopy and then by freezing with subsequent storage at \u221280C in MELFI. Microscopy at the end of culturing confirmed that the 4 day cultures grew to adulthood as the first generation for both the L1 and dauer cultures, and that the 8 day cultures grew to a second generation of adulthood.     Worms were homogenized with four rounds of 20-second beating at 5000 rpm in a Micro Smash TM MS-100 bead beater with 3 minutes of cooling on ice between rounds. Total RNA was extracted using an Isogen RNA purification kit following the manufacturer's protocol.     Total RNA was amplified using the Low Input Quick Amp Labeling Kit protocol. Cy3 labeled cRNA was produced according to manufacturer's protocol.     Labeled cRNA (1.65 ug/sample) was hybridized to a C. elegans oligo microarray using a gene expression hybridization kit at 65 C for 17 hours.     Array were scanned with an Agilent Scanner and processed with Agilent Feature Extraction Software.", "Experiment Platform": "KIBO", "Characteristics": "", "Study Grant Number": "UK MRC (G0801271) and the US NIH NIAMS (AR054342)", "Study Publication Author List": "Atsushi Higashitani  Toko Hashizume  Tomoko Sugimoto  Chihiro Mori  Kanako Nemoto  Timothy Etheridge  Nahoko Higashitani  Takako Takanami  Hiromi Suzuki  Keiji Fukui  Takashi Yamazaki  Noriaki Ishioka  Nathaniel Szewczyk  and Akira Higashibata     Timothy Etheridge  Kanako Nemoto  Toko Hashizume  Chihiro Mori  Tomoko Sugimoto  Hiromi Suzuki  Keiji Fukui  Takashi Yamazaki  Akira Higashibata  Nathaniel J. Szewczyk  Atsushi Higashitani", "Project Link": "http://iss.jaxa.jp/en/kiboexp/news/cerise_start.html", "Study Publication Title": "C. elegans RNAi space experiment (CERISE) in Japanese Experiment\nModule KIBO.     The effectiveness of RNAi in Caenorhabditis elegans is maintained during spaceflight.", "Managing NASA Center": "", "Study Description": "Microgravity effect on C. elegans gene expression was analysed by whole genome microarray. The worms were cultivated under microgravity for 8 days in the Japanese Module of the International Space Station. The samples of this study were divided three experimental groups: 1. microgravity for 8 days 2. artificial 1G control for 8 days on orbit 3. ground 1G control for 8 days This study was repeated with three biological and two technical replicates.", "organism": "Caenorhabditis elegans", "Data Source Type": "cgene", "ESA Acronym": ""}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>Space</em> Flight     Gravity, Altered", "C. elegans RNAi <em>space</em> experiment: CERISE", "Utilization\u201d promoted by the Japan <em>Space</em> Forum.", "<em>cgene</em>"]}}, {"_index": "study", "_type": "docs", "_id": "Wd_6g4QB28eYt3lGNbZs", "_score": 9.723705, "_source": {"Space Program": "", "Flight Program": "Shuttle Program", "Study Assay Measurement Type": "transcription profiling", "Study Protocol Description": "The RNA fixative RNA Later II (Ambion, Austin, TX), glutaraldehyde (16%; Sigma, St. Louis, MO), and formaldehyde (2%; Ted Pella, Redding, CA) were used as fixatives in flight experiments.     The virulent, mouse-passaged S. typhimurium derivative of SL1344 termed \u03c73339 was used as the WT strain in all flight- and ground-based experiments. Lennox broth was used as the growth medium in all experiments (5), and PBS (Invitrogen, Carlsbad, CA) was used to resuspend bacteria for use as inoculum in the FPAs. To facilitate group activation of FPAs during flight and to ensure proper containment levels, sets of eight FPAs were loaded into larger containers termed group activation packs.     SIGMA GenElute bacterial genomic DNA extraction and RNeasy kit (QIAGEN)     Incorporation of Cy5-dCTP using Klenow enzyme and random hexamers and incorporation of Cy3-dCTP with Superscript RT and random hexamers. Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201; only the first two subarrays were scanned     Overnight hyb on Corning UltraGAPS slides at 42\u00b0C in 25% formamide / 5xSSC / 0.1% BSA     Data from stored array images were obtained with QuantArray software (Packard Bioscience, Billerica, MA)", "Material Type": "Cells", "Study Identifier": "OSD-11", "Study Person": {"First Name": "Michael S. P. M. Cheryl", "Middle Initials": " A", "Last Name": "McClelland Porwollik Cheng McClelland Nickerson"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "Kennedy Space Center (KSC)", "Data Source Type": "cgene", "Mission": {"Start Date": "09/09/2006", "End Date": "09/21/2006", "Name": "STS-115"}, "Study Grant Number": "", "Experiment Platform": "Group Activation Pack (GAP)  Multiple Orbital Bioreactor with Instrumentation and Automated Sampling (MOBIAS)", "Study Factor Name": "Spaceflight", "Study Publication Author List": "Wilson J. W.  Ott C. M.  zu Bentrup K. H\u00f6ner  Ramamurthy R.  Quick L.  Porwollik S.  Cheng P.  McClelland M.  Tsaprailis G.  Radabaugh T.  Hunt A.  Fernandez D.  Richter E.  Shah M.  Kilcoyne M.  Joshi L.  Nelman-Gonzalez M.  Hing S.  Parra M.  Dumars P.  Norwood K.  Bober R.  Devich J.  Ruggles A.  Goulart C.  Rupert M.  Stodieck L.  Stafford P.  Catella L.  Schurr M. J.  Buchanan K.  Morici L.  McCracken J.  Allen P.  Baker-Coleman C.  Hammond T.  Vogel J.  Nelson R.  Pierson D. L.  Stefanyshyn-Piper H. M.  Nickerson C. A.", "Study Assay Technology Platform": "Sidney Kimmel Cancer Center non-commercial", "Authoritative Source URL": "OSD-11/", "Project Identifier": "12A", "thumbnail": "/geode-py/ws/studies/OSD-11/image", "Project Title": "Effect of Spaceflight on Microbial Gene Expression and Virulence (Microbe) (2001092)", "Study Public Release Date": 1189641600.0, "Project Link": "https://nlsp.nasa.gov/view/lsdapub/lsda_experiment/e85d2a9e-f02d-5629-a486-1a2677e8b057", "Study Publication Title": "Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq", "organism": "Salmonella enterica", "Accession": "OSD-11", "Study Assay Technology Type": "DNA microarray", "Study Title": "Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq", "Study Protocol Type": "sample collection     sample treatment protocol     RNA Extraction     Labeling     Nucleic Acid Hybridization     Data Collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "This work was supported by National Aeronautics and Space Administration Grant NCC2-1362 (to C.A.N.), Louisiana Board of Regents Grant NNG05GH22H (to C.B.-C.), the Arizona Proteomics Consortium (supported by National Institute on Environmental Health Sciences Grant ES06694 to the Southwest Environmental Health Sciences Center), National Institutes of Health/National Cancer Institute Grant CA023074 (to the Arizona Cancer Center), and the BIO5 Institute of the University of Arizona", "Study Factor Type": "Space Flight", "Factor Value": "", "Study Description": "A comprehensive analysis of both the molecular genetic and phenotypic responses of any organism to the space flight environment has never been accomplished because of significant technological and logistical hurdles. Moreover, the effects of space flight on microbial pathogenicity and associated infectious disease risks have not been studied. The bacterial pathogen Salmonella typhimurium was grown aboard Space Shuttle mission STS-115 and compared with identical ground control cultures. Global microarray and proteomic analyses revealed that 167 transcripts and 73 proteins changed expression with the conserved RNA-binding protein Hfq identified as a likely global regulator involved in the response to this environment. Hfq involvement was confirmed with a ground-based microgravity culture model. Space flight samples exhibited enhanced virulence in a murine infection model and extracellular matrix accumulation consistent with a biofilm. Strategies to target Hfq and related regulators could potentially decrease infectious disease risks during space flight missions and provide novel therapeutic options on Earth.", "Study Protocol Name": "sample collection     treatment protocol     RNA Extraction     Labeling     Nucleic Acid Hybridization     Data Collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-11", "Data Source Accession": "E-GEOD-8573  GSE8573"}, "highlight": {"all": ["Kennedy <em>Space</em> Center (KSC)", "<em>cgene</em>", "<em>Space</em> flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq", "This work was supported by National Aeronautics and <em>Space</em> Administration Grant NCC2-1362 (to C.A.N.),", "<em>Space</em> Flight"]}}, {"_index": "study", "_type": "docs", "_id": "Ot_6g4QB28eYt3lGM7YH", "_score": 9.583915, "_source": {"Space Program": "NASA", "Flight Program": "Space Transportation System (STS), International Space Station (ISS)", "Study Assay Measurement Type": "transcription profiling", "Study Protocol Description": "The worms were cultured in C. elegans maintenance medium; CeMM provided by Bioserve Space Technology, University of Colorado, USA.     The CHab was flown as part of the Commercial Generic Bioprocessing Apparatus (CGBA) Science Insert-01 (CSI-01) on the STS-116 flight (December 2006) to the International Space Station. The worms were incubated in the CGBA for six months at 25\nC and were passaged every month from one opticell to the next. Upon landing, surviving worms were extracted and RNAlater added. The asynchronous stages of C. elegans were grown through multi-generation (up to +10 generations) on the International Space Station (ISS). The worms were automatically transferred from one chamber to another chamber with fresh CeMM at approximately 1-month intervals. The ground sample was passaged synchronously to the flight sample at the same time.     Trizol extraction of total RNA was performed according to the manufacturer's instructions.     Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10ng - 100 ng total RNA (GeneChip\u00ae Expression Analysis Technical Manual, 2005-2006, Affymetrix).     Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip\u00ae C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.     The data were analyzed with GeneChip Operation Software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.     GeneChips were scanned using the GeneChip Scanner 3000.     Data were processed as described in GL-DPPD-7114 (https://github.com/nasa/GeneLab_Data_Processing/blob/master/Microarray/Affymetrix/Pipeline_GL-DPPD-7114_Versions/GL-DPPD-7114.md) using NF_MAAffymetrix version 1.0.5 (https://github.com/nasa/GeneLab_Data_Processing/tree/NF_MAAffymetrix_1.0.5/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix). In short, a RunSheet containing raw data file location and processing metadata from the study's *ISA.zip file was generated using dp_tools (version 1.3.4). The raw array data files were loaded into R (version 4.1.3) using oligo (version 1.58.0). Raw data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version 1.58.0). The raw probe level intensity data was background corrected and normalized across arrays via the oligo (version 1.58.0) quantile method. Normalized probe level data quality assurance density plot, pseudo images, MA plots, and boxplots were generated using oligo (version 1.58.0). Normalized probe level data was summarized to the probeset level using the oligo (version 1.58.0) RMA method. Ensembl gene ID mappings were retrieved for each probeset using biomaRt (version 2.50.0), Ensembl database (ensembl.org, release 107). Differential expression analysis was performed in R (version 4.1.3) using limma (version 3.50.3); all groups were compared pairwise for each probeset to generate a moderated t-statistic and associated p- and adjusted p-value. Gene annotations were assigned for every probeset that mapped to exactly one Ensembl gene ID using the custom annotation tables generated in-house as detailed in GL-DPPD-7110 (https://github.com/nasa/GeneLab_Data_Processing/blob/GL_RefAnnotTable_1.0.0/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110.md), with STRINGdb (version 2.8.4), PANTHER.db (version 1.0.11), and org.Ce.eg.db (version 3.15.0).", "Material Type": "", "Study Identifier": "OSD-42", "Study Person": {"First Name": "Sue-Mian N-F S", "Middle Initials": " M", "Last Name": "Then Jusoh Then"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "Data Source Type": "cgene", "Mission": {"Start Date": "12/09/2006", "End Date": "12/22/2006", "Name": "STS-116"}, "Study Grant Number": "UKM-ANGKASA-NBD-0018-2007", "Experiment Platform": "C. elegans Habitat (CHab)", "Study Factor Name": "Spaceflight", "Study Publication Author List": "Jamal R  Nurul-Faizah J  Then SM  Szewczyk NJ  Stodieck LS  Harun R     Celen I  Jayasinghe A  Doh J  Sabanayagam CR", "Study Assay Technology Platform": "Affymetrix", "Authoritative Source URL": "OSD-42/", "Project Identifier": "CSI-01", "thumbnail": "/geode-py/ws/studies/OSD-42/image", "Project Title": "", "Study Public Release Date": 1318550400.0, "Project Link": "http://www.ncbi.nlm.nih.gov/bioproject/PRJNA146465", "Study Publication Title": "Gene expression changes in space flown Caenorhabditis elegans exposed to a long period of microgravity.     Comparative Transcriptomic Signature of the Simulated Microgravity Response in Caenorhabditis elegans", "organism": "Caenorhabditis elegans", "Accession": "OSD-42", "Study Assay Technology Type": "DNA microarray", "Study Title": "Expression data from C. elegans", "Study Protocol Type": "grow     sample treatment protocol     nucleic_acid_extraction     labeling     hybridization     feature_extraction     image_aquisition     data transformation", "Project Type": "Spaceflight Study", "Study Funding Agency": "Universiti Kebangsaan Malaysia", "Study Factor Type": "Space Flight", "Factor Value": "", "Study Description": "We used microarrays to investigate the effects of microgravity and space radiation on the genome-wide expression of the C. elegans. Three technical replicates of wild type C. elegans (CC1 strain) which exposed to space radiation are analyzed along with ground control.", "Study Protocol Name": "P-GSE32949-3     P-GSE32949-2     P-GSE32949-4     P-GSE32949-5     P-GSE32949-6     P-GSE32949-8     P-GSE32949-7     GeneLab microarray data processing protocol", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-42", "Data Source Accession": "GSE32949"}, "highlight": {"all": ["<em>Space</em> Transportation System (STS), International <em>Space</em> Station (ISS)", "The worms were cultured in C. elegans maintenance medium; CeMM provided by Bioserve <em>Space</em> Technology,", "Apparatus (CGBA) Science Insert-01 (CSI-01) on the STS-116 flight (December 2006) to the International <em>Space</em>", "<em>cgene</em>", "<em>Space</em> Flight"]}}, {"_index": "study", "_type": "docs", "_id": "ZN_6g4QB28eYt3lGNrY7", "_score": 9.583915, "_source": {"Space Program": "Japan Aerospace Exploration Agency", "Flight Program": "JAXA", "Study Assay Measurement Type": "transcription profiling", "Study Protocol Description": "A hair root was cut into ~15 fragments by using knife under a stereoscopic microscope. Collected fragments were immersed of ISOGEN (TakaraBio, Kyoto, Japan) in tube and stirred using the Bioruptor UCD250 (Cosmo Bio, Tokyo, Japan). Next, Total RNA was purified from hair lysates by using the ISOGEN as manufacutuerer's recommendation. Total RNA was amplified using the Ambion MessageAmp aRNA kit (Thermo Fisher Scientific, MA). Each RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).     Cyanine-3 (Cy3) labeled aRNA was prepared from RNA using the MessageAmp aRNA kit (Thermo Fisher Scientific, MA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.     An 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60C for 30 minutes in a reaction volume of 0.1ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.1 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression 4x44K v2 Microarray Kit (G4845A) for 17 hours at 65C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.     Slides were scanned on the Agilent DNA Microarray Scanner (G2505B)     The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.     In each mission, five strands of hair were sampled six times from each astronaut within the period of July 2009 to February 2013. The sampling timings were as follows: 6 sampling time points (Fig 1); first preflight (Launch (L) -180 to -90 days: 6 to 3 months before launch), second preflight (L-60 to -14: 2 months to 2 weeks before launch), first inflight (L+20 to 37: 20 to 37 days after launch), second inflight (Return (R) -20 to -7: 20 to 7 days before return), first postflight (R+2 to 7: 2 to 7 days after return), and second postflight (R+30 to 90: from 1 to 3 months after return).  In sampling day, two astronauts were paired and plucked another hair sample using tweezer in the direction of hair growth without damaging the hair roots. These plucked samples were stored at -80C until analysis.", "Material Type": "Hair follicle", "Study Identifier": "OSD-174", "Study Person": {"First Name": "Masaya Masahiro", "Middle Initials": "", "Last Name": "Seki Terada"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "Data Source Type": "cgene", "Mission": {"Start Date": "", "End Date": "", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "Sex     Tim     Spaceflight     Time", "Study Publication Author List": "Terada M  Seki M  Takahashi R  Yamada S et al.", "Study Assay Technology Platform": "Agilent", "Authoritative Source URL": "OSD-174/", "Project Identifier": "", "thumbnail": "/geode-py/ws/studies/OSD-174/image", "Project Title": "", "Study Public Release Date": 1459382400.0, "Project Link": "", "Study Publication Title": "Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station.", "organism": "Homo sapiens", "Accession": "OSD-174", "Study Assay Technology Type": "DNA microarray", "Study Title": "Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station", "Study Protocol Type": "RNA extraction     labeling     nucleic acid hybridization     data collection     normalization data transformation     treatment protocol", "Project Type": "Spaceflight", "Study Funding Agency": "The experimental cost for this study was funded by Japan Aerospace Exploration Agency (JAXA).", "Study Factor Type": "Sex     root     Space Flight     time", "Factor Value": "", "Study Description": "In recent times, long-term stay has become a common occurrence in the International Space Station (ISS). However, adaptation to the space environment can sometimes pose physiological problems to the astronauts after their return. Therefore, it is important to develop healthcare technologies for astronauts. In this study, hair, an easy-to-obtain sample, was identified as the candidate. In order to investigate the genetic changes in human hair during space flight, the hair follicles of 10 astronauts were analyzed by DNA microarray and real time q-PCR analyses. Space environment induced gene expression of hair follicles of astronaut was measured 6 differnent times included 2 in flight on orbit. Ten independent experiments were performed on differing astronauts. and the sampling day was differed for each astronaut because of their schedules.", "Study Protocol Name": "RNA extraction     labeling     nucleic acid hybridization     data collection     normalization data transformation     treatment protocol", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-174", "Data Source Accession": "E-GEOD-74708"}, "highlight": {"all": ["<em>cgene</em>", "<em>Space</em> Station.", "<em>Space</em> Station", "Sex     root     <em>Space</em> Flight     time", "In order to investigate the genetic changes in human hair during <em>space</em> flight, the hair follicles of"]}}, {"_index": "study", "_type": "docs", "_id": "_9_6g4QB28eYt3lGLrW8", "_score": 9.513603, "_source": {"Space Program": "UK Space Agency, the European Space Agency (ESA)", "Flight Program": "Internation Space Station (ISS)", "Study Assay Measurement Type": "transcription profiling", "Study Protocol Description": "Total RNA was extracted from dry or CAAT seeds for each of Earth-WS, Earth, and Space seed batches, three replicates per treatment, as outlined previously. Its quality was verified using an Agilent Bioanalyzer 2100.          RNA libraries of the 18 samples were sequenced using a HiSeq V4 sequencer (Illumina) generating paired-end 125 bp reads (Vienna BioCenter Core Facilities GmbH, Austria).     Seed Material, Space Travel and Packaging: Seeds of salad rocket, Eruca sativa Mill. (TZ 5007 seed lot 09835147, Tozer Seeds Ltd. Pyports, Downside Bridge Road, Cobham, Surrey, KT11 3EH, UK) were used in the Rocket Science project. Company warehouse storage of this seed lot was at 14C with a relative humidity (RH) of 25% in foil bags. Three seed batches originating from this seed lot were used in our experimental work: (1) The seed batch \u2018Earth-WS (Warehouse Stock)\u2019 was directly taken from this seed lot stored in the described warehouse conditions (14C, 25% RH). The Earth-WS seed batch therefore provides a ground control which remained in the warehouse storage and therefore directly represents the original seed lot (no space journey, no packaging process). (2) The seed batch \u2018Earth\u2019 also provides a ground control, but in addition to the several-month warehouse storage (~22C, 25% RH) it also underwent the packaging process in March 2016. In this packaging process, individual foil packets (red) were filled with 100 seeds each (Seed Packers Ltd., Bury St Edmunds, Suffolk, IP32 6NL, UK). (3) The seed batch \u2018Space\u2019 underwent the space journey and subsequently the same packaging process in March 2016 to provide individual foil packets (blue). During the entire space journey, seed were transported and stored in sealed foil bags with a humidity of 25% inside a jiffy envelope. While Space seeds underwent the space journey (plus packaging), Earth-WS (no packaging) and Earth (plus packaging) remained in warehouse storage. Packaging of the Space and Earth seeds was conducted under the same conditions and with the same foil bags (red and blue) in the second half of March 2016.\n\nFor the space journey, Space seed were transported in the sealed foil bags by airplane from London (UK) to Baikonur (Kazakhstan) via Noordwijk (Netherlands) and Moscow (Russia) in August 2015. The transport was at room temperature (18\u201325C), but as no temperature datalogger was used, we cannot exclude occasional fluctuations beyond this temperature range. Space seeds were launched aboard Soyuz 44S (air temperature on board 18\u201325C) to the ISS on 2nd September 2015. Space seeds were stored for six months inside the ISS (with an average temperature of 22 to 23C and occasional fluctuations between 18 and 32C), and the location within the space station changed; the seeds were stored most of the time in the Columbus laboratory and occasionally were removed for photographs (still sealed within foil bags). Space seeds boarded the Soyuz capsule on 2nd March 2016 for re-entry to Earth, landing on the Kazakh Steppe. Seeds were transported to London (UK) by airplane via Moscow (Russia), Stavanger (Norway), and Houston (USA) and underwent the packaging process in the UK starting 14 March 2016. The sealed foil bag during the space journey was to maintain humidity (low), air composition, and pressure throughout. Moisture content was determined by drying 100 mg of seed in glass vials using a drying oven for 17 h at 103C and reweighing. Dry storage of the seeds in red and blue foil bags in the Seed Science Laboratory at Royal Holloway University of London was at 22C in a sealed plastic container above silica gel (generating <15% RH). Conductivity assays were conducted in May 2016, CAAT assays took place January\u2013April 2017, and RNA extraction for the transcriptome analysis was in May 2017.     Controlled Artificial Ageing Treatment (CAAT): Seeds were transferred to 2 mL Eppendorf tubes and exposed to 70% RH (in the headspace of a sealed container above 25 g/100 mL LiCl) for three days at 22C and then exposed to 35C for the specified number of days (length of CAAT). Seeds were then dried above silica beads at 35C for 2 h and subsequently stored in sealed vials at room temperature until germination assays were carried out. CAAT is a commonly used method in seed science and industry to compare the ageing sensitivity of seeds during dry storage. To achieve this in an experimentally reasonable time, the combination of increased temperature (usually to 35\u201345C) and RH (usually 70\u201390% to generate an elevated seed moisture content) is required.", "Material Type": "Seeds", "Study Identifier": "OSD-301", "Study Person": {"First Name": "Stefan", "Middle Initials": "A", "Last Name": "Rensing"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "Data Source Type": "cgene", "Mission": {"Start Date": "02-Sep-2015", "End Date": "12-Sep-2015", "Name": "Soyuz 44S"}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "Spaceflight     Treatment", "Study Publication Author List": "Chandler JO  Haas FB  Khan S  Bowden L  Ignatz M  Enfissi EMA  Gawthrop F  Griffiths A  Fraser PD  Rensing SA  Leubner-Metzger G", "Study Assay Technology Platform": "Illumina", "Authoritative Source URL": "OSD-301/", "Project Identifier": "", "thumbnail": "/geode-py/ws/studies/OSD-301/image", "Project Title": "Rocket Science", "Study Public Release Date": 1588204800.0, "Project Link": "https://www.esa.int/Space_in_Member_States/United_Kingdom/Highlights/Rocket_Science", "Study Publication Title": "Rocket Science: The Effect of Spaceflight on Germination Physiology, Ageing, and Transcriptome of Eruca sativa Seeds", "organism": "Eruca vesicaria", "Accession": "OSD-301", "Study Assay Technology Type": "RNA Sequencing (RNA-Seq)", "Study Title": "Eruca sativa Rocket Science RNA-seq", "Study Protocol Type": "nucleic acid extraction     library construction     nucleic acid sequencing     sample collection     treatment protocol", "Project Type": "Spaceflight Study", "Study Funding Agency": "Our research was supported by the Research Strategy Fund of Royal Holloway University of London to GL-M. Methods used in this work were developed as part of the ERA-CAPS SeedAdapt consortium project (www.seedadapt.eu) supported by the Deutsche Forschungsgemeinschaft (DFG grant no. RE 1697/8\u20131 to S.A.R.) and the Biotechnology and Biological Sciences Research Council (BBSRC, grant nos. BB/M00192X/1 to G.L.-M.), by the Industrial Strategy Challenge Fund (ISCF) Wave1 AgriTech by Innovate UK and the BBSRC to G.L.-M. (BB/R021147/1) and to F.G./Tozer Seeds (TSB132858), and by the BBSRC to P.D.F and E.A.M.E. (grant no. BB/P001742/1). The APC was funded by Royal Holloway University of London.", "Study Factor Type": "Space Flight     treatment", "Factor Value": "", "Study Description": "In the 'Rocket Science' citizen science project Eruca sativa (salad rocket) seeds stored for six months on board of the International Space Station caused delayed crop establishment. Here we investigated the physiological and molecular mechanisms underpinning the spaceflight effects on dry seeds. We found that 'Space' seed germination vigor was reduced and aging sensitivity increased, but the spaceflight did not compromise seed viability and the development of normal seedlings. Comparative analysis of the transcriptomes (using RNASeq) in dry seeds and upon controlled artificial aging treatment (CAAT) revealed differentially expressed genes (DEGs) associated with spaceflight and ageing. DEG categories enriched by spaceflight and CAAT included transcription and translation with reduced transcript abundances for 40S and 60S ribosomal subunit genes. Among the 'spaceflight-up' DEGs were Heat Shock Protein (HSP), DNAJ-related chaperones, a Heat Shock Factor (HSFA7a-like), and components of several DNA repair pathways (e.g. ATM, DNA ligase1). The 'response to radiation' category was especially enriched in 'spaceflight-up' DEGs including HSPs, catalases and the transcription factor HY5. The major finding from the physiological and transcriptome analysis is that spaceflight causes vigor loss and partial ageing during air-dry seed storage, for which space environmental factors and consequences for seed storage during spaceflights are discussed.", "Study Protocol Name": "nucleic acid extraction     library construction     nucleic acid sequencing     sample collection     treatment protocol", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-301", "Data Source Accession": "PRJNA606141"}, "highlight": {"all": ["UK <em>Space</em> Agency, the European <em>Space</em> Agency (ESA)", "Internation <em>Space</em> Station (ISS)", "For the <em>space</em> journey, <em>Space</em> seed were transported in the sealed foil bags by airplane from London (UK", "<em>cgene</em>", "<em>Space</em> Flight     treatment"]}}, {"_index": "study", "_type": "docs", "_id": "V9_6g4QB28eYt3lGNbZI", "_score": 9.48686, "_source": {"Authoritative Source URL": "OSD-28/", "Flight Program": "International Space Station (ISS)", "Mission": {"End Date": "Sep-11 2009", "Start Date": "Feb-07-2008", "Name": "STS-122  STS-128"}, "Material Type": "", "Project Identifier": "PROTECT", "Accession": "OSD-28", "Identifiers": "GLDS-28", "Study Identifier": "OSD-28", "Study Protocol Name": "P-GSE37124-1     P-GSE37124-6     P-GSE37124-3     P-GSE37124-8     P-GSE37124-7     sample collection     P-GSE37124-4     P-GSE37124-5", "Study Assay Technology Type": "DNA microarray", "Acknowledgments": "", "Study Assay Technology Platform": "Agilent", "Study Person": {"Last Name": "Nicholson", "Middle Initials": "L", "First Name": "Wayne"}, "Study Protocol Type": "bioassay_data_transformation     hybridization     growth protocol     feature_extraction     image_aquisition     sample collection protocol     nucleic_acid_extraction     labeling", "Space Program": "ESA", "Study Title": "Bacillus subtilis spores, PROTECT experiment, Space-exposed and Mars-exposed vs. Earth-control", "Study Factor Type": "Extraterrestrial Environment     Gravitation", "Study Public Release Date": 0, "Parameter Value": "", "thumbnail": "/geode-py/ws/studies/OSD-28/image", "Study Factor Name": "environment exposure     gravitation", "Study Assay Measurement Type": "transcription profiling", "Project Type": "Spaceflight Study", "Factor Value": "", "Data Source Accession": "E-GEOD-37124", "Project Title": "Resistance of spacecraft isolates to outer space for planetary protection purposes", "Study Funding Agency": "This study was supported in part by grants from the NASA Planetary Protection Office (NNA06CB58G and NNX10AV22G) to W.L.N. and by the DLR grant DLR-FuE Projekt ISS-Nutzung in der Biodiagnostik, Programm RF-FuW, Teilprogramm 475 to R.M.", "Study Protocol Description": "Loess normalized log2 ratio (exposed/ground control)     Identical quantities of cDNAs were used to probe 15,000-feature custom microarrays (Agilent) prepared from the B. subtilis strain 168 genomic sequence (Kunst et al., 1997).     To synchronize germination, spores in water (~1 x 10^9) were heat activated at 70C for 30 min, then harvested by centrifugation. To initiate germination, spores were resuspended in 100 ml of 2x LB medium containing the germinant L-alanine (10 mM final concentration) in a 250-ml Klett flask and agitated vigorously in a rotary water bath shaker at 37C. Germination was monitored by loss of optical density as measured in a Klett-Summerson photometer fitted with the No. 66 (660 nm; red) filter.     Raw and normalized intensities were extracted from scanned images, background subtraction, quantile and Loess normalization were performed by UF-ICBR. The microarray contained 15,209 data points equivalent to 4,103 genes with an average number of 3.7 measurements per gene; the oligos were designed such that each Open Reading Frame (ORF) was sampled at multiple locations (n = 3 or 4). Log-transformed data sets for each ORF from simulated Mars-exposed spores were compared to the same ORF from the ground control spores using one-way Analysis of Variance (ANOVA).     Scanning performed at UF-ICBR.     After 60 min of germination, spores were harvested by centrifugation and the pellets stored frozen at -20C until further analysis.     Total RNA was isolated from germinated spores using the Ribo-Pure Bacteria Kit followed by treatment with RNase-free DNase, using the protocols supplied by the manufacturer (Ambion-Life Technologies, Grand Island, NY, USA).     Total RNA samples (20C) were sent to the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR). Samples were converted into Cy3- or Cy5-labelled cDNAs at UF-ICBR.", "Experiment Platform": "EXPOSE-E", "Characteristics": "", "Study Grant Number": "NASA Grand Nos. NNA06CB58G and NNX10AV22G", "Study Publication Author List": "Nicholson WL  Moeller R; PROTECT Team  Horneck G.", "Project Link": "", "Study Publication Title": "Transcription responses of germinating Bacillus subtilis spores exposed to 1.5 years of space and simulated Martian conditions on the EXPOSE-E experiment PROTECT", "Managing NASA Center": "", "Study Description": "Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SP-beta prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.", "organism": "", "Data Source Type": "cgene", "ESA Acronym": ""}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "Bacillus subtilis spores, PROTECT experiment, <em>Space</em>-exposed and Mars-exposed vs. Earth-control", "Resistance of spacecraft isolates to outer <em>space</em> for planetary protection purposes", "As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real <em>space</em> conditions and", "<em>cgene</em>"]}}, {"_index": "study", "_type": "docs", "_id": "sd_6g4QB28eYt3lGKLWQ", "_score": 9.467521, "_source": {"Space Program": "JAXA", "Flight Program": "International Space Station (ISS)", "Study Assay Measurement Type": "transcription profiling", "Study Protocol Description": "A full description of the experimental procedures and flight hardware, including illustrations, employed on this experiment can be found in (Higashitani et al., 2010, Biol. Sci. Space, 23, 183-187). All experiments were carried out under temperature controlled conditions in the Cell Biology Experiment Facility (CBEF) within the KIBO module.Cultures for microRNA expression analysis were grown for 4 d and 8 d. Experiments were stopped by first observing the animals by light microscopy and then by freezing with subsequent storage at -80C in MELFI. Flight samples were thawed on ice with M9 buffer containing 0.05% gelatine, and approximately 10^3 adult hermaphrodites were collected in each experimental condition by picking under stereo microscopy.     Total RNA was isolated with TRIzol Reagent (Invitrogen).     Total RNA (17 micro-g) was purified by flash PAGE^TM system. Label  IT miRNA Labeling Kit (Mirus Bio Corp., cat.#MIR8305) was used for probe label with Cy5.      After pre-hybridization for 60 min at 37C with 6 x SSPE, 1% SDS, 0.2% BSA, hybridization was performed at 37C for 4 hr hybridization in Hybridization Buffer (6xSSPE, 0.8% BSA, 12% DI-Formamide, 2.5% SDS). Array was washed 4 times with 6 x SSPE, 0.05% Tween-20 (25C) for 3 min, 3 x SSPE, 0.05% Tween-20 (25C) for 3 min, 0.5 x SSPE, 0.05% Tween-20 (25C) for 3 min and 0.5 x SSPE, 0.05% Tween-20 (25C) for 3 min.     GenePix 4000B scanner (Molecular Devices)     condition: micro gravity for 4 d\n\n", "Material Type": "Whole Organism", "Study Identifier": "OSD-75", "Study Person": {"First Name": "Atsushi K", "Middle Initials": "", "Last Name": "Higashitani Nemoto"}, "ESA Acronym": "", "Acknowledgments": "We are grateful to the entire crew of the C. elegans RNAi space experiment (CERISE) for operation in STS129, STS130 and the ISS Kibo module. We thank the Caenorhabditis elegans Genetic Center for kind supply of the GFP-fusion strains and Lew Jacobson, University of Pittsburgh for the asp-4 RNAi construct. We also extend thanks to Freya Shephard who prepared some of the dauer animals used in these experiments.", "Managing NASA Center": "", "Data Source Type": "cgene", "Mission": {"Start Date": "11/16/2009", "End Date": "11/27/2009", "Name": "STS-129"}, "Study Grant Number": "Medical Research Council UK G0801271; NIH NIAMS ARO54342", "Experiment Platform": "Cell Biology Experiment Facility (CBEF)", "Study Factor Name": "Altered Gravity     Duration     Spaceflight", "Study Publication Author List": "Etheridge T  Nemoto K  Hashizume T  Mori C  Sugimoto T  Suzuki H  Fukui K  Yamazaki T  Higashibata A  Szewczyk NJ  Higashitani A.", "Study Assay Technology Platform": "Filgen", "Authoritative Source URL": "OSD-75/", "Project Identifier": "CERISE", "thumbnail": "/geode-py/ws/studies/OSD-75/image", "Project Title": "CERISE", "Study Public Release Date": 1297814400.0, "Project Link": "http://iss.jaxa.jp/en/kiboexp/news/cerise_start.html", "Study Publication Title": "The effectiveness of RNAi in Caenorhabditis elegans is maintained during spaceflight.", "organism": "Caenorhabditis elegans", "Accession": "OSD-75", "Study Assay Technology Type": "miRNA Microarray", "Study Title": "MicroRNA expression of C. elegans in space environment", "Study Protocol Type": "growth protocol     RNA extraction     labeling     nucleic acid hybridization     scan protocol     sample treatment protocol", "Project Type": "Spaceflight Study", "Study Funding Agency": "This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan, the Japan Society for the Promotion of Science, and Ground-Based Research Announcement for Space Utilization promoted by the Japan Space Forum. TE was supported by the Medical Research Council UK. NJS was supported by the National Institutes of Health.", "Study Factor Type": "Gravity, Altered     duration     Space Flight", "Factor Value": "", "Study Description": "Entire microRNA expression were analyzed using the Filgen Array miRNA Caenorhabditis elegans 232 probes (Filgen). In the microRNA expression analysis, we compared the expression data between two groups: micro-gravity samples (4 d and 8 d) and controls (4 d and 8 d ground control and 1 G centrifuge onboard ISS).", "Study Protocol Name": "growth protocol     RNA extraction     labeling     nucleic acid hybridization     scan protocol     sample treatment protocol", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-75", "Data Source Accession": "GSE27288"}, "highlight": {"all": ["International <em>Space</em> Station (ISS)", "<em>Space</em>, 23, 183-187).", "<em>cgene</em>", "Utilization promoted by the Japan <em>Space</em> Forum.", "Gravity, Altered     duration     <em>Space</em> Flight"]}}]}}