{"took": 7, "timed_out": false, "_shards": {"total": 5, "successful": 5, "skipped": 0, "failed": 0}, "hits": {"total": 55187, "max_score": 5.811479, "hits": [{"_index": "study", "_type": "docs", "_id": "bHTleY8BcirjsmJn6l3A", "_score": 5.811479, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "Immunoassay", "Study Protocol Description": "Urine aliquots were thawed and processed immediately.     Urine aliquots were thawed and processed with the NULISAseq 200plex v1 Inflammation Panel (Feng et al.) with two technical replicates (10uL each) per sample. This panel includes 203 targets spanning cytokines, chemokines, and other proteins related to immune response. NGS data were processed using the NULISAseq algorithm (Alamar Biosciences). The sample- (SMI) and target-specific (TMI) barcodes were quantified, and up to two mismatching bases or one indel and one mismatch were allowed. Intraplate normalization was performed by dividing the target counts for each sample well by that well\u2019s internal control (mCherry) counts. Interplate normalization was performed using interplate control (IPC) normalization, in which counts were divided by target-specific medians of the three IPC wells on that plate, and then rescaled by the factor 10^4. To facilitate statistical analyses, IPC-normalized counts were log2-transformed to form a more normal distribution. These log2 IPC-normalized counts are referred to as NULISA Protein Quantification (NPQ) units. Methods for data processing and normalization were extracted from Feng et al 2023 (https://www.biorxiv.org/content/10.1101/2023.04.09.536130v2.full.pdf).     To enable maximal data reuse (for machine-readable approaches), the submitted version of this dataset was subsequently transformed and edited to be aligned with a reusable template, which was created through feedback provided by subject matter experts in the ALSDA Analysis Working Group. This transformed reusable version is structured so all results are standardized into specific rows (source/subject) and columns (measures). This enables all assay results to be identically structured for efficient data mining.     All subjects were consented at an informed consent briefing (ICB) at SpaceX (Hawthorne, CA), and samples were collected and processed under the approval of the Institutional Review Board (IRB) at Weill Cornell Medicine, under Protocol 21-05023569. All crew members have consented for data and sample sharing. We analyzed samples before and after a 3-day mission to space.     Urine was collected from the Inspiration4 crew into sterile collection cups. Samples were aliquoted in a sterile hood and frozen at -80C. Aliquots were shipped to Alamar Bio (Fremont, CA) for biomarker profiling.", "Material Type": "Urine", "Study Identifier": "OSD-656", "Study Person": {"First Name": "Eliah Christopher", "Middle Initials": "G. E.", "Last Name": "Overbey Mason"}, "ESA Acronym": "", "Acknowledgments": "Thanks to the WorldQuant Foundation, NASA , the National Institutes of Health (R01MH117406, P01CA214274 R01CA249054), the LLS (MCL7001-18, LLS 9238-16), and the GI Research Foundation (GIRF).", "Managing NASA Center": "", "Data Source Type": "alsda", "Mission": {"Start Date": "09/16/2021", "End Date": "09/18/2021", "Name": "SpaceX Inspiration4"}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "Time     Spaceflight", "Study Publication Author List": "Eliah G. Overbey  Braden T. Tierney  JangKeun Kim  Kirill Grigorev  Jiwoon Park  Nadia Houerbi  Sebastian Garcia Medina  Cem Meydan  Namita Damle  Deena Najjar  Evan E. Afshin  Krista A. Ryon  Karolina Sienkiewicz  Laura Patras  Remi Klotz  Veronica Ortiz  Matthew MacKay  Annalise Schweickart  Maria A. Sierra  Ezequiel Dantas  Theodore Nelson  Egle Cekanaviciute  Gabriel Deards  Jonathan Foox  S. Anand Narayanan  Caleb M. Schmidt  Michael A. Schmidt  Julian C. Schmidt  Sean Mullane  Seth Stravers Tigchelaar  Steven Levitte  Craig Westover  Chandrima Bhattacharya  Serena Lucotti  Daniel J. Butler  Doru Paul  Christopher Mozsary  Lauren M. Sanders  Lynn E. Taylor  Chintan O. Patel  Sharib A. Khan  Mir Suhail  Syed G. Byhaqui  Burhan Aslam  Aaron S Gajadhar  Lucy Williamson  Purvi Tandel  Qiu Yang  Jessica Chu  Ryan Benz  Asim Siddiqui  Daniel Hornburg  Kelly Blease  Juan Moreno  Andrew Boddicker  Junhua Zhao  Bryan Lajoie  Ryan T. Scott  Andrew Altomare  Semyon Kruglyak  Shawn Levy  Briana M. Hudson  Aric Rininger  Sarah E. Church  Afshin Beheshti  George M. Church  Scott M. Smith  Brian E. Crucian  Sara R. Zwart  Francine Garrett-Bakelman  Jan Krumsiek  Qiuying Chen  Dawson Miller  Steven Gross  Kelly L. Bolton  Susan M. Bailey  Richard Granstein  Ari M. Melnick  Bader Shirah  Sylvain V. Costes  Irina Matei  David C. Lyden  Min Yu  Anil S. Menon  Jaime Mateus  Christopher E. Mason     Eliah G. Overbey  Krista Ryon  JangKeun Kim  Braden Tierney  Remi Klotz  Veronica Ortiz  Sean Mullane  Julian C. Schmidt  Matthew MacKay  Namita Damle  Deena Najjar  Irina Matei  Laura Patras  J. Sebastian Garcia Medina  Ashley Kleinman  Jeremy Wain Hirschberg  Jacqueline Proszynski  S. Anand Narayanan  Caleb M. Schmidt  Evan E. Afshin  Lucinda Innes  Mateo Mejia Saldarriaga  Michael A. Schmidt  Richard D. Granstein  Bader Shirah  Min Yu  David Lyden  Jaime Mateus  Christopher E. Mason", "Study Assay Technology Platform": "Alamar Biosciences", "Authoritative Source URL": "OSD-656/", "Project Identifier": "Inspiration4 Crew", "thumbnail": "/geode-py/ws/studies/OSD-656/image", "Project Title": "", "Study Public Release Date": 1715644800.0, "Project Link": "", "Study Publication Title": "The Space Omics and Medical Atlas (SOMA) and international astronaut biobank     Collection of Biospecimens from the Inspiration4 Mission Establishes the Standards for the Space Omics and Medical Atlas (SOMA)", "organism": "Homo sapiens", "Accession": "OSD-656", "Study Assay Technology Type": "Multiplex", "Study Title": "SpaceX Inspiration4 Urine Inflammation Panel (Multiplex, NULISAseq)", "Study Protocol Type": "Sample Preparation     Assay Information     data transformation     Treatment protocol     sample collection", "Project Type": "Spaceflight Study", "Study Funding Agency": "Funding provided by NASA, NIH, and philanthropic donations. NNX14AH50G, NNX17AB26G, 80NSSC22K0254, NNH18ZTT001N-FG2, NNX16AO69A.  The National Institutes of Health (R01MH117406, P01CA214274 R01CA249054), the LLS (MCL7001-18, LLS 9238-16).", "Study Factor Type": "time     Space Flight", "Factor Value": "", "Study Description": "The SpaceX Inspiration4 mission was a 3-day mission with four private astronauts to low Earth orbit that occurred in September 2021. The crew collected biospecimen samples before, during, and after flight. One of these biospecimen collections included urine from pre-flight and post-flight/recovery timepoints (L-92, L-44, L-3, R+1, R+45, R+82). 203 inflammatory, cytokine, and chemokine proteins were quantified using NULISAseq. This study derives results from the Multiplex assay, and the urine data in this study are related to other studies using data from the same experiment; OSD-569 (whole blood), OSD-570 (peripheral blood mononuclear cells), OSD-571 (plasma), OSD-572 (skin, oral, and nasal swabs),  OSD-573 (Dragon capsule samples), OSD-574 (skin biopsy), OSD-575 (serum), and OSD-630 (stool).", "Study Protocol Name": "Sample Preparation     Assay Information     ALSDA Transformed Data     Treatment Protocol     sample collection", "Characteristics": "", "Parameter Value": "", "Identifiers": "LSDS-64", "Data Source Accession": ""}, "highlight": {"all": ["with a reusable template, which was created through feedback provided by subject matter experts in the <em>ALSDA</em>", "<em>alsda</em>", "Sample Preparation     Assay Information     <em>ALSDA</em> Transformed Data     Treatment Protocol     sample"]}}, {"_index": "study", "_type": "docs", "_id": "bXTleY8BcirjsmJn7V2V", "_score": 4.777042, "_source": {"Authoritative Source URL": "OSD-575/", "Flight Program": "", "Mission": {"End Date": "09/18/2021", "Start Date": "09/16/2021", "Name": "SpaceX Inspiration4"}, "Material Type": "Serum", "Project Identifier": "Inspiration4 Crew", "Accession": "OSD-575", "Identifiers": "LSDS-8     GLDS-579", "Study Identifier": "OSD-575", "Study Protocol Name": "ALSDA Transformed Data     Sample Preparation - Alamar Biosciences     Assay Information - Alamar Biosciences     Sample Preparation - Immune HD71     Assay Information - Immune HD71     Sample Preparation - Cardiovascular HDCVD9     Assay Information - Cardiovascular HDCVD9     Treatment Protocol     sample collection     Comprehensive Metabolic Panel", "Study Assay Technology Type": "Multiplex     Multiplex     Multiplex     Comprehensive Metabolic Panel", "Acknowledgments": "Thanks to the WorldQuant Foundation, NASA , the National Institutes of Health (R01MH117406, P01CA214274 R01CA249054), the LLS (MCL7001-18, LLS 9238-16), and the GI Research Foundation (GIRF).", "Study Assay Technology Platform": "Eve Technologies Panel HDCVD9     Eve Technologies Panel HD71     Alamar Biosciences     Quest Diagnostics", "Study Person": {"Last Name": "Mason Overbey Grigorev Nelson", "Middle Initials": "E G M", "First Name": "Christopher Eliah Kirill Theodore"}, "Study Protocol Type": "data transformation     Sample Preparation     Assay Information     Sample Preparation     Assay Information     Sample Preparation     Assay Information     Treatment Protocol     sample collection     Comprehensive Metabolic Panel", "Space Program": "", "Study Title": "SpaceX Inspiration4 Blood Serum Metabolic Panel and Immune/Cardiac Cytokine Arrays (Comprehensive Metabolic Panel and Multiplex)", "Study Factor Type": "time     Space Flight", "Study Public Release Date": 1715644800.0, "Parameter Value": "", "thumbnail": "/geode-py/ws/studies/OSD-575/image", "Study Factor Name": "Time     Spaceflight", "Study Assay Measurement Type": "Immunoassay     Immunoassay     Immunoassay     Analytical Chemistry", "Project Type": "Spaceflight Study", "Factor Value": "", "Data Source Accession": "", "Project Title": "", "Study Funding Agency": "Funding provided by NASA, NIH, and philanthropic donations NNX14AH50G, NNX17AB26G, 80NSSC22K0254, NNH18ZTT001N-FG2, NNX16AO69A", "Study Protocol Description": "To enable maximal data reuse (for machine-readable approaches), the submitted version of this dataset was subsequently transformed and edited to be aligned with a reusable template, which was created through feedback provided by subject matter experts in the ALSDA Analysis Working Group. This transformed reusable version is structured so all results are standardized into specific rows (source/subject) and columns (measures). This enables all assay results to be identically structured for efficient data mining.     Frozen serum aliquots were shipped to Alamar Biosciences (Fremont, CA).     The NULISA-seq Inflammation Panel was performed, which targets 124 cytokines/chemokines and 80 other proteins related to immune response. NGS data were processed using the NULISAseq algorithm (Alamar Biosciences). The sample- (SMI) and target-specific (TMI) barcodes were quantified, and up to two mismatching bases or one indel and one mismatch were allowed. Intraplate normalization was performed by dividing the target counts for each sample well by that well\u2019s internal control (mCherry) counts. Interplate normalization was performed using interplate control (IPC) normalization, in which counts were divided by target-specific medians of the three IPC wells on that plate, and then rescaled by the factor 10^4. To facilitate statistical analyses, IPC-normalized counts were log2-transformed to form a more normal distribution. These log2 IPC-normalized counts are referred to as NULISA Protein Quantification (NPQ) units. Methods for data processing and normalization were extracted from Feng et al 2023 (https://www.biorxiv.org/content/10.1101/2023.04.09.536130v2.full.pdf).     Frozen serum samples were submitted to Eve Technologies (Calgary, Canada) for biomarker profiling.     The biomarker profiling panel Human Cytokine/Chemokine 71-Plex Discovery Assay\u00ae Array (HD71) was used. Concentration values were extrapolated using a 4 of 5 parameter logic standard curve. Measurements were normalized by average of pre-flight values from all crew.     Frozen serum samples were submitted to Eve Technologies (Calgary, Canada) for biomarker profiling.     The biomarker profiling panel Human Cardiovascular Disease Panel 3 9-Plex Discovery Assay\u00ae Array (HDCVD9) was used. Concentration values were extrapolated using a 4 of 5 parameter logic standard curve. Measurements were normalized by average of pre-flight values from all crew.     All subjects were consented at an informed consent briefing (ICB) at SpaceX (Hawthorne, CA), and samples were collected and processed under the approval of the Institutional Review Board (IRB) at Weill Cornell Medicine, under Protocol 21-05023569. All crew members have consented for data and sample sharing. We analyzed samples before and after a 3-day mission to space.     Serum separator tubes (SSTs, BD Biosciences:  367987) were spun at 1300xg for 10 minutes. Fresh serum was sent at room temperature to Quest Diagnostics for a comprehensive metabolic panel (CMP). The remaining serum was frozen at -80C.     Fresh serum was submitted to Quest Diagnostics (test code 10231) and run on a Beckman Coulter AU5800.", "Experiment Platform": "", "Characteristics": "", "Study Grant Number": "", "Study Publication Author List": "Eliah G. Overbey  Braden T. Tierney  JangKeun Kim  Kirill Grigorev  Jiwoon Park  Nadia Houerbi  Sebastian Garcia Medina  Cem Meydan  Namita Damle  Deena Najjar  Evan E. Afshin  Krista A. Ryon  Karolina Sienkiewicz  Laura Patras  Remi Klotz  Veronica Ortiz  Matthew MacKay  Annalise Schweickart  Maria A. Sierra  Ezequiel Dantas  Theodore Nelson  Egle Cekanaviciute  Gabriel Deards  Jonathan Foox  S. Anand Narayanan  Caleb M. Schmidt  Michael A. Schmidt  Julian C. Schmidt  Sean Mullane  Seth Stravers Tigchelaar  Steven Levitte  Craig Westover  Chandrima Bhattacharya  Serena Lucotti  Daniel J. Butler  Doru Paul  Christopher Mozsary  Lauren M. Sanders  Lynn E. Taylor  Chintan O. Patel  Sharib A. Khan  Mir Suhail  Syed G. Byhaqui  Burhan Aslam  Aaron S Gajadhar  Lucy Williamson  Purvi Tandel  Qiu Yang  Jessica Chu  Ryan Benz  Asim Siddiqui  Daniel Hornburg  Kelly Blease  Juan Moreno  Andrew Boddicker  Junhua Zhao  Bryan Lajoie  Ryan T. Scott  Andrew Altomare  Semyon Kruglyak  Shawn Levy  Briana M. Hudson  Aric Rininger  Sarah E. Church  Afshin Beheshti  George M. Church  Scott M. Smith  Brian E. Crucian  Sara R. Zwart  Francine Garrett-Bakelman  Jan Krumsiek  Qiuying Chen  Dawson Miller  Steven Gross  Kelly L. Bolton  Susan M. Bailey  Richard Granstein  Ari M. Melnick  Bader Shirah  Sylvain V. Costes  Irina Matei  David C. Lyden  Min Yu  Anil S. Menon  Jaime Mateus  Christopher E. Mason     Eliah G. Overbey  Krista Ryon  JangKeun Kim  Braden Tierney  Remi Klotz  Veronica Ortiz  Sean Mullane  Julian C. Schmidt  Matthew MacKay  Namita Damle  Deena Najjar  Irina Matei  Laura Patras  J. Sebastian Garcia Medina  Ashley Kleinman  Jeremy Wain Hirschberg  Jacqueline Proszynski  S. Anand Narayanan  Caleb M. Schmidt  Evan E. Afshin  Lucinda Innes  Mateo Mejia Saldarriaga  Michael A. Schmidt  Richard D. Granstein  Bader Shirah  Min Yu  David Lyden  Jaime Mateus  Christopher E. Mason     Eliah G. Overbey  Krista A. Ryon  JangKeun Kim  Christopher E. Mason", "Project Link": "", "Study Publication Title": "The Space Omics and Medical Atlas (SOMA) and international astronaut biobank     Collection of Biospecimens from the Inspiration4 Mission Establishes the Standards for the Space Omics and Medical Atlas (SOMA)     CAMbank: SST Field Processing v1", "Managing NASA Center": "", "Study Description": "The SpaceX Inspiration4 mission was a 3-day mission with four private astronauts to low Earth orbit that occurred in September 2021. The crew collected biospecimen samples before, during, and after flight. One of these biospecimen collections included whole blood collected via venipuncture, with serum extracted from blood using a serum separator tube (SST). Samples were collected pre-flight (L-92, L-44, L-3) and post-flight (R+1, R+45, R+82). Serum samples were submitted for immune and cardiovascular cytokine biomarker profiling panels at two different companies (Eve Technologies and Alamar), and to Quest Diagnostics for comprehensive metabolic panel testing. Data was used to measure changes in cytokines and metabolic measures during spaceflight. This study derives results from the Comprehensive Metabolic Panel and Multiplex assays, and the blood serum data in this study are related to other studies using data from the same experiment; OSD-569 (whole blood), OSD-570 (peripheral blood mononuclear cells), OSD-571 (plasma), OSD-572 (skin, oral, and nasal swabs),  OSD-573 (Dragon capsule samples), OSD-574 (skin biopsy), OSD-656 (urine), and OSD-630 (stool).", "organism": "Homo sapiens", "Data Source Type": "alsda", "ESA Acronym": ""}, "highlight": {"all": ["<em>ALSDA</em> Transformed Data     Sample Preparation - Alamar Biosciences     Assay Information - Alamar Biosciences", "with a reusable template, which was created through feedback provided by subject matter experts in the <em>ALSDA</em>", "<em>alsda</em>"]}}, {"_index": "study", "_type": "docs", "_id": "a3TleY8BcirjsmJn6F3z", "_score": 3.9872966, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "Complete Blood Count     transcription profiling     genome sequencing     transcription profiling     Targeted Genome Sequencing", "Study Protocol Description": "All subjects were consented at an informed consent briefing (ICB) at SpaceX (Hawthorne, CA), and samples were collected and processed under the approval of the Institutional Review Board (IRB) at Weill Cornell Medicine, under Protocol 21-05023569. All crew members have consented for data and sample sharing. We analyzed samples before and after a 3-day mission to space.     For long-read RNAseq and bulkRNAseq, 2.5 mL of whole blood was collected in PAXgene Blood RNA tubes (BD Biosciences, cat no. 762165). Tube was gently inverted 8-10 times. Tube was stored upright for a minimum of 2 hours, then was placed at -20\u00b0C until nucleic acid extraction. For whole genome sequencing and panel clonal hematopoiesis assay, 10mL of whole blood was collected into a Streck cfDNA blood collection tube (cat  230470). Tube centrifuged for 20min at 300g. The red blood cell (RBC) pellet was frozen at -80C. For Complete Blood Count (CBC), one 4mL tube of whole blood was collected in a K2 EDTA tube (BD Biosciences, cat  367844) and submitted to Quest Diagnostics ( test code 6399) for processing.     Total RNA was extracted using the PAXgene Blood RNA kit (Qiagen, cat no. Qiagen 762164) according to the manufacturer's protocol.     Poly-A mRNA was isolated from approximately 50-500 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The resulting mRNA was converted into cDNA using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). After end repair/dA-tailing, adaptor ligation, and USER-enzyme digestion, indexing PCR was carried out using the UG Library Amplification Kit (Ultima Genomics) with custom indexing primers that amplify the TruSeq Read1 and Read 2 sequences, but are appended with Ultima Genomics adapter sequences. After 11 cycles of PCR, amplification products were cleaned up using a 1.0x ratio of AMPure XP beads (Beckman Coulter). Overhang generation was carried out using components from the UG Library Amplification Kit (Ultima Genomics) and material was size selected using a dsSPRI approach with 0.6x/0.85x AMPure XP beads. Quality control of the resulting libraries was carried out using the DNA High Sensitivity Bioanalyzer Reagents (Agilent Technologies) and concentrations were measured via Qubit HS DNA Quantification Kit (ThermoFisher).     Sample pools were then seeded onto UG sequencing beads, pre-enriched, and amplified by emulsion PCR, leveraging UG\u2019s automated sequencing bead preparation system (AMP). Sequencing was performed on UG100 sequencing systems, running 464 flow-cycles (116 cycles across each of the four nucleotides [T, G, C, A]).     Fastq format was checked with fastq_utils v0.25.1. Quality assessment of reads was performed with FastQC v0.11.9 and reports were combined with MultiQC v1.12. rRNA percentages of reads were estimated with the 'hts_SeqScreener' program of htstream v1.3.3 screened against a fasta file of H-sapiens rRNA sequences retrieved from NCBI on 01-Sep-2021.     Oxford Nanopore Technologies\u2019 direct RNA library prep protocol (SQK-RNA002) for PromethION was used. Input amount for each sample library preparation was 500 ng of total RNA.     Each library was divided in two, and brought up to loading volume by adding ONT\u2019s EB (Elution Buffer). One PromethION flow cell (FLO-PRO002) was used per library (i.e per sample), and libraries were sequenced on PromethION 48 beta for 72 hours using the MinKNOW software. Runs were paused and the remaining half of each library was reloaded ~18 hours into the sequencing run onto their respective flow cells. Following this, runs were continued for the remainder of 72 hours.     Fast5 files were basecalled with Guppy version 6.2.1 [community.nanoporetech.com], and alignment of raw nanopore events to the basecalled sequences was done with the f5c module eventalign5. Quality assessment was performed with pycoQC and MultiQC. The Oxford Nanopore Technologies pipeline, pipeline-transcriptome-de, was used to quantify transcripts and to subsequently perform the differential expression analysis. pipeline-transcriptome-de performs the quantification with salmon, accounting for multi-mapping reads; therefore, we included the highest-scoring secondary minimap2 alignments (minimap2 switch -p1.0) in the input for the pipeline. Differential gene expression results, which pipeline-transcriptome-de generates with edgeR while collapsing transcripts into respective genes. Differentially expressed genes were also calculated using minimap2, featureCounts, DESeq2, and the SARTools wrapper package. m6Anet was used to detect m6A modifications. As required by m6anet, the transcriptomic alignments were filtered to retain primary mappings only (minimap2 switch --secondary equals no). Sites of m6A modifications were annotated with probabilities of methylation via m6anet, and methylKit was then used to discover differentially methylated sites between conditions; sites were deemed significant if the resultant methylKit q-value fell below 0.01, as recommended by the tool's authors.     One 4mL tube of whole blood collected in a K2EDTA tube (BD Biosciences, Cat. 367844) was submitted to Quest Diagnostics, test code 6399. The Sysmex XN analyzer performs hematology analysis according to the hydrodynamic focusing (DC Detection), flow cytometry method (semiconductor laser), and SLS hemoglobin method.     To enable maximal data reuse (for machine-readable approaches), the submitted version of this dataset was subsequently transformed and edited to be aligned with a reusable template, which was created through feedback provided by subject matter experts in the ALSDA Analysis Working Group. This transformed reusable version is structured so all results are standardized into specific rows (source/subject) and columns (measures). This enables all assay results to be identically structured for efficient data mining.     Red blood cell (RBC) pellet was thawed at RT and DNA was extracted with the QIAamp Blood Maxi Kit (Qiagen  51192).     The extracted DNA was shipped to Element Biosciences (San Diego, CA) for library preparation. The extracted DNA was quantified using Thermo Fisher Qubit dsDNA HS Assay Kit (cat  Q238253). KAPA HyperPrep Kit (Roche, cat  07962363001) was used for preparing all extracted DNA samples per manufacturer\u2019s instructions. Adapters used were KAPA Unique-Dual Indexed Adapter Kit (Roche, cat  08861919702). 8 DNA samples were library prepared, Covaris sheared and PCR-free. The DNA libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay Kit (cat  Q238253) and sized using Agilent High Sensitivity DNA Kit (cat  5067-4626).     The 8 DNA libraries generated with the KAPA HyperPrep Kit were processed using Adept Library Compatibility Kit (Element Biosciences, cat  830-00003). Each library was circularized individually with an input of 0.5pmol (30 ul of 16.67nM). The final circularized libraries were quantified using qPCR standard and primer mix provided in the Adept Compatibility Workflow Kit (cat  830-00007). The 8 circular libraries were pooled into 4 separate 2-plex pools. Each 2-plex pool was denatured and sequenced on Element AVITI system (Element Biosciences, Part  88-00001) using 2x150 paired end reads with indexing.     Fastq format was checked with fastq_utils v0.25.1. Quality assessment of reads was performed with FastQC v0.11.9 and reports were combined with MultiQC v1.12.     Illumina sequencing adapters containing unique molecular identifiers were ligated onto short-read fragments according to the Kapa Bio-systems HyperPrep protocol (Roche, cat  07962363001). Targeted enrichment of 9 genes (DNMT3A, TET2, ASXL1, TP53, CHEK2, JAK2, SRSF2, SF3B1, PPM1D) involved in clonal hematopoiesis was performed following the standard Invitae capture protocol.     Deep sequencing was performed to a depth of ~ 15,000x using Novaseq 6000 and 150x150 S4 chemistry.     Fastq format was checked with fastq_utils v0.25.1. Quality assessment of reads was performed with FastQC v0.11.9 and reports were combined with MultiQC v1.12.", "Material Type": "RBC pellet     Whole Blood", "Study Identifier": "OSD-569", "Study Person": {"First Name": "Christopher Eliah Kirill Theodore J. Sebastian", "Middle Initials": "E G. M", "Last Name": "Mason Overbey Grigorev Nelson Garcia Medina"}, "ESA Acronym": "", "Acknowledgments": "Thanks to the WorldQuant Foundation, NASA, the National Institutes of Health (R01MH117406, P01CA214274 R01CA249054), the LLS (MCL7001-18, LLS 9238-16), and the GI Research Foundation (GIRF).", "Managing NASA Center": "", "Data Source Type": "cgene     alsda", "Mission": {"Start Date": "9/16/21", "End Date": "9/18/21", "Name": "SpaceX Inspiration4"}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "Time     Spaceflight", "Study Publication Author List": "Eliah G. Overbey  JangKeun Kim  Braden T. Tierney  Jiwoon Park  Nadia Houerbi  Alexander G. Lucaci  Sebastian Garcia Medina  Namita Damle  Deena Najjar  Kirill Grigorev  Evan E. Afshin  Krista A. Ryon  Karolina Sienkiewicz  Laura Patras  Remi Klotz  Veronica Ortiz  Matthew MacKay  Annalise Schweickart  Christopher R. Chin  Maria A. Sierra  Matias F. Valenzuela  Ezequiel Dantas  Theodore M. Nelson  Egle Cekanaviciute  Gabriel Deards  Jonathan Foox  S. Anand Narayanan  Caleb M. Schmidt  Michael A. Schmidt  Julian C. Schmidt  Sean Mullane  Seth Stravers Tigchelaar  Steven Levitte  Craig Westover  Chandrima Bhattacharya  Serena Lucotti  Jeremy Wain Hirschberg  Jacqueline Proszynski  Marissa Burke  Ashley Kleinman  Daniel J. Butler  Conor Loy  Omary Mzava  Joan Lenz  Doru Paul  Christopher Mozsary  Lauren M. Sanders  Lynn E. Taylor  Chintan O. Patel  Sharib A. Khan  Mir Suhail  Syed G. Byhaqui  Burhan Aslam  Aaron S Gajadhar  Lucy Williamson  Purvi Tandel  Qiu Yang  Jessica Chu  Ryan W. Benz  Asim Siddiqui  Daniel Hornburg  Kelly Blease  Juan Moreno  Andrew Boddicker  Junhua Zhao  Bryan Lajoie  Ryan T. Scott  Rachel R. Gilbert  San-huei Lai Polo  Andrew Altomare  Semyon Kruglyak  Shawn Levy  Ishara Ariyapala  Joanne Beer  Bingqing Zhang  Briana M. Hudson  Aric Rininger  Sarah E. Church  Afshin Beheshti  George M. Church  Scott M. Smith  Brian E. Crucian  Sara R. Zwart  Irina Matei  David C. Lyden  Francine Garrett-Bakelman  Jan Krumsiek  Qiuying Chen  Dawson Miller  Joe Shuga  Stephen Williams  Corey Nemec  Guy Trudel  Martin Pelchat  Odette Laneuville  Iwijn De Vlaminck  Steven Gross  Kelly L. Bolton  Susan M. Bailey  Richard Granstein  David Furman  Ari M. Melnick  Sylvain V. Costes  Bader Shirah  Min Yu  Anil S. Menon  Jaime Mateus  Cem Meydan  Christopher E. Mason     Kirill Grigorev  Theodore M. Nelson  Eliah G. Overbey  Nadia Houerbi  JangKeun Kim  Deena Najjar  Namita Damle  Evan E. Afshin  Krista A. Ryon  Jean Thierry-Mieg  Danielle Thierry-Mieg  Ari M. Melnick  Jaime Mateus  Christopher E. Mason     Eliah G. Overbey  Krista Ryon  JangKeun Kim  Braden Tierney  Remi Klotz  Veronica Ortiz  Sean Mullane  Julian C. Schmidt  Matthew MacKay  Namita Damle  Deena Najjar  Irina Matei  Laura Patras  J. Sebastian Garcia Medina  Ashley Kleinman  Jeremy Wain Hirschberg  Jacqueline Proszynski  S. Anand Narayanan  Caleb M. Schmidt  Evan E. Afshin  Lucinda Innes  Mateo Mejia Saldarriaga  Michael A. Schmidt  Richard D. Granstein  Bader Shirah  Min Yu  David Lyden  Jaime Mateus  Christopher E. Mason     J Sebastian Garcia-Medina  Karolina Sienkiewicz  S Anand Narayanan  Eliah G Overbey  Kirill Grigorev  Krista A Ryon  Marissa Burke  Jacqueline Proszynski  Braden Tierney  Caleb M Schmidt  Nuria Mencia-Trinchant  Remi Klotz  Veronica Ortiz  Jonathan Foox  Christopher Chin  Deena Najjar  Irina Matei  Irenaeus Chan  Carlos Cruchaga  Ashley Kleinman  JangKeun Kim  Alexander Lucaci  Conor Loy  Omary Mzava  Iwijn De Vlaminck  Anvita Singaraju  Lynn E Taylor  Julian C Schmidt  Michael A Schmidt  Kelly Blease  Juan Moreno  Andrew Boddicker  Junhua Zhao  Bryan Lajoie  Andrew Altomare  Semyon Kruglyak  Shawn Levy  Min Yu  Duane C Hassane  Susan M Bailey  Kelly Bolton  Jaime Mateus  Christopher E Mason     Eliah G. Overbey  Krista Ryon  JangKeun Kim  Christopher E Mason", "Study Assay Technology Platform": "Quest Diagnostics     Oxford Nanopore Technologies     Element Biosciences     Ultima Genomics     Illumina", "Authoritative Source URL": "OSD-569/", "Project Identifier": "Inspiration4 Crew", "thumbnail": "/geode-py/ws/studies/OSD-569/image", "Project Title": "", "Study Public Release Date": 1715644800.0, "Project Link": "", "Study Publication Title": "The Space Omics and Medical Atlas (SOMA) and international astronaut biobank     Direct RNA sequencing of astronauts reveals spaceflight-associated m6A increases and hematopoietic transcriptional responses     Collection of Biospecimens from the Inspiration4 Mission Establishes the Standards for the Space Omics and Medical Atlas (SOMA)     Genome and clonal hematopoiesis stability contrasts with immune, cfDNA, mitochondrial, and telomere length changes during short duration spaceflight.     CAMbank: cfDNA BCT Field Processing v1", "organism": "Homo sapiens", "Accession": "OSD-569", "Study Assay Technology Type": "Hematology Analyzer     long read RNA Sequencing     nucleotide sequencing     RNA Sequencing (RNA-Seq)     nucleotide sequencing", "Study Title": "Whole Blood Measurements from the SpaceX Inspiration4 Mission (RNA-seq, epitranscriptome, WGS, clonal hematopoiesis, CBC)", "Study Protocol Type": "treatment protocol     sample collection     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     data transformation     Library Construction     Nucleic Acid Sequencing     Sequence Analysis Data Transformation     Complete Blood Count     data transformation     Nucleic Acid Extraction     Library Construction     Nucleic Acid Sequencing     data transformation     Library Construction     Nucleic Acid Sequencing     data transformation", "Project Type": "Spaceflight Study", "Study Funding Agency": "Funding provided by NASA, NIH, and philanthropic donations NNX14AH50G, NNX17AB26G, 80NSSC22K0254, NNH18ZTT001N-FG2, NNX16AO69A", "Study Factor Type": "time     Space Flight", "Factor Value": "", "Study Description": "The SpaceX Inspiration4 mission was a 3-day mission with four private astronauts to low Earth orbit that occurred in September 2021. The crew collected biospecimen samples before, during, and after flight. One of these biospecimen collections included whole blood collected via venipuncture into PaxGene Blood RNA tubes (BD Biosciences, #762165), collected pre-flight (L-92, L-44, L-3) and post-flight (R+1, R+45, R+82, R+194). Total RNA was purified from each tube and mRNA was sequenced using the Oxford Nanopore Technologies direct RNA-sequencing kit on the PromethION. Data was used to generate differential gene expression profiles and annotate sites of m6A modification. Additionally, whole genome sequencing was performed on crew members at L-44 and R+45 and a clonal hematopoiesis panel was performed on a subset of 9 genes (DNMT3A, TET2, ASXL1, TP53, CHEK2, JAK2, SRSF2, SF3B1, PPM1D). For these, DNA was isolated from the pellet of a cfDNA blood collection tube (Streck, cat #230470) (L-44, L-3, R+1, R+45, R+82, R+194). Finally, whole blood collected in K2 EDTA tubes (BD Biosciences, cat# 367844) were submitted to Quest Diagnostics for a complete blood count at all ground timepoints (L-92, L-44, L-3, R+1, R+45, R+82, R+194).", "Study Protocol Name": "Treatment protocol     sample collection     Nucleic Acid Extraction - long read RNA sequencing and bulkRNAseq     Library Construction - bulkRNAseq     Nucleic Acid Sequencing - bulkRNAseq     GeneLab raw data processing protocol - long read RNA sequencing and bulkRNAseq     Library Construction - long read RNA sequencing     Nucleic Acid Sequencing - long read RNA sequencing     Sequence Analysis Data Transformation - long read RNA sequencing     Complete Blood Count     ALSDA Transformed Data     Nucleic Acid Extraction - whole genome sequencing and clonal hematopoiesis     Library Construction - whole genome sequencing     Nucleic Acid Sequencing - whole genome sequencing     GeneLab raw data processing protocol - whole genome sequencing     Library Construction - clonal hematopoiesis     Nucleic Acid Sequencing - clonal hematopoiesis     GeneLab raw data processing protocol - clonal hematopoiesis", "Characteristics": "", "Parameter Value": "", "Identifiers": "GLDS-561     LSDS-7", "Data Source Accession": ""}, "highlight": {"all": ["with a reusable template, which was created through feedback provided by subject matter experts in the <em>ALSDA</em>", "<em>cgene</em>     <em>alsda</em>", "sequencing     Sequence Analysis Data Transformation - long read RNA sequencing     Complete Blood Count     <em>ALSDA</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PRD000294", "_score": 3.7341497, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "", "Study Identifier": "", "Study Person": {"First Name": "Yuan", "Middle Initials": "", "Last Name": "Fang"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "instrument model LTQ FT", "Authoritative Source URL": "PRD000294", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1281783600, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PRD000294", "Study Assay Technology Type": "", "Study Title": "TransSILAC", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": ["Not available"], "Study Description": "TransSILAC-allSpectra.iso_0_singlets_Part1", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PRD000294"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PRD000417", "_score": 3.7285507, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "", "Study Identifier": "", "Study Person": {"First Name": "ATHANASIOS", "Middle Initials": "", "Last Name": "DIDANGELOS"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "instrument model LTQ Orbitrap", "Authoritative Source URL": "PRD000417", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1342695600, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PRD000417", "Study Assay Technology Type": "", "Study Title": "HUMAN AORTA VS AAA", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": ["Not available"], "Study Description": "AAA1", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PRD000417"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PRD000005", "_score": 3.7188258, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "", "Study Identifier": "", "Study Person": {"First Name": "Ronald", "Middle Initials": "", "Last Name": "Beavis"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "instrument model", "Authoritative Source URL": "PRD000005", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1124103600, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PRD000005", "Study Assay Technology Type": "", "Study Title": "GPMDB Submission: Aurum Spectra", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": ["Not available"], "Study Description": "Not available", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PRD000005"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PXD011999", "_score": 3.7133503, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "cell culture", "Study Identifier": "", "Study Person": {"First Name": "Forest", "Middle Initials": "", "Last Name": "White"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "Q Exactive", "Authoritative Source URL": "PXD011999", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1548676800, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PXD011999", "Study Assay Technology Type": "", "Study Title": "DARPin_study", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": [], "Study Description": "Studying signaling networks downstream of HER2 inhibition", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PXD011999"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PRD000671", "_score": 3.7036269, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "cell culture", "Study Identifier": "", "Study Person": {"First Name": "Richard", "Middle Initials": "", "Last Name": "Green"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "instrument model LTQ Orbitrap", "Authoritative Source URL": "PRD000671", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1333278000, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PRD000671", "Study Assay Technology Type": "", "Study Title": "BradelTretheway_2011_Comprehensive_proteomic_analysis_of_Influenza_Virus_Polymerase", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": ["Not available"], "Study Description": "Not available", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PRD000671"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PRD000443", "_score": 3.6982734, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "", "Study Identifier": "", "Study Person": {"First Name": "Jenny J.", "Middle Initials": "", "Last Name": "Fischer"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "instrument model LTQ Orbitrap", "Authoritative Source URL": "PRD000443", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1318935600, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PRD000443", "Study Assay Technology Type": "", "Study Title": "SAHA CCMS", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": ["Not available"], "Study Description": "SAHA CCMS in HepG2", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PRD000443"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PXD001043", "_score": 3.6833184, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "", "Study Identifier": "", "Study Person": {"First Name": "Fabre", "Middle Initials": "", "Last Name": "Bertrand"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "LTQ Orbitrap", "Authoritative Source URL": "PXD001043", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1467975600, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PXD001043", "Study Assay Technology Type": "", "Study Title": "Proteasome composition analysis", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": [], "Study Description": "Proteasome complexes diversity was studied by AP-MS approaches.", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PXD001043"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PRD000607", "_score": 3.6735992, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "", "Study Identifier": "", "Study Person": {"First Name": "Agnes", "Middle Initials": "", "Last Name": "JOURNET"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "instrument model LTQ Orbitrap", "Authoritative Source URL": "PRD000607", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1338462000, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PRD000607", "Study Assay Technology Type": "", "Study Title": "PALMITO", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": ["Not available"], "Study Description": "Palmitoyl proteins enriched by ABE chemistry.", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PRD000607"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PXD009917", "_score": 3.6735992, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "lung", "Study Identifier": "", "Study Person": {"First Name": "weixuan", "Middle Initials": "", "Last Name": "wang"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "LTQ Orbitrap", "Authoritative Source URL": "PXD009917", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1531306800, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PXD009917", "Study Assay Technology Type": "", "Study Title": "A549 CD38 phosphoproteomics analysis", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": [], "Study Description": "A549 CD38 overexpression cells phosphoproteomics analysis", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PXD009917"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PXD004809", "_score": 3.6735992, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "cell culture", "Study Identifier": "", "Study Person": {"First Name": "Yagnesh", "Middle Initials": "", "Last Name": "Umrania"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "LTQ Orbitrap", "Authoritative Source URL": "PXD004809", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1488456000, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PXD004809", "Study Assay Technology Type": "", "Study Title": "mitoSILAC", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": [], "Study Description": "Comparison of control and promoter mutant mitochondrial proteomes.", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PXD004809"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PXD006594", "_score": 3.6735992, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "cell culture", "Study Identifier": "", "Study Person": {"First Name": "Ren\u00e9", "Middle Initials": "", "Last Name": "Zahedi"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "Orbitrap Fusion Lumos", "Authoritative Source URL": "PXD006594", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1516795200, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PXD006594", "Study Assay Technology Type": "", "Study Title": "ChaFRAtip", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": [], "Study Description": "Temporal profiling of proteolytic cleavage during apoptosis.", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PXD006594"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PRD000168", "_score": 3.6735992, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "", "Study Identifier": "", "Study Person": {"First Name": "Juergen", "Middle Initials": "", "Last Name": "Hartler"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "instrument model LTQ Orbitrap XL", "Authoritative Source URL": "PRD000168", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1262865600, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PRD000168", "Study Assay Technology Type": "", "Study Title": "HEL bosutinib/dasatinib profiling", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": ["Not available"], "Study Description": "Not available", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PRD000168"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "PRD000172", "_score": 3.668484, "_source": {"Space Program": "", "Flight Program": "", "Study Assay Measurement Type": "", "Study Protocol Description": "", "Material Type": "blood serum breast cancer cell line", "Study Identifier": "", "Study Person": {"First Name": "Thomas", "Middle Initials": "", "Last Name": "Lau"}, "ESA Acronym": "", "Acknowledgments": "", "Managing NASA Center": "", "links": [""], "Data Source Type": "ebi_pride", "Mission": {"Start Date": "0000000000", "End Date": "0000000000", "Name": ""}, "Study Grant Number": "", "Experiment Platform": "", "Study Factor Name": "", "Study Publication Author List": "", "Study Assay Technology Platform": "instrument model", "Authoritative Source URL": "PRD000172", "Project Identifier": "", "thumbnail": "", "Project Title": "", "Study Public Release Date": 1264507200, "Project Link": "", "Study Publication Title": "", "organism": ["Homo sapiens (Human)"], "Accession": "PRD000172", "Study Assay Technology Type": "", "Study Title": "Hs578T paper", "Study Protocol Type": "", "Project Type": "", "Study Funding Agency": "", "Study Factor Type": [], "Factor Value": ["Not available"], "Study Description": "Depleted SCX frxns", "Study Protocol Name": "", "Characteristics": ["Homo sapiens (Human)"], "Parameter Value": [""], "Data Source Accession": "PRD000172"}, "highlight": {"all": ["<em>ebi_pride</em>"]}}, {"_index": "study", "_type": "docs", "_id": "1IkWkJ8BgAsf-Ud5zezO", "_score": 3.6557777, "_source": {"Authoritative Source URL": "OSD-818/", "Flight Program": "", "Mission": {"End Date": "", "Start Date": "", "Name": ""}, "Material Type": "Culture Media", "Project Identifier": "Simulated_Environmental_Factors", "Accession": "OSD-818", "Identifiers": "LSDS-132", "Study Identifier": "OSD-818", "Study Protocol Name": "Growth Protocol     sample collection     Protein Blot Transfer Info     Blocking Protocol     Labeling Information - FN     Primary Antibody - FN     Secondary Antibody - FN     Western Blot Imaging     Image Metadata     ALSDA Transformed Data     Labeling Information - COLIV     Primary Antibody - COLIV     Secondary Antibody - COLIV", "Study Assay Technology Type": "Western Blot     Western Blot", "Acknowledgments": "", "Study Assay Technology Platform": "ChemiDoc MP     ChemiDoc MP", "Study Person": {"Last Name": "Peng Curry Liu Lohawala Sharma Sharma", "Middle Initials": " P.", "First Name": "Michael Stacy M. Yang Husain Gaurav Tasneem P."}, "Study Protocol Type": "growth protocol     sample collection     Protein Blot Transfer Info     Blocking Protocol     Labeling Information     Primary Antibody     Secondary Antibody     Western Blot Imaging     Image Metadata     data transformation     Labeling Information     Primary Antibody     Secondary Antibody", "Space Program": "", "Study Title": "The ex vivo human translaminar autonomous system to study spaceflight associated neuro-ocular syndrome pathogenesis (Culture Media, Western Blot)", "Study Factor Type": "Treatment Pressure (ICP:IOP)     Optic Nerve Tilt", "Study Public Release Date": 1784764800.0, "Parameter Value": "", "thumbnail": "/geode-py/ws/studies/OSD-818/image", "Study Factor Name": "Treatment Pressure (ICP:IOP)     Optic Nerve Tilt", "Study Assay Measurement Type": "protein quantification     protein quantification", "Project Type": "Ground Study", "Factor Value": "", "Data Source Accession": "", "Project Title": "", "Study Funding Agency": "Translational Research Institute for Space Health grant through NASA Cooperative Agreement NNX16AO69A", "Study Protocol Description": "The human samples utilized were de-identified human donor eyes. The methods were performed in accordance with relevant guidelines and regulations and approved by North Texas Health Science Center on Not Human Subject Research (NHSR). The research activity involved de-identified biospecimens obtained from an external vendor (Lions Eye Institute for Transplant and Research) which meets the federal definition of NHSR. Therefore, the samples were not a part of Human Subject Research and did not require Institutional Review Board and Human Subjects Office review of non-human subjects\u2019 research. The human donor eyes utilized for our study were assessed in an unbiased manner using well-established serological testing performed by the Lions Eye Institute. Only eyes having a non-reactive serology were utilized, including negative COVID-19 serologies. We used male (n equals\u200910) and female (n equals\u20098) donors regardless of sex bias. All experiments were performed in three independent repeats and relevant analysis performed in a masked manner. Human posterior segment culture experiments from human donors were performed in accordance with University of North Texas Health Science Center Institutional Biosafety Committee approval (proposal number IBC-2019-0110). Our data complies with the inclusion and ethics criterion in research. Left (OS or Oculus Sinister) and right (OD or Oculus Dexter) human donor eyes were harvested within 6-12\u2009h of death and cultured within 24\u2009h in the translaminar autonomous system (TAS) model. Culture media consisted of a neurobasal perfusion medium, which was prepared fresh prior to receipt of the eyes. The neurobasal perfusion medium was prepared according to previously established protocols. Briefly, neurobasal/B27 medium (ThermoFisher Scientific) was utilized with 100\u2009U/ml penicillin (Sigma Aldrich), 100\u2009 ug/ml streptomycin (Sigma Aldrich), 1\u2009mM (millimolar) pyruvate (ThermoFisher Scientific), 2\u2009mM glutamine (ThermoFisher Scientific), 5\u2009ug/ml insulin (Sigma Aldrich), 100\u2009 ug/ml transferrin (Sigma Aldrich), 100\u2009ug/ml bovine serum albumin (Sigma Aldrich), 60\u2009ng/ml progesterone (Sigma Aldrich), 16\u2009microgram/ml putrescine (Sigma), 40\u2009ng/ml sodium selenite (Sigma Aldrich), 40\u2009ng/ml thyroxine (Sigma Aldrich), 40\u2009ng/ml tri-iodothyronine (Sigma Aldrich), 5\u2009uM (micromolar) forskolin (Sigma Aldrich) and 1 percent human serum (Sigma Aldrich). Under sterile conditions, whole eyes were initially soaked in a povidone-iodine solution for 2\u2009min followed by a wash in sterile phosphate-buffered solution (PBS). Excess adnexa was dissected from the globe, and the eye was bisected at the equator into anterior and posterior segments. Vitreous humor, lens, and the optic nerve sheath were removed from the posterior segment 2\u2009mm from the posterior end of the globe for all samples. Additional sclera was trimmed, if necessary, to ensure a proper fit over the rounded dome of the intraocular pressure (IOP) chamber (bottom compartment) with the ON facing upwards. The chamber dome is slightly flattened at the top which ensures effective perfusion of the retina. The posterior segment was secured with a circular ring sealed using an epoxy resin O-ring with four screws, ensuring a tight seal. Inflow and outflow tubing was inserted into their respective ports, and the posterior eye cup was manually infused with neurobasal perfusion medium using the push/pull method to remove any air bubbles through the outflow port. The intracranial pressure (ICP) chamber (top compartment) was subsequently placed directly on top of the IOP chamber and sealed with four screws, ensuring that the optic nerve (ON) was encased within the ICP chamber. Inflow and outflow tubing was inserted and the ICP chamber was infused with neurobasal perfusion medium as described above. The entire TAS unit was incubated at 37\u2009C in 5 percent carbon dioxide for the duration of the perfusion study. Each chamber was connected to its own hydrostatic pressure transducer attached to a multichannel bridge amplifier. Each pressure transducer was manually calibrated just prior to the study using a two-point liquid calibration method. Medium was perfused through the inlets at an adjustable flow rate using an automated syringe pump system to maintain the desired pressure, and the conditioned medium was collected every 48-72\u2009hour from the chamber outlets. Pressure data was recorded every 1\u2009min and averaged over a 24-hour period with the LabChart software system. Flow rates were adjusted manually to maintain the targeted pressures. Basic flow rates ranged from 100 to 300\u2009uL/min to mimic the approximate range of physiologic flow rates. The mean and standard deviations of IOP, ICP, and translaminar pressure difference (TLPD) were calculated for every 24-hour period. After a 10 to 12-day period, tissue was collected for further analysis. Measurements were taken from distinct samples. Six experimental groups were defined by combinations of intracranial pressure (ICP) to intraocular pressure (IOP) and optic nerve tilt: Group 1 (ICP:IOP 12:16 mmHg, 0 degree tilt), Group 2 (15:16 mmHg, 0 degree tilt), Group 3 (12:21 mmHg for 7 days followed by 12:16 mmHg for 7 days, 0 degree tilt), Group 4 (21:16 mmHg, 0 degree tilt), Group 5 (15:16 mmHg, 6 degree optic nerve tilt), and Group 6 (15:16 mmHg, 10 degree optic nerve tilt). The raw data compressed folder contains .adicht files, which are the raw pressure recording data collected by the LabChart program. These can be opened in the free version of the software, LabChart Reader (https://www.adinstruments.com/products/labchart-reader). We have also provided the data exported in csv format using (https://github.com/JimHokanson/adinstruments_sdk_python). The pressure processed data files provided by the research team contain a truncated version of the raw data, which is a mean value for each hour of the full raw data set.     After a 14-day period, conditioned perfusion medium from both the IOP and ICP chambers was sampled for analysis. Concentrating beads (StrataClean Resin, Agilent) were\nadded to the conditioned medium and centrifuged, after which the supernatant was discarded.     For western immunoblot analysis, conditioned perfusion medium was collected. Concentrating beads (StrataClean Resin, Agilent) were added to the conditioned medium and centrifuged, after which the supernatant was discarded. An equal volume of 2X Laemmli buffer was added, boiled, and separated by SDS-PAGE. Protein was transferred to nitrocellulose membranes.     Protein was transferred to nitrocellulose membranes and blocked with SuperBlock T20 (Thermo Fisher Scientific).     Blots for the conditioned medium were incubated with one primary antibody: mouse anti-FN.     Blots for the conditioned medium were incubated with the following primary antibody overnight at room temperature: mouse anti-FN (0.5\u20131 ug/ml, AB200541; Abcam).     The blots were then incubated for 1 h at room temperature with HRP-linked anti-mouse secondary antibody (goat anti-mouse, SC-2005, 1:1,000).     Chemiluminescent signal was developed with SuperSignal West Femto Substrate (Thermo Fisher Scientific) and images were captured with the ChemiDoc MP Imaging System (Bio-Rad, Hercules, CA).     Each gel consisted of 12 lanes with one sample occupying each lane. There  are four different gels and the order of the samples within them are as follows:\nGel A:  Lane_1: 7346_OD_ICP, Lane_2: 7346_OD_IOP, Lane_3: 7346_OS_ICP, Lane_4: 7346_OS_IOP, Lane_5: 15373_OD_ICP, Lane_6: 15373_OD_IOP, Lane_7: 15373_OS_ICP, Lane_8: 15373_OS_IOP, Lane_9: 15380_OD_ICP, Lane_10: 15380_OD_IOP, Lane_11: 15380_OS_ICP, Lane_12: 15380_OS_IOP;\n\nGel B: Lane_1: 18004_OD_ICP, Lane_2: 18004_OD_IOP, Lane_3: 18004_OS_ICP, Lane_4: 18004_OS_IOP, Lane_5: 20779_OD_ICP, Lane_6: 20779_OD_IOP, Lane_7: 20779_OS_ICP, Lane_8: 20779_OS_IOP, Lane_9: 22196_OD_ICP, Lane_10: 22196_OD_IOP, Lane_11: 22196_OS_ICP, Lane_12: 22196_OS_IOP;\n\nGel C: Lane_1: 22536_OD_ICP, Lane_2: 22536_OD_IOP, Lane_3: 22536_OS_ICP, Lane_4: 22536_OS_IOP, Lane_5: 32115_OD_ICP, Lane_6: 32115_OD_IOP, Lane_7: 32115_OS_ICP, Lane_8: 32115_OS_IOP, Lane_9: 34085_OD_ICP, Lane_10: 34085_OD_IOP, Lane_11: 34085_OS_ICP, Lane_12: 34085_OS_IOP;\n\nGel D: Lane_3: 37718_OD_ICP, Lane_4: 37718_OD_IOP, Lane_5: 37350_OD_ICP, Lane_6: 37350_OD_IOP, Lane_7: 37350_OS_ICP, Lane_8: 37350_OS_IOP, Lane_9: 39574_OD_ICP, Lane_10: 39574_OD_IOP, Lane_11: 39574_OS_ICP, Lane_12: 39574_OS_IOP, Lane_13: 41204_OS_ICP, Lane_14: 41204_OS_IOP     To enable maximal data reuse (for machine-readable approaches), the submitted version of this dataset was subsequently transformed and edited to be aligned with a reusable template, which was created through feedback provided by subject matter experts in the ALSDA Analysis Working Group. This transformed reusable version is structured so all results are standardized into specific rows (source/subject) and columns (measures). This enables all assay results to be identically structured for efficient data mining.     Blots for the conditioned medium were incubated with one primary antibody: rabbit anti-COLIV.     Blots for the conditioned medium were incubated with the following primary antibody overnight at room temperature: rabbit anti-COLIV (1:1000, NB120-6586; Novus).     The blots were then incubated for 1 h at room temperature with HRP-linked anti-rabbit secondary antibody (goat anti-rabbit, SC-2004, 1:1,000).", "Experiment Platform": "", "Characteristics": "", "Study Grant Number": "", "Study Publication Author List": "Peng M  Curry SM  Liu Y  Lohawala H  Sharma G  Sharma TP.", "Project Link": "", "Study Publication Title": "The ex vivo human translaminar autonomous system to study spaceflight associated neuro-ocular syndrome pathogenesis", "Managing NASA Center": "", "Study Description": "Spaceflight-Associated Neuro-ocular Syndrome (SANS) is a significant unexplained adverse reaction to long-duration spaceflight. We employ an ex vivo translaminar autonomous system (TAS) to recreate a human ocular ground-based spaceflight analogue model to study SANS pathogenesis. To recapitulate the human SANS conditions, human ocular posterior segments are cultured in the TAS model for 14 days. Translaminar pressure differentials are generated by simulating various flow rates within intracranial pressure (ICP) and intraocular (IOP) chambers to maintain hydrostatic pressures of ICP: IOP (12:16, 15:16, 12:21, 21:16 mmHg). In addition, optic nerves are mechanically kinked by 6- and 10-degree tilt inserts for the ICP: IOP - 15:16 mmHg pressure paradigm. The TAS model successfully maintains various pressure differentials for all experimental groups over 14 days. Post culture, we determine inflammatory and extracellular component expression changes within posterior segments. To further characterize the SANS pathogenesis, axonal transport capacity, optic nerve degeneration and retinal functional are measured. Identifiable pathogenic alterations are observed in posterior segments by morphologic, apoptotic, and inflammatory changes including transport and functional deficits under various simulated SANS conditions. Here we report our TAS model provides a unique preclinical application system to mimic SANS pathology and a viable therapeutic testing device for countermeasures. 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