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The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment.","name":"sample collection","parameters":[{"@id":"#140294576560352","parameterName":{"@id":"61mpJeBmV9Y5BEvAImmp28SWa286XWbVfznlqMWH","annotationValue":"Sample Storage Method","comments":[],"termAccession":"","termSource":""}},{"@id":"#140294576559056","parameterName":{"@id":"Xv0M9pE0aUSn3kUQ9KB3uLrvghDs8N2ndH4aj4iN","annotationValue":"Sample Preservation Method","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"9AKy01Zo5kzawArYiQYhNN82sV5bfwRsBjaGG7pr","annotationValue":"sample collection","comments":[],"termAccession":"","termSource":"EFO"},"uri":"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2516735","version":""},{"@id":"#140294570266192","comments":[],"components":[],"description":"Seedlings stored in RNAlater were recovered from -80C freezer. Each tube containing the seedlings was allowed to thaw in the fridge overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. Roots of the preserved seedlings from the spaceflight and ground control harvests were dissected and the rest of the seedlings were saved in RNAlater and stored back to -80C freezer.For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis. Total RNA extraction: Total RNA was extracted using Qiashredder and RNAeasy kits from QIAGEN (QIAGEN Sciences, MD, USA) according to the manufacturer\u2019s instructions. Residual DNA was removed by performing an on-column digestion using an RNase Free DNase (QIAGEN GmbH, Hilden, Germany). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).","name":"nucleic acid extraction","parameters":[{"@id":"#140292877609520","parameterName":{"@id":"Hop5C9AJDN9g3VYqtIJtB2A611oQjKFpzG6shAoZ","annotationValue":"QA Instrument","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"LtJv4qkDYGdWEWf7KNMHXmtYiTXfoN2URUaMmE28","annotationValue":"nucleic acid extraction","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#140294570264320","comments":[],"components":[],"description":"Library preparation was performed at the University of Florida\u2019s Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core. RNA integrity was verified using the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, United States). Of the total RNA, 10 ng were used to construct cDNA libraries with the ClonTech SMART-Seq v4 ultra-low input RNA kit for sequencing (Clontech Laboratories, Inc., Cat : 634890), according to the manufacturer\u2019s instructions. Briefly, 1st strand cDNA was primed by the SMART-Seq v4 oligonucleotide, which then base-pairs with these additional nucleotides, creating an extended template. The reverse transcriptase then switches templates and continues transcribing to the end of the oligonucleotide, resulting full-length cDNA that contains an anchor sequence that serves as a universal priming site for second strand synthesis. Then, cDNA was amplified with primer II A for 8 PCR cycles. Illumina sequencing libraries were then generated with 150 pg of cDNA using the Illumina Nextera DNA Sample Preparation Kit (Cat : FC-131-1024) according to the manufacturer\u2019s instructions. Briefly, 150 pg of cDNA were fragmented by tagmentation reaction and adapter sequences were added onto template cDNA by PCR amplification. Libraries were quantitated using both the 2100 BioAnalyzer and qPCR (Kapa Biosystems, catalog number: KK4824).","name":"library construction","parameters":[{"@id":"#140294596582128","parameterName":{"@id":"4a5FiDbDQsdVjo0pSH9bDjaOpun5U1omQLtGKcSM","annotationValue":"library selection","comments":[],"termAccession":"","termSource":""}},{"@id":"#140294596579680","parameterName":{"@id":"IGq9rbNXpEWfC8vEpombTe2NvK8MUiWnl5X0tOmQ","annotationValue":"library layout","comments":[],"termAccession":"","termSource":""}},{"@id":"#140294596583232","parameterName":{"@id":"jyn3HUjeRkcCJW1MOoUHArZWd187DkjSM5JL8A3E","annotationValue":"Stranded","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}},{"@id":"#140294596579584","parameterName":{"@id":"8WYoCyz2C7EHCUeJopWqPTSkwz6WD98uPi77l4Ik","annotationValue":"Library Kit","comments":[],"termAccession":"https://osdr.nasa.gov/","termSource":""}}],"protocolType":{"@id":"guvtidVm5oDIR6gcuJvLrTydPC0nu2TRi1vDGfOz","annotationValue":"library construction","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#140292877610576","comments":[],"components":[],"description":"Sequencing experiments were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) gene expression and sequencing core, University of Florida. In preparation for sequencing, barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT and qPCR (Kapa Biosystems, catalog number: KK4824). Individual samples were pooled equimolarly at 4 nM. This working pool was used as input in the NextSeq500 instrument sample preparation protocol (Illumina, Part 15048776, Rev A). Typically, a 1.3 pM library concentration resulted in optimum clustering density in our instrument (i.e., ~200,000 clusters per mm2). Samples were sequenced on 5 flowcells (5 NextSeq 500 runs), using a 2x76 cycles (paired-end) configuration. A typical sequencing run in the NextSeq500 produced 750-800 million paired-end read with a Q30 equals to or greater than 85%. For RNA seq, around 40 million reads provided sufficient depth for transcriptome analysis.","name":"nucleic acid sequencing","parameters":[{"@id":"#140294596580304","parameterName":{"@id":"CbsOsBKhJANDso5kTtTkkEkONmwFxYPLJsPgkVT2","annotationValue":"sequencing instrument","comments":[],"termAccession":"","termSource":""}},{"@id":"#140294596582848","parameterName":{"@id":"DOWz9RyvfMoltYGyC7An2WqtHdVXvLLJU32JiRbM","annotationValue":"Read Length","comments":[],"termAccession":"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl","termSource":"NCIT"}}],"protocolType":{"@id":"c5S03CdvRWecZ6JPFmdhDQYahJ6XZiDguENvcClH","annotationValue":"nucleic acid sequencing","comments":[],"termAccession":"","termSource":"EFO"},"uri":"","version":""},{"@id":"#140292877610000","comments":[],"components":[],"description":"The data analysis was performed at the ICBR bioinformatics core, University of Florida. 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The cuffdiff output files were parsed with custom scripts to generate the final annotated tables of differentially expressed genes.","name":"sequence analysis data transformation","parameters":[{"@id":"#140294596580544","parameterName":{"@id":"3Hq6ViAPdhnUQVpmPN4g5qe1Sc2CIbQALaTc3jdF","annotationValue":"","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"jkzxN21qOEKADpe9AFD1WXMrrCUeWOZcIJnXtOv8","annotationValue":"sequence analysis data transformation","comments":[],"termAccession":"","termSource":"EFO"},"uri":"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2516735","version":""},{"@id":"#140292877608176","comments":[],"components":[],"description":"Raw fastq files from each sample were assessed for % rRNA using HTStream SeqScreener (version 1.3.3) screened against a fasta file of Arabidopsis thaliana rRNA sequences retrieved from NCBI on Sept-2021. 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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. Arabidopsis Thaliana STAR and RSEM references were built using STAR (version 2.7.11b) and RSEM (version 1.3.3), respectively, Ensembl Plants release 59, genome assembly TAIR10 (Arabidopsis_thaliana.TAIR10.dna.toplevel.fa) and the following gtf annotation file: Arabidopsis_thaliana.TAIR10.59.gtf. Trimmed reads were aligned to the Arabidopsis Thaliana STAR reference with STAR (version 2.7.11b) 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 RSEM (version 1.3.3), with strandedness set to none and RSEM count log files were compiled with MultiQC (version 1.26). To create a set of rRNA-removed quantification data, Ensembl IDs mapping to ribosomal RNA (rRNA) were removed from the RSEM gene count data. Both the original set of RSEM 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) with tximport (version 1.34.0) 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 (<a href=\"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\" target=\"_\" >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</a>), with STRINGdb (version 2.16.4), PANTHER.db (version 1.0.12), and org.At.tair.db (version 3.19.1).","name":"GeneLab RNAseq data processing protocol","parameters":[{"@id":"#140292976274928","parameterName":{"@id":"W9tes96RPBkIuuA0eNexPPFOXF4m5lLPOIBTnVsM","annotationValue":"trimmed sequence 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