SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions. PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Genome_build: Escherichia coli (DH10B) PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: excel file include RPKM values for each Sample PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively. PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer[linebreak]s recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.). PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	17.6A_Space_50 PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	treatment_protocol	Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	strain: ATCC 4157 PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	location: Space PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	gentamycin concentration (ug/ml): 50 PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL. PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	17.6A_Space_50 PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	treatment_protocol	Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses. PGCGROWTHCONDITIONS
SRR3643541	GSE82341	GSM2190865	GPL18133	PMID_27806055	17.6A	A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	contact_name	Luis,,Zea PGCGROWTHCONDITIONS