title: F. tularensis with prolonged growth - rep3

status: Public on Apr 23 2021

city: Umea

first: Kemal

last: Avican

address: Building 6L

department: Department of Molecular Biology

country: Sweden

institute: Umea University

description:
rRNA depleted total RNA
FRAT_processed.txt

data_processing:
The RNA-seq libraries generated by RNAtag-Seq were sequenced by either single end or paired end Illumina sequencing. Each library harboring a pool of 36 RNA samples was demultiplexed according to the unique 8 nt on the ligated barcode adaptors to separate reads from each replicate by CLC Genomic Workbench version 20.
RNA-seq reads we aligned to the reference genome with CLC Genomic workbench version 20
For differential gene expression analysis, the trimmed mean of M values (TMM) (Robinson and Oshlack, 2010) normalization method was used to normalize the sequencing depth of the individual libraries. For each bacterial species, the comparisons were performed between multiple groups and the control sample so that the full dataset could be used for fitting the generalized linear model.
Genome_build: CP025774, CP008706, NC_017846, NC_001318, NC_006350, NC_006351, NC_008787, NC_008770, NC_08790, NC_017316, NC_011601, NC_017633, NC_017721, NC_017722, NC_017723, NC_017724, NC_008253, C_019551, NC_007146, NC_011333, NC_000921, NC_009648, NC_009649, NC_009650,NC_009651, NC_009652, NC_009653, NC_002942, NC_003210, NC_009525, NC_002946, NC_008767, NC_002516, NC_016810, NC_017718, NC_017719, NC_017720, , CM001474, NC_002952, NC_002953, NC_005951, CP020462, CP020463, NC_004368, NC_008533, NZ_CP008776, NC_012925, NC_002505, NC_002506, NC_010465
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample for each species

organism: Francisella tularensis

source_name: in vitro bacterial culture

growth_protocol: All bacterial strains  were grown in their optimal growth medium and temperatures as indicated in laboratories specialized in each species. Three bacterial cultures were grown overnight and then subcultured to a new culture vial with 1:50-1:100 dilution. The cultures were grown until the exponential phase with an OD600 of 0.1-0.6 and exposed to the 11 stresses separately. The stress conditions, reagents used to generate them, and the exposure times are given in Table S1. Un-exposed cultures at exponential growth were used as controls for differential expression analysis. For nutritional downshift, the three bacterial cultures were spun down at 9000 rpm for 2 minutes, the supernatant removed, the pellets resuspended in 1X M9 supplemented with 0.1 M MgCl2 and 0.1 M CaCl2, and incubated for 30 minutes. For hypoxia, 2 ml screw cap tubes were filled with bacterial culture at exponential growth and the caps were screwed on without leaving space for air. The exposure to the stress conditions was stopped by adding 5% (final concentration) phenol:ethanol solution.

extract_protocol:
One milliliter of triplicate bacterial cultures exposed to the stresses and un-exposed control culture were immediately pelleted by centrifugation at 9000 rpm at room temperature for 2 minutes after adding phenol:ethanol. The supernatant were removed and the pellets resuspended in 0.5 ml Trizol solution. For Gram-negative bacteria, the cells were homogenized in Trizol solution by pipetting up and down 15 times. For Gram-positive bacteria, culture suspensions in Trizol were transferred to previously cooled bead beater tubes containing 0.1-mm glass beads and treated with Mini-Beadbeater (Biospec Products Inc, USA) twice at a fixed speed for 45 seconds, and then cooled on ice for 1 minute between the treatments. Culture homogenates were incubated at room temperature for 5 minutes and then supplemented with 0.2 ml chloroform, thoroughly mixed by shaking 10 times, and incubated for 3 minutes. After centrifugation at 12 000 g at 4°C for 15 minutes, the aqueous upper phase was carefully transferred to new RNase free tubes. An equal volume of 99% ethanol was added to the transferred aqueous phase and isolation continued using the Direct-Zol RNA Miniprep Plus (Zymo Research, USA) RNA purification kit protocol. Total RNAs were eluted in RNase free water in RNase free tubes. The total RNA concentrations were measured using the Qubit BR RNA Assay Kit (ThermoFisher Scientific, USA) and RNA integrity confirmed on a 0.8% agarose gel in TBE buffer.
All rRNA-depleted RNA-seq library preparations were performed according to Shishkin et al.,2015 with minor modifications. RNAtag-Seq allows multiple library preparations in one tube, with initial tagging of total RNA samples with modified (5’P and 3’ddC) DNA barcoded adaptors, each harboring a unique 8 nt sequence used to demultiplex individual libraries after sequencing. We combined the library preparation of three biological replicates from 11 stress-exposed samples and the un-exposed control sample, resulting in 36 library preparations in one tube for each bacterial strain. Therefore, 36 unique barcoded adaptors were used to tag the 36 replicates, with every three barcodes used for samples from the same stress conditions in all bacterial species (Table S2). A total of 100 ng total RNA was used for each biological replicate. The total RNA was fragmented in 2X FastAP Thermosensitive Alkaline Phosphatase buffer for 3 minutes at 94°C, DNase treated, and dephosphorylated with a combination of TURBO DNase and Thermosensitive Alkaline Phosphatase in 1X FastAP buffer for 30 minutes at 37°C. Fragmented, DNase-treated, and dephosphorylated total RNAs were cleaned with a 2X reaction volume of Agencourt RNAClean XP beads. Cleaned total RNAs were incubated with 100 pmol of a unique DNA barcode adaptor at 70°C for 3 minutes, and then ligated with T4 RNA ligase 1 for 90 minutes at 22°C. The ligation was stopped and the enzyme denatured by the addition of RLT buffer. The 36 denatured ligation mixes were then pooled and cleaned in a Zymo Clean & ConcentratorTM-5 column according to the manufacturer’s 200 nt cut-off protocol. The RNAs were eluted in 32 l of RNase free water. The ribosomal RNA was depleted using the Ribo-ZeroTM Magnetic Gold Kit (Bacteria) according to the manufacturer’s instructions. The first strand cDNA of each pool was generated using an AffinityScript Multiple Temperature cDNA synthesis kit with 50 pmol of AR2 primer at 55°C for 55 minutes. The RNA was degraded by adding a 10% reaction volume of 1 N NaOH at 70°C for 12 minutes and the reaction neutralized with an 18% reaction volume of 0.5 M acetic acid. After cleaning the reverse transcription primers with a 2X reaction volume of RNAClean XP beads, the 3Tr3 adapter was ligated with T4 RNA ligase 1 at 22°C with overnight incubation. The second ligation was cleaned first with a 2X, and secondly 1.5X, reaction volume of RNAClean XP beads. The cDNA was then used as the template for PCR reaction with FailSafeTM PCR enzyme mix using 12.5 pmol 2P_univP5 as forward primers and 12.5 pmol ScriptSeqTM Index (barcode) PCR primers as reverse primers. The PCR cycles were as follows: 95°C for 3 minutes, followed by 12 cycles at 95°C for 30 seconds, 55°C for 30 seconds, and 68°C for 3 minutes, and then finishing at 68°C for 7 minutes. The PCR product was cleaned first with a 1.5X, and secondly 0.8X, reaction volume of AMPure beads and eluted in RNAse free water. The library concentrations were measured using the QubitTM dsDNA HS Assay Kit and the library insert size determined by the Agilent DNA 1000 Kit in a 2100 Electrophoresis Bioanalyser Instrument (Agilent, USA).
RNAtag-Seq

treatment_protocol: Bacterial cultures were treated with 11 infection-related stress conditions and a control (Ctrl) sample not treated with any stress: acidic stress (As), pH 3-5 for 10 minutes; bile stress (Bs), 0.5% bile salts for 10 minutes; low iron (Li), 250 μM 2,2-dipyridryl for 10 minutes; hypoxia (Hyp), low oxygen for 4 hours; nutritional downshift (Nd), incubation in 1X M9 salts for 30 minutes; nitrosative stress (Ns), 250 μM Spermine NONOate for 10 minutes; osmotic stress (Oss), 0.5% NaCl for 10 minutes; oxidative stress (Oxs), 0.5-10 mM H2O2 for 10 minutes; stationary phase (Sp); temperature (Tm), 41°C for 20 minutes; varied virulence inducing condition (Vic).

tag: treatment

value: Four hours prolonged growth

value: Francisella tularensis subsp. holarctica FSC200


title: F. tularensis with prolonged growth - rep2

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: strain


title: ChIPseq_ESC_wt_Banp_r3

status: Public on May 17 2021

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (MiSeq) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. ChIP-seq samples were aligned to the mm10/hg19 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters, allowing only for uniquely mapping reads.
Genome_build: mm10/hg19
wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and setting shift to the inferred shifts (Methods). The scores in the wig file therefore represent the number of shifted alignments per 100bp window and per million reads in the library. Peaks were identified using MACS2 using default parameters, except for the option -g, which was set to the mappable genome size for mm10 and hg19 respectively. For the mouse samples, MACS2 was run using the IgG samples as a control, for the human samples, no control was used. Resulting peaks were then filtered for mappability, whereby only peaks that were at least 80% mappable were retained for further analysis. Mappability was defined as the fraction of all possible 50mers contained in a given region that were mappable using the same alignment parameters as used to map the ChIP-seq data. For all downstream analysis, only reproducible peaks, i.e. peaks that occured in all replicates, were used. Scores in the bed files correspond to log2 enrichment over IgG for mouse or log2 read counts for human samples.
Banp motif matches for mm10 and hg19 (PredictedBanpMotifs_withChIPsignal_mm10.csv, PredictedBanpMotifs_withChIPsignal_hg19.csv) were defined as matches to the Banp weight matrix with a log2-odds score (versus a uniform background) of at least 12.5 (Methods). ChIP signal was calculated in a 201 bp window centered on each motif. File columns described in file header.

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). The human cancer cell lines (HCT116 and HCC1954) were cultured in DMEM medium supplemented with 10% fetal calf serum, 1× nonessential amino acids and 1× L-glutamine (37°C, 7% CO2).

extract_protocol:
DNA was purified by Phenol:Chloroform extraction.
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 10 PCR cycles.

treatment_protocol: Cells (1x107) were seeded into 10 cm plates the day before the experiment. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) chromatin was sonicated for ~22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (2) 75-200ug of chromatin was used per IP, (3) protein A/G magnetic Dynabeads (Thermo Fisher Scientific) were used.

tag: cell type

value: embryonic stem cells

tag: genotype

value: wild type

tag: chip antibody

value: AbCam, ab72076


title: F. tularensis with prolonged growth - rep1


title: F. tularensis at stationary phase - rep3

value: Grown until stationary phase


title: F. tularensis at stationary phase - rep1


title: F. tularensis at stationary phase - rep2


title: F. tularensis under oxidative stress - rep3

value: Treated with H2O2


title: F. tularensis under high temperature - rep3

value: Treated with 41C


title: F. tularensis under high temperature - rep2


title: F. tularensis under osmotic stress - rep1

value: Treated with NaCl


title: F. tularensis under nitrosative stress - rep3

value: Treated with spermin NONOate complex


title: F. tularensis under osmotic stress - rep2


title: F. tularensis under nitrosative stress - rep2


title: F. tularensis under osmotic stress - rep3


title: F. tularensis under nitrosative stress - rep1


title: F. tularensis under nutritional downshift - rep3

value: Treated with removal of nutrients


title: F. tularensis under hypoxia - rep3

value: Treated with oxygen deprivation


title: F. tularensis under oxidative stress - rep1


title: F. tularensis under nutritional downshift - rep2


title: F. tularensis under hypoxia - rep1


title: F. tularensis under hypoxia - rep2


title: F. tularensis under nutritional downshift - rep1


title: F. tularensis under low iron - rep3

value: Treated with 2,2-dipyridryl


title: F. tularensis under low iron - rep1


title: F. tularensis under low iron - rep2


title: F. tularensis under high temperature - rep1


title: F. tularensis untreated (control) - rep3

value: Untreated


title: F. tularensis untreated (control) - rep2


title: F. tularensis under oxidative stress - rep2


title: F. tularensis under bile stress - rep3

value: Bile salts treated


title: F. tularensis untreated (control) - rep1


title: F. tularensis under bile stress - rep2


title: F. tularensis under acidic stress - rep2

value: Acetic acid treated


title: K. pneumoniae under human serum treatment - rep3

description:
rRNA depleted total RNA
KLEBS_processed.txt

organism: Klebsiella pneumoniae

value: Treated with human serum

value: Klebsiella pneumoniae subsp. pneumoniae MGH 78578


title: K. pneumoniae under human serum treatment - rep2


title: K. pneumoniae under high temperature - rep3


title: F. tularensis under acidic stress - rep1

value: Francisella tularensis subsp. holarctica FSC200


title: F. tularensis under bile stress - rep1


title: F. tularensis under acidic stress - rep3


title: K. pneumoniae under human serum treatment - rep1


title: K. pneumoniae under high temperature - rep2


title: K. pneumoniae under high temperature - rep1


title: K. pneumoniae under nitrosative stress - rep1


title: K. pneumoniae under nitrosative stress - rep3


title: K. pneumoniae at stationary phase - rep1


title: K. pneumoniae at stationary phase - rep3


title: K. pneumoniae at stationary phase - rep2


title: K. pneumoniae under oxidative stress - rep1


title: K. pneumoniae under osmotic stress - rep2


title: K. pneumoniae under oxidative stress - rep2


title: K. pneumoniae under nutritional downshift - rep2


title: K. pneumoniae under nitrosative stress - rep2


title: K. pneumoniae under osmotic stress - rep3


title: K. pneumoniae under nutritional downshift - rep3


title: K. pneumoniae under oxidative stress - rep3


title: K. pneumoniae under nutritional downshift - rep1


title: K. pneumoniae under hypoxia - rep3


title: K. pneumoniae under hypoxia - rep2


title: K. pneumoniae under hypoxia - rep1


title: K. pneumoniae under osmotic stress - rep1


title: K. pneumoniae under bile stress - rep3


title: K. pneumoniae untreated (control) - rep3


title: K. pneumoniae untreated (control) - rep1


title: K. pneumoniae untreated (control) - rep2


title: K. pneumoniae under low iron - rep2


title: K. pneumoniae under bile stress - rep2


title: K. pneumoniae under low iron - rep3


title: K. pneumoniae under acidic stress - rep2


title: K. pneumoniae under bile stress - rep1


title: K. pneumoniae under acidic stress - rep3


title: H. pylori G27 under NiCl2 treatment - rep1

description:
rRNA depleted total RNA
HPG27_processed.txt

organism: Helicobacter pylori

value: Treated with NiCl2

value: Helicobacter pylori G27


title: H. pylori G27 under high temperature - rep2


title: H. pylori G27 under high temperature - rep3


title: H. pylori G27 at stationary phase - rep1


title: H. pylori G27 under high temperature - rep1


title: H. pylori G27 at stationary phase - rep2


title: H. pylori G27 at stationary phase - rep3


title: H. pylori G27 under NiCl2 treatment - rep3


title: H. pylori G27 under osmotic stress - rep2


title: H. pylori G27 under oxidative stress - rep1


title: H. pylori G27 under osmotic stress - rep1


title: H. pylori G27 under osmotic stress - rep3


title: H. pylori G27 under NiCl2 treatment - rep2


title: K. pneumoniae under low iron - rep1


title: H. pylori G27 under nitrosative stress - rep3


title: H. pylori G27 under nutritional downshift - rep1


title: H. pylori G27 under nitrosative stress - rep1


title: H. pylori G27 under nitrosative stress - rep2


title: H. pylori G27 under hypoxia - rep3


title: H. pylori G27 under oxidative stress - rep2


title: H. pylori G27 under hypoxia - rep2


title: H. pylori G27 under nutritional downshift - rep2


title: H. pylori G27 under hypoxia - rep1


title: H. pylori G27 under nutritional downshift - rep3


title: H. pylori G27 under low iron - rep2


title: K. pneumoniae under acidic stress - rep1


title: H. pylori G27 under oxidative stress - rep3


title: H. pylori G27 under low iron - rep3


title: H. pylori G27 under low iron - rep1


title: L. pneumophila under high temperature - rep3

description:
rRNA depleted total RNA
LEGIP_processed.txt

organism: Legionella pneumophila

value: Legionella pneumophila subsp. pneumophila Philadelphia 1


title: H. pylori G27 untreated (control) - rep3


title: L. pneumophila at stationary phase - rep3

value: Grown until stationary phase


title: L. pneumophila under high temperature - rep2


title: H. pylori G27 untreated (control) - rep1


title: L. pneumophila at stationary phase - rep2


title: H. pylori G27 untreated (control) - rep2


title: L. pneumophila under oxidative stress - rep2

value: Treated with H2O2


title: L. pneumophila under oxidative stress - rep3


title: H. pylori G27 under acidic stress - rep3


title: L. pneumophila under high temperature - rep1

value: Treated with 41C


title: H. pylori G27 under acidic stress - rep2


title: H. pylori G27 under acidic stress - rep1


title: L. pneumophila at stationary phase - rep1


title: L. pneumophila under oxidative stress - rep1


title: L. pneumophila under osmotic stress - rep3

value: Treated with NaCl


title: L. pneumophila under nitrosative stress - rep2

value: Treated with spermin NONOate complex


title: L. pneumophila under nitrosative stress - rep1


title: L. pneumophila under nutritional downshift - rep3

value: Treated with removal of nutrients


title: L. pneumophila under nitrosative stress - rep3


title: L. pneumophila under osmotic stress - rep1


title: L. pneumophila under low iron - rep1


title: L. pneumophila under hypoxia - rep1

value: Treated with oxygen deprivation


title: L. pneumophila under low iron - rep3

value: Treated with 2,2-dipyridryl


title: L. pneumophila under low iron - rep2


title: L. pneumophila under acidic stress - rep3


title: L. pneumophila under nutritional downshift - rep1


title: L. pneumophila under acidic stress - rep2


title: L. pneumophila under acidic stress - rep1


title: L. pneumophila under nutritional downshift - rep2


title: L. pneumophila under hypoxia - rep2


title: L. pneumophila under hypoxia - rep3


title: P. aeruginosa in phosphate medium - rep2

description:
rRNA depleted total RNA
PSEUDO_processed.txt

organism: Pseudomonas aeruginosa

value: Growth in phosphate medium

value: Pseudomonas aeruginosa PAO1


title: L. pneumophila  untreated (control) - rep3

value: Untreated


title: L. pneumophila  untreated (control) - rep2


title: L. pneumophila under osmotic stress - rep2


title: P. aeruginosa under high temperature - rep3


title: L. pneumophila  untreated (control) - rep1

value: untreated


title: P. aeruginosa in phosphate medium - rep1


title: P. aeruginosa at stationary phase - rep2


title: P. aeruginosa at stationary phase - rep1


title: P. aeruginosa under high temperature - rep1


title: P. aeruginosa under oxidative stress - rep2


title: P. aeruginosa at stationary phase - rep3


title: P. aeruginosa under oxidative stress - rep3


title: P. aeruginosa under oxidative stress - rep1


title: P. aeruginosa under osmotic stress - rep3


title: P. aeruginosa under osmotic stress - rep2


title: P. aeruginosa under nitrosative stress - rep1


title: P. aeruginosa under nitrosative stress - rep3


title: P. aeruginosa under osmotic stress - rep1


title: P. aeruginosa under nitrosative stress - rep2


title: P. aeruginosa under nutritional downshift - rep1


title: P. aeruginosa under hypoxia - rep2


title: P. aeruginosa under nutritional downshift - rep2


title: P. aeruginosa under hypoxia - rep1


title: P. aeruginosa under high temperature - rep2


title: P. aeruginosa under hypoxia - rep3


title: P. aeruginosa under nutritional downshift - rep3


title: P. aeruginosa in phosphate medium - rep3


title: L. monocytogenes under Amberlite XAD4 treatment - rep3

description:
rRNA depleted total RNA
Listeria_processed.txt

organism: Listeria monocytogenes

value: Treated with Amberlite XAD4

value: Listeria monocytogenes EGD-e


title: P. aeruginosa untreated (control) - rep1


title: P. aeruginosa under bile stress - rep3

value: Bile salts treated


title: P. aeruginosa under bile stress - rep2


title: P. aeruginosa under acidic stress - rep1

value: Acetic acid treated


title: P. aeruginosa under acidic stress - rep3


title: L. monocytogenes under Amberlite XAD4 treatment - rep1


title: P. aeruginosa under acidic stress - rep2


title: L. monocytogenes under high temperature - rep3


title: P. aeruginosa untreated (control) - rep2


title: L. monocytogenes under Amberlite XAD4 treatment - rep2


title: P. aeruginosa under low iron - rep3


title: P. aeruginosa untreated (control) - rep3


title: P. aeruginosa under low iron - rep1


title: L. monocytogenes under high temperature - rep2


title: L. monocytogenes under oxidative stress - rep3


title: L. monocytogenes at stationary phase - rep2


title: L. monocytogenes under oxidative stress - rep2


title: L. monocytogenes under osmotic stress - rep1


title: L. monocytogenes at stationary phase - rep1


title: L. monocytogenes under osmotic stress - rep2


title: L. monocytogenes under osmotic stress - rep3


title: L. monocytogenes under nitrosative stress - rep2


title: L. monocytogenes under nitrosative stress - rep1


title: P. aeruginosa under bile stress - rep1


title: P. aeruginosa under low iron - rep2


title: L. monocytogenes at stationary phase - rep3


title: L. monocytogenes under nutritional downshift - rep1


title: L. monocytogenes under hypoxia - rep3


title: L. monocytogenes under nutritional downshift - rep2


title: L. monocytogenes under high temperature - rep1


title: L. monocytogenes under hypoxia - rep1


title: L. monocytogenes under low iron - rep2


title: L. monocytogenes under nutritional downshift - rep3


title: L. monocytogenes under hypoxia - rep2


title: L. monocytogenes under low iron - rep3


title: L. monocytogenes under low iron - rep1


title: L. monocytogenes untreated (control) - rep3


title: L. monocytogenes untreated (control) - rep2


title: L. monocytogenes under bile stress - rep3


title: L. monocytogenes untreated (control) - rep1


title: L. monocytogenes under bile stress - rep1


title: L. monocytogenes under oxidative stress - rep1


title: L. monocytogenes under bile stress - rep2


title: L. monocytogenes under nitrosative stress - rep3


title: L. monocytogenes under acidic stress - rep1


title: L. monocytogenes under acidic stress - rep2


title: L. monocytogenes under acidic stress - rep3


title: H. pylori J99 under high temperature - rep3

description:
rRNA depleted total RNA
HPJ99_processed.txt

value: Helicobacter pylori J99


title: H. pylori J99 under NiCl2 treatment - rep3

value: Treated with NiCl2


title: H. pylori J99 under NiCl2 treatment - rep2


title: H. pylori J99 at stationary phase - rep2

value: Grown until stationary phase


title: H. pylori J99 at stationary phase - rep3


title: H. pylori J99 under high temperature - rep2

value: Treated with 41C


title: H. pylori J99 under high temperature - rep1


title: H. pylori J99 at stationary phase - rep1


title: H. pylori J99 under oxidative stress - rep3

value: Treated with H2O2


title: H. pylori J99 under oxidative stress - rep1


title: H. pylori J99 under osmotic stress - rep1

value: Treated with NaCl


title: H. pylori J99 under nitrosative stress - rep2

value: Treated with spermin NONOate complex


title: H. pylori J99 under oxidative stress - rep2


title: H. pylori J99 under osmotic stress - rep3


title: H. pylori J99 under nitrosative stress - rep1


title: H. pylori J99 under nutritional downshift - rep3

value: Treated with removal of nutrients


title: H. pylori J99 under nutritional downshift - rep2


title: H. pylori J99 under osmotic stress - rep2


title: H. pylori J99 under hypoxia - rep3

value: Treated with oxygen deprivation


title: H. pylori J99 under NiCl2 treatment - rep1


title: H. pylori J99 under hypoxia - rep1


title: H. pylori J99 under low iron - rep3

value: Treated with 2,2-dipyridryl


title: H. pylori J99 under low iron - rep2


title: H. pylori J99 under low iron - rep1


title: H. pylori J99 under hypoxia - rep2


title: H. pylori J99 untreated (control) - rep2


title: H. pylori J99 untreated (control) - rep1


title: H. pylori J99 under acidic stress - rep1


title: S. flexneri under congo red treatment - rep1

description:
rRNA depleted total RNA
SHIF_processed.txt

organism: Shigella flexneri

value: Treated with congo red

value: Shigella flexneri 5a str. M90T


title: S. flexneri under congo red treatment - rep2


title: H. pylori J99 under nitrosative stress - rep3


title: S. flexneri under congo red treatment - rep3


title: S. flexneri under high temperature - rep2


title: S. flexneri under high temperature - rep3


title: H. pylori J99 under acidic stress - rep2


title: S. flexneri at stationary phase - rep3


title: S. flexneri at stationary phase - rep2


title: S. flexneri at stationary phase - rep1


title: S. flexneri under oxidative stress - rep2


title: S. flexneri under oxidative stress - rep1


title: S. flexneri under oxidative stress - rep3


title: H. pylori J99 untreated (control) - rep3

value: Untreated


title: S. flexneri under osmotic stress - rep2


title: S. flexneri under osmotic stress - rep3


title: S. flexneri under nitrosative stress - rep1


title: S. flexneri under nitrosative stress - rep2


title: S. flexneri under nitrosative stress - rep3


title: H. pylori J99 under nutritional downshift - rep1


title: S. flexneri under osmotic stress - rep1


title: S. flexneri under hypoxia - rep3


title: S. flexneri under nutritional downshift - rep3


title: S. flexneri under nutritional downshift - rep2


title: S. flexneri under nutritional downshift - rep1


title: S. flexneri under high temperature - rep1


title: H. pylori J99 under acidic stress - rep3


title: S. flexneri under hypoxia - rep1


title: S. flexneri under low iron - rep3


title: S. flexneri under low iron - rep1


title: S. flexneri untreated (control) - rep2


title: S. flexneri untreated (control) - rep3


title: S. flexneri untreated (control) - rep1


title: S. flexneri under bile stress - rep2


title: S. flexneri under bile stress - rep1


title: S. flexneri under acidic stress - rep2


title: S. flexneri under bile stress - rep3


title: H. influenzae under high temperature - rep2

description:
rRNA depleted total RNA
HINF_processed.txt

organism: Haemophilus influenzae

value: Haemophilus influenzae 86-028NP


title: H. influenzae under high temperature - rep1


title: S. flexneri under acidic stress - rep3


title: H. influenzae at stationary phase - rep2


title: H. influenzae under cold shock - rep3

value: Treated with 20C


title: H. influenzae under oxidative stress - rep3


title: H. influenzae at stationary phase - rep3


title: H. influenzae under oxidative stress - rep1


title: H. influenzae under cold shock - rep2


title: S. flexneri under acidic stress - rep1


title: H. influenzae at stationary phase - rep1


title: H. influenzae under cold shock - rep1


title: S. flexneri under hypoxia - rep2


title: H. influenzae under oxidative stress - rep2


title: H. influenzae under osmotic stress - rep1


title: S. flexneri under low iron - rep2


title: H. influenzae under nitrosative stress - rep3


title: H. influenzae under osmotic stress - rep3


title: H. influenzae under nitrosative stress - rep2


title: H. influenzae under nitrosative stress - rep1


title: H. influenzae under osmotic stress - rep2


title: H. influenzae under nutritional downshift - rep3


title: H. influenzae under low iron - rep3


title: H. influenzae under hypoxia - rep1


title: H. influenzae under low iron - rep1


title: H. influenzae under low iron - rep2


title: H. influenzae under hypoxia - rep2


title: H. influenzae untreated (control) - rep2


title: H. influenzae under nutritional downshift - rep2


title: H. influenzae under hypoxia - rep3


title: H. influenzae under nutritional downshift - rep1


title: H. influenzae under acidic stress - rep3


title: A. baumannii under ethanol treatment - rep3

description:
rRNA depleted total RNA
ACIB_processed.txt

organism: Acinetobacter baumannii

value: Treated with Ethanol

value: Acinetobacter baumannii AB5075-UW


title: H. influenzae under acidic stress - rep1

value: Acetic acid treated


title: A. baumannii under ethanol treatment - rep1


title: A. baumannii under high temperature - rep3


title: A. baumannii under high temperature - rep1


title: A. baumannii under high temperature - rep2


title: A. baumannii at stationary phase - rep3


title: A. baumannii at stationary phase - rep2


title: A. baumannii at stationary phase - rep1


title: A. baumannii under oxidative stress - rep1


title: H. influenzae untreated (control) - rep3


title: A. baumannii under oxidative stress - rep2


title: A. baumannii under oxidative stress - rep3


title: A. baumannii under osmotic stress - rep3


title: H. influenzae untreated (control) - rep1


title: H. influenzae under acidic stress - rep2


title: A. baumannii under osmotic stress - rep2


title: A. baumannii under ethanol treatment - rep2


title: A. baumannii under osmotic stress - rep1


title: A. baumannii under nitrosative stress - rep2


title: A. baumannii under nutritional downshift - rep3


title: A. baumannii under nitrosative stress - rep1


title: A. baumannii under hypoxia - rep3


title: A. baumannii under nutritional downshift - rep1


title: A. baumannii under hypoxia - rep1


title: A. baumannii under nutritional downshift - rep2


title: A. baumannii under hypoxia - rep2


title: H. influenzae under high temperature - rep3


title: A. baumannii under low iron - rep1


title: A. baumannii under low iron - rep2


title: S. pyogenes under human serum treatment - rep3

description:
rRNA depleted total RNA
SPYO_processed.txt

organism: Streptococcus pyogenes

value: Treated with human serum

value: Streptococcus pyogenes 5448


title: A. baumannii untreated (control) - rep3


title: A. baumannii untreated (control) - rep2


title: S. pyogenes under human serum treatment - rep2


title: A. baumannii untreated (control) - rep1


title: S. pyogenes under human serum treatment - rep1


title: A. baumannii under bile stress - rep3

value: Bile salts treated


title: A. baumannii under nitrosative stress - rep3


title: A. baumannii under bile stress - rep2


title: S. pyogenes under high temperature - rep2

value: Treated with 41C


title: A. baumannii under low iron - rep3


title: S. pyogenes under high temperature - rep3


title: S. pyogenes under high temperature - rep1


title: A. baumannii under bile stress - rep1


title: S. pyogenes at stationary phase - rep3

value: Grown until stationary phase


title: A. baumannii under acidic stress - rep3


title: S. pyogenes at stationary phase - rep2


title: A. baumannii under acidic stress - rep2


title: A. baumannii under acidic stress - rep1


title: S. pyogenes under oxidative stress - rep3

value: Treated with H2O2


title: S. pyogenes under oxidative stress - rep2


title: S. pyogenes under osmotic stress - rep3

value: Treated with NaCl


title: S. pyogenes under oxidative stress - rep1


title: S. pyogenes under osmotic stress - rep1


title: S. pyogenes under osmotic stress - rep2


title: S. pyogenes under nitrosative stress - rep2

value: Treated with spermin NONOate complex


title: S. pyogenes at stationary phase - rep1


title: S. pyogenes under nitrosative stress - rep1


title: S. pyogenes under hypoxia - rep3

value: Treated with oxygen deprivation


title: S. pyogenes under hypoxia - rep1


title: S. pyogenes under hypoxia - rep2


title: S. pyogenes under nutritional downshift - rep1

value: Treated with removal of nutrients


title: S. pyogenes under nutritional downshift - rep2


title: S. pyogenes under nitrosative stress - rep3


title: S. pyogenes under low iron - rep3

value: Treated with 2,2-dipyridryl


title: S. pyogenes under low iron - rep1


title: S. pyogenes under low iron - rep2


title: S. pyogenes under nutritional downshift - rep3


title: S. pyogenes untreated (control) - rep3

value: Untreated


title: S. pyogenes untreated (control) - rep2


title: S. pyogenes under bile stress - rep3


title: S. pyogenes under bile stress - rep2


title: S. pyogenes untreated (control) - rep1


title: S. pyogenes under acidic stress - rep3


title: S. pyogenes under acidic stress - rep1


title: S. pyogenes under bile stress - rep1


title: S. Typhimurium in MM5.8 medium - rep3

description:
rRNA depleted total RNA
SALMT_processed.txt

organism: Salmonella enterica

value: Growth in MM5.8 medium

value: Salmonella enterica subsp. enterica serovar Typhimurium SL1344


title: S. Typhimurium in MM5.8 medium - rep2


title: S. Typhimurium at stationary phase - rep2


title: S. Typhimurium in MM5.8 medium - rep1


title: S. Typhimurium at stationary phase - rep3


title: S. Typhimurium under high temperature - rep1


title: S. Typhimurium at stationary phase - rep1


title: S. Typhimurium under oxidative stress - rep2


title: S. Typhimurium under nitrosative stress - rep3


title: S. Typhimurium under oxidative stress - rep1


title: S. Typhimurium under osmotic stress - rep3


title: S. Typhimurium under oxidative stress - rep3


title: S. Typhimurium under osmotic stress - rep1


title: S. Typhimurium under osmotic stress - rep2


title: S. Typhimurium under nitrosative stress - rep2


title: S. Typhimurium under nutritional downshift - rep1


title: S. Typhimurium under nutritional downshift - rep2


title: S. pyogenes under acidic stress - rep2


title: S. Typhimurium under nutritional downshift - rep3


title: S. Typhimurium under low iron - rep3


title: S. Typhimurium under nitrosative stress - rep1


title: S. Typhimurium under high temperature - rep2


title: S. Typhimurium under low iron - rep2


title: S. Typhimurium under hypoxia - rep1


title: S. Typhimurium under hypoxia - rep2


title: S. Typhimurium under low iron - rep1


title: S. Typhimurium untreated (control) - rep3


title: S. Typhimurium under high temperature - rep3


title: S. Typhimurium untreated (control) - rep2


title: S. Typhimurium untreated (control) - rep1


title: S. Typhimurium under bile stress - rep2


title: S. Typhimurium under bile stress - rep1


title: S. Typhimurium under acidic stress - rep3


title: S. Typhimurium under bile stress - rep3


title: S. Typhimurium under acidic stress - rep2


title: S. Typhimurium under acidic stress - rep1


title: S. Typhimurium under hypoxia - rep3


title: A. xylosoxidans under cold shock - rep3

description:
rRNA depleted total RNA
ACHX_processed.txt

organism: Achromobacter xylosoxidans

value: Treated with 20C

value: Achromobacter xylosoxidans SOLR10


title: A. xylosoxidans under nitrosative stress - rep2


title: A. xylosoxidans under nutritional downshift - rep3


title: A. xylosoxidans under nitrosative stress - rep1


title: A. xylosoxidans under nitrosative stress - rep3


title: A. xylosoxidans under nutritional downshift - rep2


title: A. xylosoxidans under hypoxia - rep3


title: A. xylosoxidans under low iron - rep2


title: A. xylosoxidans under nutritional downshift - rep1


title: A. xylosoxidans untreated (control) - rep3


title: A. xylosoxidans under low iron - rep1


title: A. xylosoxidans under hypoxia - rep1


title: A. xylosoxidans under high temperature - rep1


title: A. xylosoxidans under high temperature - rep3


title: A. xylosoxidans under cold shock - rep2


title: A. xylosoxidans under cold shock - rep1


title: A. xylosoxidans under low iron - rep3


title: A. xylosoxidans under high temperature - rep2


title: A. xylosoxidans at stationary phase - rep3


title: A. xylosoxidans under oxidative stress - rep3


title: A. xylosoxidans under oxidative stress - rep1


title: A. xylosoxidans under osmotic stress - rep2


title: A. xylosoxidans under osmotic stress - rep3


title: A. xylosoxidans at stationary phase - rep2


title: A. xylosoxidans under oxidative stress - rep2


title: A. xylosoxidans at stationary phase - rep1


title: A. xylosoxidans untreated (control) - rep2


title: A. xylosoxidans under hypoxia - rep2


title: A. xylosoxidans under osmotic stress - rep1


title: A. xylosoxidans untreated (control) - rep1


title: A. xylosoxidans under bile stress - rep3


title: A. xylosoxidans under bile stress - rep1


title: A. xylosoxidans under bile stress - rep2


title: A. xylosoxidans under acidic stress - rep3

value: Acetic acid treated


title: A. xylosoxidans under acidic stress - rep2


title: A. xylosoxidans under acidic stress - rep1


title: S. suis under porcine serum treatment - rep3

description:
rRNA depleted total RNA
SSUIS_processed.txt

organism: Streptococcus suis

value: Treated with porcine serum

value: Streptococcus suis S10 - P1/7


title: S. suis under high temperature - rep2


title: S. suis untreated (control) - rep2


title: S. suis under oxidative stress - rep2


title: S. suis under oxidative stress - rep1


title: S. suis under high temperature - rep1


title: S. suis under bile stress - rep3

value: Bile salts treated


title: S. suis under high temperature - rep3

value: Treated with 41C


title: S. suis under nitrosative stress - rep1


title: S. suis under oxidative stress - rep3


title: S. suis under nutritional downshift - rep3


title: S. suis under nutritional downshift - rep2


title: S. suis under nutritional downshift - rep1


title: S. suis under osmotic stress - rep3


title: S. suis untreated (control) - rep1


title: S. suis under low iron - rep3


title: S. suis under porcine serum treatment - rep1


title: S. suis under low iron - rep1


title: S. suis under nitrosative stress - rep3


title: S. suis under low iron - rep2


title: S. suis under nitrosative stress - rep2


title: S. suis under porcine serum treatment - rep2


title: S. suis untreated (control) - rep3


title: S. suis under osmotic stress - rep1


title: S. suis under osmotic stress - rep2


title: S. suis under bile stress - rep1


title: S. suis under acidic stress - rep2


title: S. suis under bile stress - rep2


title: S. suis under acidic stress - rep3


title: E. coli (EPEC) under low iron - rep3

description:
rRNA depleted total RNA
EPEC_processed.txt

organism: Escherichia coli

value: Escherichia coli EPEC 0127:H6 E2348/69


title: E. coli (EPEC) under low iron - rep1


title: E. coli (EPEC) under low iron - rep2


title: E. faecalis treated with FBS - rep2

description:
rRNA depleted total RNA
ENTFA_processed.txt

organism: Enterococcus faecalis

value: Treated with fetal bovine serum

value: Enterococcus faecalis OG1RF


title: E. faecalis under high temperature - rep2


title: E. faecalis under high temperature - rep3


title: E. coli (EPEC) untreated (control) - rep2


title: E. faecalis treated with FBS - rep1


title: E. faecalis under high temperature - rep1


title: E. coli (EPEC) untreated (control) - rep1


title: E. coli (EPEC) under bile stress - rep1


title: E. faecalis at stationary phase - rep3

value: Grown until stationary phase


title: E. faecalis at stationary phase - rep1


title: E. coli (EPEC) under acidic stress - rep3


title: E. coli (EPEC) under bile stress - rep2


title: E. faecalis under oxidative stress - rep2

value: Treated with H2O2


title: E. faecalis under oxidative stress - rep1


title: E. coli (EPEC) under acidic stress - rep1


title: E. faecalis under osmotic stress - rep3

value: Treated with NaCl


title: E. coli (EPEC) under acidic stress - rep2


title: E. faecalis at stationary phase - rep2


title: E. faecalis treated with FBS - rep3


title: E. coli (EPEC) under bile stress - rep3


title: S. suis under acidic stress - rep1


title: E. faecalis under osmotic stress - rep2


title: E. faecalis under osmotic stress - rep1


title: E. coli (EPEC) untreated (control) - rep3


title: E. coli (UPEC)  with prolonged growth - rep1

description:
rRNA depleted total RNA
UPEC_processed.txt

value: One and a half hour prolonged growth

value: Escherichia coli UPEC 536


title: E. faecalis under oxidative stress - rep3


title: E. coli (UPEC)  with prolonged growth - rep3


title: E. faecalis under nitrosative stress - rep3

value: Treated with spermin NONOate complex


title: E. coli (UPEC) under high temperature - rep2


title: E. coli (UPEC) under high temperature - rep3


title: E. faecalis under nitrosative stress - rep2


title: E. faecalis under nutritional downshift - rep3

value: Treated with removal of nutrients


title: E. faecalis under nutritional downshift - rep2


title: E. faecalis under nutritional downshift - rep1


title: E. coli (UPEC) at stationary phase - rep3


title: E. coli (UPEC) at stationary phase - rep2


title: E. faecalis under hypoxia - rep2

value: Treated with oxygen deprivation


title: E. coli (UPEC) at stationary phase - rep1


title: E. coli (UPEC)  with prolonged growth - rep2


title: E. coli (UPEC) under oxidative stress - rep3


title: E. faecalis under hypoxia - rep1


title: E. faecalis under low iron - rep3

value: Treated with 2,2-dipyridryl


title: E. coli (UPEC) under oxidative stress - rep2


title: E. coli (UPEC) under oxidative stress - rep1


title: E. faecalis under low iron - rep2


title: E. coli (UPEC) under osmotic stress - rep2


title: E. faecalis under low iron - rep1


title: E. faecalis under nitrosative stress - rep1


title: E. coli (UPEC) under osmotic stress - rep3


title: E. faecalis untreated (control) - rep3

value: Untreated


title: E. coli (UPEC) under high temperature - rep1


title: E. coli (UPEC) under osmotic stress - rep1


title: E. faecalis untreated (control) - rep2


title: E. faecalis untreated (control) - rep1


title: E. coli (UPEC) under nitrosative stress - rep2


title: E. faecalis under bile stress - rep3


title: E. coli (UPEC) under nitrosative stress - rep3


title: E. faecalis under hypoxia - rep3


title: E. faecalis under bile stress - rep2


title: E. faecalis under bile stress - rep1


title: E. coli (UPEC) under nutritional downshift - rep3


title: E. coli (UPEC) under nutritional downshift - rep2


title: E. faecalis under acidic stress - rep3

value: Acetic acid treated


title: E. coli (UPEC) under nutritional downshift - rep1


title: E. faecalis under acidic stress - rep2


title: E. faecalis under acidic stress - rep1


title: E. coli (UPEC) under hypoxia - rep2


title: E. coli (UPEC) under hypoxia - rep1


title: E. coli (UPEC) under low iron - rep3


title: E. coli (UPEC) untreated (control) - rep3


title: E. coli (UPEC) under low iron - rep1


title: A. actinomycetemcomitans under human serum treatment - rep3

description:
rRNA depleted total RNA
AGGA_processed.txt

organism: Aggregatibacter actinomycetemcomitans

value: Treated with human serum


title: E. coli (UPEC) under hypoxia - rep3


title: E. coli (UPEC) under low iron - rep2


title: E. coli (UPEC) under nitrosative stress - rep1


title: A. actinomycetemcomitans under human serum treatment - rep1


title: A. actinomycetemcomitans under high temperature - rep2


title: A. actinomycetemcomitans under human serum treatment - rep2


title: A. actinomycetemcomitans under high temperature - rep3


title: E. coli (UPEC) under bile stress - rep3

value: Bile salts treated


title: E. coli (UPEC) untreated (control) - rep1


title: A. actinomycetemcomitans under high temperature - rep1

value: Treated with 41C


title: E. coli (UPEC) under bile stress - rep1


title: A. actinomycetemcomitans at stationary phase - rep3


title: E. coli (UPEC) under bile stress - rep2


title: A. actinomycetemcomitans at stationary phase - rep2


title: A. actinomycetemcomitans at stationary phase - rep1


title: E. coli (UPEC) under acidic stress - rep2


title: E. coli (UPEC) under acidic stress - rep3


title: A. actinomycetemcomitans under oxidative stress - rep3


title: E. coli (UPEC) under acidic stress - rep1


title: A. actinomycetemcomitans under oxidative stress - rep1


title: E. coli (UPEC) untreated (control) - rep2


title: E. coli (ETEC)  with prolonged growth - rep3

description:
rRNA depleted total RNA
ETEC_processed.txt

value: Escherichia coli ETEC H10407


title: A. actinomycetemcomitans under osmotic stress - rep2


title: E. coli (ETEC)  with prolonged growth - rep2


title: A. actinomycetemcomitans under nitrosative stress - rep2


title: A. actinomycetemcomitans under osmotic stress - rep1


title: E. coli (ETEC)  with prolonged growth - rep1


title: A. actinomycetemcomitans under nitrosative stress - rep1


title: E. coli (ETEC) under high temperature - rep3


title: E. coli (ETEC) under high temperature - rep2


title: E. coli (ETEC) at stationary phase - rep3


title: E. coli (ETEC) under high temperature - rep1


title: A. actinomycetemcomitans under oxidative stress - rep2


title: A. actinomycetemcomitans under nutritional downshift - rep1


title: A. actinomycetemcomitans under nutritional downshift - rep2


title: A. actinomycetemcomitans under osmotic stress - rep3


title: A. actinomycetemcomitans under nutritional downshift - rep3


title: E. coli (ETEC) at stationary phase - rep2


title: E. coli (ETEC) at stationary phase - rep1


title: E. coli (ETEC) under oxidative stress - rep3


title: E. coli (ETEC) under oxidative stress - rep2


title: A. actinomycetemcomitans under hypoxia - rep3


title: A. actinomycetemcomitans under hypoxia - rep1


title: E. coli (ETEC) under osmotic stress - rep3


title: A. actinomycetemcomitans under hypoxia - rep2


title: A. actinomycetemcomitans under low iron - rep2


title: A. actinomycetemcomitans under low iron - rep3


title: A. actinomycetemcomitans under nitrosative stress - rep3


title: E. coli (ETEC) under osmotic stress - rep1


title: E. coli (ETEC) under nitrosative stress - rep3


title: A. actinomycetemcomitans under low iron - rep1


title: E. coli (ETEC) under nitrosative stress - rep2


title: A. actinomycetemcomitans untreated (control) - rep3


title: E. coli (ETEC) under nitrosative stress - rep1


title: A. actinomycetemcomitans untreated (control) - rep1


title: A. actinomycetemcomitans untreated (control) - rep2


title: A. actinomycetemcomitans under bile stress - rep3


title: A. actinomycetemcomitans under bile stress - rep2


title: E. coli (ETEC) under nutritional downshift - rep3


title: E. coli (ETEC) under nutritional downshift - rep2


title: E. coli (ETEC) under oxidative stress - rep1


title: E. coli (ETEC) under osmotic stress - rep2


title: A. actinomycetemcomitans under acidic stress - rep3


title: E. coli (ETEC) under nutritional downshift - rep1


title: A. actinomycetemcomitans under bile stress - rep1


title: A. actinomycetemcomitans under acidic stress - rep2


title: E. coli (ETEC) under hypoxia - rep3


title: A. actinomycetemcomitans under acidic stress - rep1


title: Y. pseudotuberculosis with growth at 37C and Ca2+ depletion - rep2

description:
rRNA depleted total RNA
YPSTB_processed.txt

organism: Yersinia pseudotuberculosis

value: Growth at 37C with Ca2+ depletion

value: Yersinia pseudotuberculosis YPIII


title: Y. pseudotuberculosis with growth at 37C and Ca2+ depletion - rep3


title: Y. pseudotuberculosis with growth at 37C and Ca2+ depletion - rep1


title: E. coli (ETEC) under low iron - rep2


title: E. coli (ETEC) under low iron - rep3


title: E. coli (ETEC) under low iron - rep1


title: E. coli (ETEC) untreated (control) - rep3


title: E. coli (ETEC) untreated (control) - rep2


title: Y. pseudotuberculosis under high temperature - rep2


title: E. coli (ETEC) untreated (control) - rep1


title: Y. pseudotuberculosis under high temperature - rep1


title: E. coli (ETEC) under bile stress - rep3


title: Y. pseudotuberculosis at stationary phase - rep2

value: Grown until stationary phase


title: Y. pseudotuberculosis at stationary phase - rep3


title: Y. pseudotuberculosis at stationary phase - rep1


title: E. coli (ETEC) under hypoxia - rep2


title: Y. pseudotuberculosis under oxidative stress - rep3

value: Treated with H2O2


title: E. coli (ETEC) under acidic stress - rep3


title: E. coli (ETEC) under hypoxia - rep1


title: Y. pseudotuberculosis under oxidative stress - rep1


title: E. coli (ETEC) under acidic stress - rep2


title: Y. pseudotuberculosis under oxidative stress - rep2


title: Y. pseudotuberculosis under osmotic stress - rep3

value: Treated with NaCl


title: E. coli (EPEC)  with prolonged growth - rep3

value: One and a half hour prolonged growth

value: Escherichia coli EPEC 0127:H6 E2348/69


title: Y. pseudotuberculosis under high temperature - rep3


title: Y. pseudotuberculosis under osmotic stress - rep2


title: E. coli (EPEC)  with prolonged growth - rep2


title: Y. pseudotuberculosis under osmotic stress - rep1


title: E. coli (EPEC)  with prolonged growth - rep1


title: E. coli (EPEC) under high temperature - rep3


title: E. coli (EPEC) under high temperature - rep2


title: E. coli (EPEC) under high temperature - rep1


title: E. coli (ETEC) under bile stress - rep2


title: E. coli (EPEC) at stationary phase - rep3


title: Y. pseudotuberculosis under nitrosative stress - rep1

value: Treated with spermin NONOate complex


title: Y. pseudotuberculosis under nitrosative stress - rep2


title: Y. pseudotuberculosis under nutritional downshift - rep3

value: Treated with removal of nutrients


title: E. coli (EPEC) at stationary phase - rep1


title: E. coli (EPEC) at stationary phase - rep2


title: E. coli (ETEC) under bile stress - rep1


title: Y. pseudotuberculosis under nutritional downshift - rep2


title: E. coli (ETEC) under acidic stress - rep1


title: Y. pseudotuberculosis under nutritional downshift - rep1


title: Y. pseudotuberculosis under hypoxia - rep3

value: Treated with oxygen deprivation


title: E. coli (EPEC) under oxidative stress - rep3


title: Y. pseudotuberculosis under hypoxia - rep1


title: E. coli (EPEC) under oxidative stress - rep2


title: E. coli (EPEC) under oxidative stress - rep1


title: Y. pseudotuberculosis under hypoxia - rep2


title: V. cholerae with growth at 37C - rep2

description:
rRNA depleted total RNA
Vibrio_processed.txt

organism: Vibrio cholerae

value: Growth at 37C

value: Vibrio cholerae O1 biovar El Tor str. N16961


title: Y. pseudotuberculosis under low iron - rep3

value: Treated with 2,2-dipyridryl


title: Y. pseudotuberculosis under nitrosative stress - rep3


title: V. cholerae with growth at 37C - rep1


title: E. coli (EPEC) under osmotic stress - rep3


title: Y. pseudotuberculosis under low iron - rep2


title: V. cholerae with growth at 37C - rep3


title: V. cholerae under high temperature - rep3


title: E. coli (EPEC) under osmotic stress - rep2


title: Y. pseudotuberculosis under low iron - rep1


title: V. cholerae under high temperature - rep2


title: E. coli (EPEC) under osmotic stress - rep1


title: Y. pseudotuberculosis untreated (control) - rep2

value: Untreated


title: Y. pseudotuberculosis untreated (control) - rep3


title: E. coli (EPEC) under nitrosative stress - rep3


title: Y. pseudotuberculosis untreated (control) - rep1


title: V. cholerae under high temperature - rep1


title: E. coli (EPEC) under nitrosative stress - rep1


title: Y. pseudotuberculosis under bile stress - rep2

value: Bile salts treated


title: Y. pseudotuberculosis under bile stress - rep3


title: E. coli (EPEC) under nitrosative stress - rep2


title: E. coli (EPEC) under nutritional downshift - rep3


title: V. cholerae at stationary phase - rep3


title: V. cholerae at stationary phase - rep2


title: V. cholerae at stationary phase - rep1


title: E. coli (EPEC) under nutritional downshift - rep1


title: V. cholerae under oxidative stress - rep3


title: E. coli (EPEC) under nutritional downshift - rep2


title: Y. pseudotuberculosis under bile stress - rep1


title: Y. pseudotuberculosis under acidic stress - rep2

value: Acetic acid treated


title: V. cholerae under osmotic stress - rep2


title: V. cholerae under oxidative stress - rep1


title: V. cholerae under oxidative stress - rep2


title: Y. pseudotuberculosis under acidic stress - rep3


title: E. coli (EPEC) under hypoxia - rep3


title: V. cholerae under osmotic stress - rep3


title: E. coli (EPEC) under hypoxia - rep2


title: Y. pseudotuberculosis under acidic stress - rep1


title: E. coli (EPEC) under hypoxia - rep1


title: N. gonorrhoeae under L-lactate treatment - rep3

description:
rRNA depleted total RNA
NGON_processed.txt

organism: Neisseria gonorrhoeae

value: Treated with L-lactate

value: Neisseria gonorrhoeae FA 1090


title: M. tuberculosis under high temperature - rep3

description:
rRNA depleted total RNA
MTB_processed.txt

organism: Mycobacterium tuberculosis

value: Treated with 41C

value: Mycobacterium tuberculosis H37Ra


title: N. gonorrhoeae under L-lactate treatment - rep2


title: V. cholerae under nitrosative stress - rep2


title: M. tuberculosis under high temperature - rep2


title: M. tuberculosis at stationary phase - rep3

value: Grown until stationary phase


title: V. cholerae under nitrosative stress - rep1


title: N. gonorrhoeae under high temperature - rep3


title: M. tuberculosis under high temperature - rep1


title: N. gonorrhoeae under high temperature - rep2


title: N. gonorrhoeae under high temperature - rep1


title: V. cholerae under nutritional downshift - rep2


title: V. cholerae under nutritional downshift - rep3


title: M. tuberculosis at stationary phase - rep2


title: N. gonorrhoeae at stationary phase - rep3


title: V. cholerae under nutritional downshift - rep1


title: N. gonorrhoeae at stationary phase - rep2


title: M. tuberculosis at stationary phase - rep1


title: V. cholerae under osmotic stress - rep1

value: Treated with NaCl


title: M. tuberculosis under oxidative stress - rep2

value: Treated with H2O2


title: V. cholerae under hypoxia - rep3


title: N. gonorrhoeae at stationary phase - rep1


title: M. tuberculosis under oxidative stress - rep1


title: N. gonorrhoeae under oxidative stress - rep3


title: V. cholerae under hypoxia - rep2


title: M. tuberculosis under osmotic stress - rep3


title: V. cholerae under hypoxia - rep1


title: V. cholerae under nitrosative stress - rep3


title: M. tuberculosis under osmotic stress - rep2


title: N. gonorrhoeae under oxidative stress - rep2


title: N. gonorrhoeae under L-lactate treatment - rep1


title: N. gonorrhoeae under oxidative stress - rep1


title: M. tuberculosis under osmotic stress - rep1


title: M. tuberculosis under nitrosative stress - rep3


title: V. cholerae under low iron - rep2


title: N. gonorrhoeae under osmotic stress - rep3


title: V. cholerae untreated (control) - rep3


title: M. tuberculosis under oxidative stress - rep3


title: V. cholerae under low iron - rep1


title: N. gonorrhoeae under osmotic stress - rep2


title: M. tuberculosis under nitrosative stress - rep2


title: N. gonorrhoeae under osmotic stress - rep1


title: N. gonorrhoeae under nitrosative stress - rep3


title: N. gonorrhoeae under nitrosative stress - rep2


title: M. tuberculosis under nitrosative stress - rep1


title: V. cholerae untreated (control) - rep1


title: M. tuberculosis under nutritional downshift - rep3


title: V. cholerae untreated (control) - rep2


title: V. cholerae under bile stress - rep3


title: M. tuberculosis under nutritional downshift - rep2


title: V. cholerae under low iron - rep3


title: M. tuberculosis under nutritional downshift - rep1


title: V. cholerae under bile stress - rep2


title: N. gonorrhoeae under nitrosative stress - rep1


title: N. gonorrhoeae under nutritional downshift - rep2


title: N. gonorrhoeae under nutritional downshift - rep3


title: V. cholerae under bile stress - rep1


title: V. cholerae under acidic stress - rep3


title: M. tuberculosis under hypoxia - rep3


title: V. cholerae under acidic stress - rep2


title: N. gonorrhoeae under hypoxia - rep3


title: M. tuberculosis under hypoxia - rep2


title: N. gonorrhoeae under hypoxia - rep1


title: M. tuberculosis under hypoxia - rep1


title: N. gonorrhoeae under nutritional downshift - rep1


title: C. jejuni with prolonged growth - rep1

description:
rRNA depleted total RNA
Campy_processed.txt

organism: Campylobacter jejuni

value: One and a half hour prolonged growth

value: Campylobacter jejuni subsp. jejuni 81-176


title: M. tuberculosis under low iron - rep1


title: N. gonorrhoeae under low iron - rep3


title: M. tuberculosis under low iron - rep3


title: N. gonorrhoeae under hypoxia - rep2


title: M. tuberculosis untreated (control) - rep3


title: N. gonorrhoeae under low iron - rep1


title: C. jejuni with prolonged growth - rep3


title: C. jejuni under high temperature - rep2


title: N. gonorrhoeae under low iron - rep2


title: M. tuberculosis under bile stress - rep3


title: C. jejuni under high temperature - rep1


title: C. jejuni under high temperature - rep3


title: C. jejuni at stationary phase - rep3


title: C. jejuni at stationary phase - rep2


title: N. gonorrhoeae untreated (control) - rep1


title: M. tuberculosis untreated (control) - rep2


title: M. tuberculosis under bile stress - rep2


title: V. cholerae under acidic stress - rep1


title: M. tuberculosis under low iron - rep2


title: M. tuberculosis untreated (control) - rep1


title: N. gonorrhoeae untreated (control) - rep3


title: M. tuberculosis under bile stress - rep1


title: N. gonorrhoeae untreated (control) - rep2


title: C. jejuni with prolonged growth - rep2


title: N. gonorrhoeae under bile stress - rep3


title: M. tuberculosis under acidic stress - rep3


title: C. jejuni under oxidative stress - rep2


title: C. jejuni at stationary phase - rep1


title: N. gonorrhoeae under bile stress - rep2


title: M. tuberculosis under acidic stress - rep2


title: C. jejuni under osmotic stress - rep3


title: C. jejuni under osmotic stress - rep2


title: N. gonorrhoeae under acidic stress - rep1


title: C. jejuni under oxidative stress - rep3


title: N. gonorrhoeae under bile stress - rep1


title: C. jejuni under osmotic stress - rep1


title: M. tuberculosis under acidic stress - rep1


title: N. gonorrhoeae under acidic stress - rep3


title: B. pseudomallei with prolonged growth - rep3

description:
rRNA depleted total RNA
BURK_processed.txt

organism: Burkholderia pseudomallei

value: Four hours prolonged growth

value: Burkholderia pseudomallei K96243


title: B. pseudomallei with prolonged growth - rep2


title: C. jejuni under nitrosative stress - rep3

value: Treated with spermin NONOate complex


title: C. jejuni under nutritional downshift - rep3

value: Treated with removal of nutrients


title: N. gonorrhoeae under acidic stress - rep2


title: B. pseudomallei under high temperature - rep1


title: C. jejuni under nitrosative stress - rep2


title: B. pseudomallei under high temperature - rep2


title: B. pseudomallei under high temperature - rep3


title: C. jejuni under nutritional downshift - rep1


title: C. jejuni under nutritional downshift - rep2


title: B. pseudomallei at stationary phase - rep3


title: B. pseudomallei at stationary phase - rep2


title: C. jejuni under hypoxia - rep2

value: Treated with oxygen deprivation


title: C. jejuni under hypoxia - rep3


title: C. jejuni under oxidative stress - rep1


title: C. jejuni under low iron - rep3

value: Treated with 2,2-dipyridryl


title: C. jejuni under low iron - rep2


title: C. jejuni under low iron - rep1


title: B. pseudomallei under oxidative stress - rep2


title: B. pseudomallei with prolonged growth - rep1


title: C. jejuni under nitrosative stress - rep1


title: B. pseudomallei under osmotic stress - rep3


title: C. jejuni untreated (control) - rep3

value: Untreated


title: B. pseudomallei under osmotic stress - rep2


title: C. jejuni untreated (control) - rep2


title: B. pseudomallei under nitrosative stress - rep3


title: C. jejuni untreated (control) - rep1


title: B. pseudomallei under nitrosative stress - rep2


title: C. jejuni under bile stress - rep3

value: Bile salts treated


title: B. pseudomallei under osmotic stress - rep1


title: B. pseudomallei under nitrosative stress - rep1


title: B. pseudomallei at stationary phase - rep1


title: C. jejuni under bile stress - rep2


title: B. pseudomallei under nutritional downshift - rep2


title: B. pseudomallei under nutritional downshift - rep3


title: C. jejuni under bile stress - rep1


title: B. pseudomallei under nutritional downshift - rep1


title: C. jejuni under acidic stress - rep3

value: Acetic acid treated


title: B. pseudomallei under oxidative stress - rep3


title: B. pseudomallei under hypoxia - rep3


title: C. jejuni under acidic stress - rep1


title: C. jejuni under hypoxia - rep1


title: C. jejuni under acidic stress - rep2


title: B. pseudomallei under hypoxia - rep2


title: B. pseudomallei under oxidative stress - rep1


title: S. agalactiae under human serum treatment - rep3

description:
rRNA depleted total RNA
STAGA_processed.txt

organism: Streptococcus agalactiae

value: Treated with human serum

value: Streptococcus agalactiae NEM316


title: B. pseudomallei under hypoxia - rep1


title: S. agalactiae under human serum treatment - rep1


title: B. pseudomallei under low iron - rep2


title: B. pseudomallei under low iron - rep3


title: S. agalactiae under high temperature - rep3

value: Treated with 41C


title: S. agalactiae under high temperature - rep2


title: B. pseudomallei untreated (control) - rep3


title: B. pseudomallei under low iron - rep1


title: S. agalactiae under high temperature - rep1


title: B. pseudomallei untreated (control) - rep2


title: B. pseudomallei untreated (control) - rep1


title: S. agalactiae at stationary phase - rep2

value: Grown until stationary phase


title: S. agalactiae at stationary phase - rep3


title: B. pseudomallei under acidic stress - rep3


title: B. pseudomallei under acidic stress - rep2


title: B. pseudomallei under acidic stress - rep1


title: S. agalactiae at stationary phase - rep1


title: S. pneumoniae under human serum treatment - rep2

description:
rRNA depleted total RNA
STRPN_processed.txt

organism: Streptococcus pneumoniae

value: Streptococcus pneumoniae D39


title: S. agalactiae under oxidative stress - rep3

value: Treated with H2O2


title: S. pneumoniae under human serum treatment - rep1


title: S. pneumoniae under human serum treatment - rep3


title: S. pneumoniae under high temperature - rep3


title: S. agalactiae under osmotic stress - rep3

value: Treated with NaCl


title: S. agalactiae under osmotic stress - rep2


title: S. agalactiae under oxidative stress - rep1


title: S. agalactiae under osmotic stress - rep1


title: S. pneumoniae under high temperature - rep2


title: S. agalactiae under nitrosative stress - rep3


title: S. agalactiae under human serum treatment - rep2


title: S. agalactiae under nitrosative stress - rep2


title: S. agalactiae under nitrosative stress - rep1


title: S. pneumoniae at stationary phase - rep2


title: S. agalactiae under nutritional downshift - rep3


title: S. pneumoniae at stationary phase - rep1


title: S. pneumoniae under oxidative stress - rep3


title: S. pneumoniae at stationary phase - rep3


title: S. agalactiae under nutritional downshift - rep1


title: S. agalactiae under hypoxia - rep3


title: S. pneumoniae under oxidative stress - rep1


title: S. pneumoniae under oxidative stress - rep2


title: S. agalactiae under hypoxia - rep2


title: S. agalactiae under oxidative stress - rep2


title: S. agalactiae under low iron - rep3


title: S. agalactiae under hypoxia - rep1


title: S. agalactiae under low iron - rep2


title: S. pneumoniae under osmotic stress - rep2


title: S. agalactiae under low iron - rep1


title: S. pneumoniae under osmotic stress - rep1


title: S. pneumoniae under nitrosative stress - rep3


title: S. pneumoniae under high temperature - rep1


title: S. agalactiae untreated (control) - rep2


title: S. agalactiae untreated (control) - rep3


title: S. pneumoniae under nitrosative stress - rep2


title: S. pneumoniae under nutritional downshift - rep3


title: S. agalactiae untreated (control) - rep1


title: S. pneumoniae under nutritional downshift - rep2


title: S. agalactiae under bile stress - rep3


title: S. agalactiae under bile stress - rep2


title: S. pneumoniae under nutritional downshift - rep1


title: S. pneumoniae under osmotic stress - rep3


title: S. agalactiae under acidic stress - rep3


title: S. pneumoniae under hypoxia - rep1


title: S. agalactiae under acidic stress - rep2


title: S. agalactiae under nutritional downshift - rep2


title: S. pneumoniae under hypoxia - rep3


title: S. pneumoniae under hypoxia - rep2


title: S. pneumoniae under low iron - rep3


title: S. pneumoniae under low iron - rep2


title: N. meningitidis under L-lactate treatment - rep3

description:
rRNA depleted total RNA
NMEN_processed.txt

organism: Neisseria meningitidis

value: Treated with L-lactate

value: Neisseria meningitidis serogroup C FAM18


title: S. pneumoniae under low iron - rep1


title: N. meningitidis under L-lactate treatment - rep2


title: S. pneumoniae untreated (control) - rep3


title: S. pneumoniae under nitrosative stress - rep1


title: N. meningitidis under high temperature - rep2


title: S. pneumoniae untreated (control) - rep1


title: N. meningitidis under high temperature - rep3


title: S. pneumoniae under bile stress - rep3


title: S. pneumoniae untreated (control) - rep2


title: N. meningitidis under high temperature - rep1


title: S. pneumoniae under bile stress - rep1


title: N. meningitidis under L-lactate treatment - rep1


title: N. meningitidis at stationary phase - rep3


title: N. meningitidis at stationary phase - rep2


title: S. agalactiae under acidic stress - rep1


title: S. pneumoniae under acidic stress - rep2


title: N. meningitidis under osmotic stress - rep3


title: N. meningitidis at stationary phase - rep1


title: N. meningitidis under oxidative stress - rep1


title: N. meningitidis under oxidative stress - rep3


title: N. meningitidis under nitrosative stress - rep3


title: N. meningitidis under nitrosative stress - rep1


title: S. pneumoniae under acidic stress - rep1


title: N. meningitidis under nutritional downshift - rep3


title: S. agalactiae under bile stress - rep1


title: S. pneumoniae under acidic stress - rep3


title: N. meningitidis under nutritional downshift - rep2


title: N. meningitidis under nitrosative stress - rep2


title: N. meningitidis under hypoxia - rep2


title: N. meningitidis under low iron - rep2


title: N. meningitidis under low iron - rep3


title: N. meningitidis under oxidative stress - rep2


title: N. meningitidis under low iron - rep1


title: N. meningitidis untreated (control) - rep3


title: N. meningitidis under hypoxia - rep3


title: N. meningitidis untreated (control) - rep2


title: S. pneumoniae under bile stress - rep2


title: N. meningitidis under osmotic stress - rep1


title: N. meningitidis under osmotic stress - rep2


title: N. meningitidis untreated (control) - rep1


title: N. meningitidis under nutritional downshift - rep1


title: B. burgdorferi with prolonged growth - rep2

description:
rRNA depleted total RNA
BBURG_processed.txt

organism: Borreliella burgdorferi

value: One hour prolonged growth

value: Borrelia burgdorferi B31


title: N. meningitidis under acidic stress - rep3


title: N. meningitidis under bile stress - rep3


title: N. meningitidis under bile stress - rep1


title: N. meningitidis under acidic stress - rep2


title: B. burgdorferi at stationary phase - rep3


title: N. meningitidis under acidic stress - rep1


title: B. burgdorferi under oxidative stress - rep3


title: N. meningitidis under bile stress - rep2


title: B. burgdorferi at stationary phase - rep1


title: B. burgdorferi under oxidative stress - rep2


title: B. burgdorferi with prolonged growth - rep1


title: B. burgdorferi under high temperature - rep2


title: B. burgdorferi under high temperature - rep1


title: N. meningitidis under hypoxia - rep1


title: B. burgdorferi at stationary phase - rep2


title: B. burgdorferi under high temperature - rep3


title: B. burgdorferi under nitrosative stress - rep1

value: Treated with spermin NONOate complex


title: B. burgdorferi under nitrosative stress - rep2


title: B. burgdorferi under nutritional downshift - rep3

value: Treated with removal of nutrients


title: B. burgdorferi under oxidative stress - rep1


title: B. burgdorferi under osmotic stress - rep1


title: B. burgdorferi under osmotic stress - rep3


title: B. burgdorferi under nitrosative stress - rep3


title: B. burgdorferi under nutritional downshift - rep2


title: B. burgdorferi under hypoxia - rep3

value: Treated with oxygen deprivation


title: B. burgdorferi with prolonged growth - rep3


title: B. burgdorferi under nutritional downshift - rep1


title: B. burgdorferi under low iron - rep2

value: Treated with 2,2-dipyridryl


title: B. burgdorferi under low iron - rep3


title: B. burgdorferi untreated (control) - rep3

value: Untreated


title: B. burgdorferi under low iron - rep1


title: B. burgdorferi untreated (control) - rep1


title: B. burgdorferi untreated (control) - rep2


title: B. burgdorferi under hypoxia - rep1


title: B. burgdorferi under hypoxia - rep2


title: B. burgdorferi under osmotic stress - rep2


title: B. burgdorferi under acidic stress - rep3

value: Acetic acid treated


title: B. burgdorferi under acidic stress - rep2


title: PD170

status: Public on Apr 21 2021

city: Bethesda

first: Niki

last: Moutsopoulos

address: 30 convent Dr

country: USA

institute: NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v2.0.0 (GM136, GM143, GM183, GM184a, PD134) or v3.0.1 ( BM150, BM152, BM156, BM157, BM158, BM165, BM168, BM169, GM144, GM147, GM148, GM238, GM241, GM242, GM169, GM283, GM289, PD153, PD161, PD161b, PD164, PD164b, PD164c, PD170) using default settings.
Secondary analysis was performed using Seurat v3 and nichenetr R packages.
Genome_build: hg38
Supplementary_files_format_and_content: CellRanger v3.0.1 gene counts matrices.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
To prepare single cell suspensions biopsies were minced and digested using Collagenase II (Worthington Biochemical Corporation) and DNase (Sigma) and processed through the gentleMACS Dissociator (Miltenyl) utilizing a nasal mucosa protocol for processing36. Following tissue dissociation, cells were passed through a 70μm filter (Falcon, Corning), washed, and counted with a Cellometer Auto 2000 (Nexcelom).
Single-cell suspensions were loaded onto a 10X Chromium Controller (10X Genomics) and library preparation was performed according to the manufacturer’s instructions for the 10X Chromium Next GEM Single Cell Library kit v3 (10X Genomics).  Libraries were then pooled in groups of 4 and sequenced on 4 lanes on a NextSeq500 sequencer (Illumina) using 10X Genomics recommended reads configuration.

tag: disease state

value: Periodontitis

tag: tissue

value: Gingiva


title: GM289

value: Healthy


title: PD164c


title: PD164b


title: GM283


title: B. burgdorferi under acidic stress - rep1


title: GM169


title: BM169

value: Buccal


title: BM168


title: BM165


title: PD134

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v2.0.0 (GM136, GM143, GM183, GM184a, PD134) or v3.0.1 ( BM150, BM152, BM156, BM157, BM158, BM165, BM168, BM169, GM144, GM147, GM148, GM238, GM241, GM242, GM169, GM283, GM289, PD153, PD161, PD161b, PD164, PD164b, PD164c, PD170) using default settings. using default settings.
Secondary analysis was performed using Seurat v3 and nichenetr R packages.
Genome_build: hg38
Supplementary_files_format_and_content: CellRanger v3.0.1 gene counts matrices.


title: PD164


title: PD153


title: PD161b


title: PD161


title: GM242


title: GM241


title: GM238


title: GM184a


title: GM183


title: GM144


title: GM147


title: BM158


title: GM143


title: BM157


title: BM152


title: BM156


title: GM136


title: BM150


title: sample.20729_d6_ciml

status: Public on Apr 15 2021

city: St. Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.24.
Genome_build: Human GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: donor 20729

growth_protocol: Sample-specific, see methods from manuscript.

extract_protocol:
NK cells (5x10^5) from each step of activation to memory-like differentiation were centrifuged, lysed in TRIzol (Invitrogen), and immediately flash frozen and stored at -80°C.
Libraries were generated with the Clontech SMARTer ultra-law input kit according to manufacturer's protocols.

tag: donor

value: NK cell

tag: timepoint

value: day 6

value: CIML


title: sample.20729_d6_ld

treatment_protocol: Sample-specific, see methods from manuscript.

value: low-dose


title: sample.20729_overnight_ld

value: overnight


title: sample.20729_overnight_hcw9201


title: sample.20729_overnight_ciml


title: sample.20729_overnight_hcw9207


title: sample.20729_d6_hcw9207


title: sample.20729_d6_hcw9201


title: sample.20552_d6_ld

source_name: donor 20552


title: sample.20552_d6_hcw9207


title: sample.20552_overnight_hcw9207


title: sample.20552_overnight_hcw9201


title: GM148


title: sample.20552_d6_ciml


title: sample.20552_overnight_ld


title: sample.18331_overnight_hcw9207

source_name: donor 18331


title: sample.20552_baseline_nk

value: baseline

value: unstimulated


title: sample.18331_overnight_ld


title: sample.18331_overnight_hcw9201


title: sample.20552_d6_hcw9201


title: sample.18331_d6_ld


title: sample.18331_overnight_ciml


title: sample.18331_d6_hcw9201


title: sample.18331_baseline_nk


title: WT3CpG12h

status: Public on Apr 01 2021

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

country: Germany

institute: University of Duesseldorf

data_processing:
Illumina bcl2fastq v2.17.1.4 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Illumina TrueSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2), then mapped to mm10 whole genome using CLC Genomics Workbench v11.0.1 with standard parameters.
Counts per million (cpm) were calculated using EdgeR on usegalaxy.org with standard parameters. Multi-group comparisons were calculated using edgeR after grouping of samples (three biological replicates each) according to their respective experimental condition and filtering of low expressing genes based on a formula from Chen, Y., Lun, A.T., and Smyth, G.K. (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Res 5, 1438. . The resulting p values were corrected for multiple testing by FDR. A p value of ≤ 0.05 was considered significant. Cut-off for differential gene expression was set to 2 fold.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each sample.

organism: Mus musculus

source_name: bone marrow

growth_protocol: BM-derived Flt3-L cultured cDCs and pDCs were generated as previously described (Scheu et al, PNAS 2008).

extract_protocol:
For RNA-Seq, BM-derived pDCs (CD3-CD19-CD11c+CD11blowB220+SiglecH+mPDCA1+) were FACS purified using FACS Aria III (BD).
Libraries were prepared according to Illumina® ‘TruSeq Stranded mRNA Library Prep Kit’. Briefly, 200 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA), following the manufacturer's protocols, with a read setup of 1 × 150 bp.

treatment_protocol: The pDCs were left untreated or stimulated with 1µM CpG 2216 (Tib Molbiol, Nr. 930507l) complexed to transfection reagent DOTAP (Roche) for 2, 6 or 12 hours. RNA was isolated by using NucleoSpin II RNA mini kit (Macherey- Nagel) and subjected to RNA-Seq.

value: bone marrow

value: pDC

tag: condition

value: CpG 12h

value: wild type


title: WT2CpG12h


title: sample.20729_baseline_nk


title: sample.20552_overnight_ciml


title: WT2CpG6h

value: CpG 6h


title: WT1CpG6h


title: WT3CpG6h


title: WT1CpG12h


title: WT1CpG2h

value: CpG 2h


title: WT3

value: naive


title: WT3CpG2h


title: WT2CpG2h


title: WT2


title: P08_M

status: Public on Feb 09 2021

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

description:
snRNA-seq iCell8
icell8.counts.txt

data_processing:
Pre-processing of the raw sequencing reads were performed using the Bioinformatics ExperT SYstem (BETSY). Read counts for iCell8 were determined using an in-house pipeline using the STAR aligner followed by featureCounts.  10X data were preprocessed with CellRanger using the mRNA procedure recommended for nuclei sequencing.
Genome_build: hg19, GRCh38
Supplementary_files_format_and_content: tab-delimited text files with feature counts matrix for each patient

source_name: tumor

extract_protocol:
RNA was extracted from single nuclei as the Takara SMARTer ICELL8 3’ DE Reagent Kit V2 or 10X Genomics Chromium Single Cell 3’ V3 Kit  following manufacturer’s protocol.
snRNA-seq libraries were prepared using the Takara SMARTer ICELL8 3’ DE Reagent Kit V2 or 10X Genomics Chromium Single Cell 3’ V3 Kit  following manufacturer’s protocol.

value: Cells from breast tumor

tag: patient

tag: treatment arm

value: C

value: letrozole + ribo

tag: ribo schedule

value: continuous

tag: response

value: Non-responder

tag: platform

tag: time point

value: mid

tag: days treated


title: P09_S

description:
snRNA-seq iCell8
icell8.counts.txt

value: B

tag: treatment

value: intermittent

value: Responder

value: start


title: P08_E

description:
snRNA-seq iCell8
icell8.counts.txt

value: end


title: P09_M

description:
snRNA-seq iCell8
icell8.counts.txt


title: P07_S

description:
snRNA-seq iCell8
icell8.counts.txt


title: P05_S

description:
snRNA-seq iCell8
icell8.counts.txt


title: sample.18331_d6_hcw9207

value: NK cell

value: day 6


title: P08_S

description:
snRNA-seq iCell8
icell8.counts.txt


title: P04_M

description:
snRNA-seq iCell8
icell8.counts.txt


title: WT1

value: bone marrow

tag: strain

value: pDC

value: wild type


title: P04_S

description:
snRNA-seq iCell8
icell8.counts.txt

tag: cell type


title: P05_M

description:
snRNA-seq iCell8
icell8.counts.txt


title: sample.18331_d6_ciml

value: CIML


title: P01_S

description:
snRNA-seq iCell8
icell8.counts.txt

value: Cells from breast tumor


title: P02_S

description:
snRNA-seq iCell8
icell8.counts.txt

value: C


title: P04_E

description:
snRNA-seq iCell8
icell8.counts.txt

value: letrozole + ribo


title: HGSOC_P03 Time2 scRNA-seq

description:
scRNA-seq iCell8
P03.counts.txt

data_processing:
Pre-processing of the raw sequencing reads were performed using the Bioinformatics ExperT SYstem (BETSY). Read counts for iCell8 were determined using an in-house pipeline using the STAR aligner followed by featureCounts.  10X data were preprocessed with CellRanger.
Genome_build: hg19, GRCh38
Supplementary_files_format_and_content: tab-delimited text files with feature counts matrix for each patient

source_name: ascites

extract_protocol:
RNA was extracted from single cells as the Takara SMARTer ICELL8 3’ DE Reagent Kit V2 or 10X Genomics Chromium Single Cell 3’ V3 Kit  following manufacturer’s protocol.
scRNA-seq libraries were prepared using the Takara SMARTer ICELL8 3’ DE Reagent Kit V2 or 10X Genomics Chromium Single Cell 3’ V3 Kit  following manufacturer’s protocol.

value: Cells from ovarian tumor

tag: days since surgery


title: HGSOC_P02 Time3 scRNA-seq

description:
scRNA-seq iCell8
P02.counts.txt


title: HGSOC_P03 Time1 scRNA-seq

description:
scRNA-seq iCell8
P03.counts.txt


title: HGSOC_P02 Time2 scRNA-seq

description:
scRNA-seq iCell8
P02.counts.txt


title: HGSOC_P03 Time3 scRNA-seq

description:
scRNA-seq iCell8
P03.counts.txt


title: HGSOC_P02 Time1 scRNA-seq

description:
scRNA-seq iCell8
P02.counts.txt


title: P46_S

description:
snRNA-seq 10X
10x.counts.txt


title: HGSOC_P01 Time1 scRNA-seq

description:
scRNA-seq iCell8
P01.counts.txt


title: P44_S

description:
snRNA-seq 10X
10x.counts.txt

value: A

value: letrozole

value: Non-responder


title: P45_M

description:
snRNA-seq 10X
10x.counts.txt

value: mid


title: P44_M

description:
snRNA-seq 10X
10x.counts.txt


title: P45_S

description:
snRNA-seq 10X
10x.counts.txt

value: Responder


title: P43_M

description:
snRNA-seq 10X
10x.counts.txt


title: P41_S

description:
snRNA-seq 10X
10x.counts.txt

value: start


title: P41_M

description:
snRNA-seq 10X
10x.counts.txt


title: P41_E

description:
snRNA-seq 10X
10x.counts.txt

value: end


title: P40_E

description:
snRNA-seq 10X
10x.counts.txt

value: continuous


title: P43_E

description:
snRNA-seq 10X
10x.counts.txt


title: P43_S

description:
snRNA-seq 10X
10x.counts.txt


title: P40_S

description:
snRNA-seq 10X
10x.counts.txt


title: P40_M

description:
snRNA-seq 10X
10x.counts.txt


title: P38_E

description:
snRNA-seq 10X
10x.counts.txt


title: P39_M

description:
snRNA-seq 10X
10x.counts.txt


title: P37_S

description:
snRNA-seq 10X
10x.counts.txt

value: B

value: intermittent


title: P37_E

description:
snRNA-seq 10X
10x.counts.txt


title: P36_S

description:
snRNA-seq 10X
10x.counts.txt


title: P36_M

description:
snRNA-seq 10X
10x.counts.txt


title: P46_M

description:
snRNA-seq 10X
10x.counts.txt


title: HGSOC_P01 Time2 scRNA-seq

description:
scRNA-seq iCell8
P01.counts.txt


title: P34_M

description:
snRNA-seq 10X
10x.counts.txt


title: P34_S

description:
snRNA-seq 10X
10x.counts.txt


title: P35_M

description:
snRNA-seq 10X
10x.counts.txt


title: P35_S

description:
snRNA-seq 10X
10x.counts.txt


title: P35_E

description:
snRNA-seq 10X
10x.counts.txt


title: P33_M

description:
snRNA-seq 10X
10x.counts.txt


title: P33_E

description:
snRNA-seq 10X
10x.counts.txt


title: P34_E

description:
snRNA-seq 10X
10x.counts.txt


title: P32_S

description:
snRNA-seq 10X
10x.counts.txt


title: P31_S

description:
snRNA-seq 10X
10x.counts.txt


title: P30_M

description:
snRNA-seq 10X
10x.counts.txt


title: P31_M

description:
snRNA-seq 10X
10x.counts.txt


title: P39_S

description:
snRNA-seq 10X
10x.counts.txt


title: P29_S

description:
snRNA-seq 10X
10x.counts.txt


title: P29_M

description:
snRNA-seq 10X
10x.counts.txt


title: P28_M

description:
snRNA-seq 10X
10x.counts.txt


title: P31_E

description:
snRNA-seq 10X
10x.counts.txt


title: P30_E

description:
snRNA-seq 10X
10x.counts.txt


title: P27_S

description:
snRNA-seq 10X
10x.counts.txt


title: P29_E

description:
snRNA-seq 10X
10x.counts.txt


title: P27_M

description:
snRNA-seq 10X
10x.counts.txt


title: P28_S

description:
snRNA-seq 10X
10x.counts.txt


title: P33_S

description:
snRNA-seq 10X
10x.counts.txt


title: P28_E

description:
snRNA-seq 10X
10x.counts.txt


title: P26_M

description:
snRNA-seq 10X
10x.counts.txt


title: P26_S

description:
snRNA-seq 10X
10x.counts.txt


title: P27_E

description:
snRNA-seq 10X
10x.counts.txt


title: P25_S

description:
snRNA-seq 10X
10x.counts.txt


title: P25_M

description:
snRNA-seq 10X
10x.counts.txt


title: P24_S

description:
snRNA-seq 10X
10x.counts.txt


title: P23_S

description:
snRNA-seq 10X
10x.counts.txt


title: P25_E

description:
snRNA-seq 10X
10x.counts.txt


title: P24_M

description:
snRNA-seq 10X
10x.counts.txt


title: P22_S

description:
snRNA-seq 10X
10x.counts.txt


title: P32_M

description:
snRNA-seq 10X
10x.counts.txt


title: P23_M

description:
snRNA-seq 10X
10x.counts.txt


title: P22_E

description:
snRNA-seq 10X
10x.counts.txt


title: P20_E

description:
snRNA-seq 10X
10x.counts.txt


title: P20_M

description:
snRNA-seq 10X
10x.counts.txt


title: P19_S

description:
snRNA-seq 10X
10x.counts.txt


title: P16_S

description:
snRNA-seq 10X
10x.counts.txt


title: P16_M

description:
snRNA-seq 10X
10x.counts.txt


title: P17_M

description:
snRNA-seq 10X
10x.counts.txt


title: P15_S

description:
snRNA-seq 10X
10x.counts.txt


title: P19_M

description:
snRNA-seq 10X
10x.counts.txt


title: P15_M

description:
snRNA-seq 10X
10x.counts.txt


title: P14_E

description:
snRNA-seq 10X
10x.counts.txt


title: P14_S

description:
snRNA-seq 10X
10x.counts.txt


title: P13_S

description:
snRNA-seq 10X
10x.counts.txt


title: P15_E

description:
snRNA-seq 10X
10x.counts.txt


title: P13_M

description:
snRNA-seq 10X
10x.counts.txt


title: HGSOC_P24 Post-treatment scRNA-seq

description:
scRNA-seq 10X
P24.counts.txt

source_name: pleural fluid

tag: days progression


title: P12_M

description:
snRNA-seq 10X
10x.counts.txt


title: P13_E

description:
snRNA-seq 10X
10x.counts.txt


title: P11_M

description:
snRNA-seq 10X
10x.counts.txt


title: P22_M

description:
snRNA-seq 10X
10x.counts.txt


title: P21_S

description:
snRNA-seq 10X
10x.counts.txt


title: P12_E

description:
snRNA-seq 10X
10x.counts.txt


title: HGSOC_P18 Post-treatment scRNA-seq

description:
scRNA-seq 10X
P18.counts.txt


title: HGSOC_P21 Post-treatment scRNA-seq

description:
scRNA-seq 10X
P21.counts.txt


title: HGSOC_P20 Post-treatment scRNA-seq

description:
scRNA-seq 10X
P20.counts.txt


title: HGSOC_P19 Post-treatment scRNA-seq

description:
scRNA-seq 10X
P19.counts.txt


title: P20_S

description:
snRNA-seq 10X
10x.counts.txt


title: P21_M

description:
snRNA-seq 10X
10x.counts.txt


title: HGSOC_P23 Post-treatment scRNA-seq

description:
scRNA-seq 10X
P23.counts.txt


title: P16_E

description:
snRNA-seq 10X
10x.counts.txt


title: HGSOC_P17 Pre-treatment scRNA-seq

description:
scRNA-seq 10X
P17.counts.txt


title: HGSOC_P16 Pre-treatment scRNA-seq

description:
scRNA-seq 10X
P16.counts.txt


title: HGSOC_P13 Pre-treatment scRNA-seq

description:
scRNA-seq 10X
P13.counts.txt


title: HGSOC_P15 Pre-treatment scRNA-seq

description:
scRNA-seq 10X
P15.counts.txt


title: P21_E

description:
snRNA-seq 10X
10x.counts.txt


title: HGSOC_P14 Pre-treatment scRNA-seq

description:
scRNA-seq 10X
P14.counts.txt


title: HGSOC_P12 Pre-treatment scRNA-seq

description:
scRNA-seq 10X
P12.counts.txt


title: HGSOC_P11 Pre-treatment scRNA-seq

description:
scRNA-seq 10X
P11.counts.txt


title: HGSOC_P10 Pre-treatment scRNA-seq

description:
scRNA-seq 10X
P10.counts.txt


title: HGSOC_P09 Time2 scRNA-seq

description:
scRNA-seq 10X
P09.counts.txt


title: HGSOC_P08 Time3 scRNA-seq

description:
scRNA-seq 10X
P08.counts.txt


title: HGSOC_P09 Time3 scRNA-seq

description:
scRNA-seq 10X
P09.counts.txt


title: HGSOC_P08 Time2 scRNA-seq

description:
scRNA-seq 10X
P08.counts.txt


title: HGSOC_P09 Time1 scRNA-seq

description:
scRNA-seq 10X
P09.counts.txt


title: HGSOC_P08 Time1 scRNA-seq

description:
scRNA-seq 10X
P08.counts.txt


title: HGSOC_P07 Time2 scRNA-seq

description:
scRNA-seq 10X
P07.counts.txt


title: HGSOC_P07 Time1 scRNA-seq

description:
scRNA-seq 10X
P07.counts.txt


title: HGSOC_P06 Time3 scRNA-seq

description:
scRNA-seq 10X
P06.counts.txt


title: HGSOC_P05 Time3 scRNA-seq

description:
scRNA-seq 10X
P05.counts.txt


title: HGSOC_P06 Time1 scRNA-seq

description:
scRNA-seq 10X
P06.counts.txt


title: HGSOC_P05 Time2 scRNA-seq

description:
scRNA-seq 10X
P05.counts.txt


title: HGSOC_P06 Time2 scRNA-seq

description:
scRNA-seq 10X
P06.counts.txt


title: HGSOC_P04 Time3 scRNA-seq

description:
scRNA-seq 10X
P04.counts.txt


title: HGSOC_P04 Time2 scRNA-seq

description:
scRNA-seq 10X
P04.counts.txt


title: donor6_truseq_fludrocortisone

status: Public on Jan 22 2021

city: Iowa city

first: Alejandro

middle: Pezzulo

last: Colmenares

state: Iowa

address: 169 Newton Road

department: Internal medicine

institute: University of Iowa

data_processing:
Total 36 fastq files for samples (single-end read) prepared with  Smart-3SEQ library were pre-processed by trimming the adapters, removing polyA tails and, extracting UMI sequence and G overhang as described in Foley et al., 2019. The fastq files were then aligned using HISAT2-2.1.0 (Kim De et al., 2019) and Homo sapiens GhCh38 NCBI Assembly (GCF_000001405.39,annotation-date 12/05/2019). Uniquely aligned reads  were counted using featureCounts from subread-1.6.4 package. 4  fastq files for each TruSeq sample (Paired read 1 and read 2 for same library across three lanes, total 72) were processed similarly to the Smart-3SEQ fastq files except for the pre-processing steps.
Differential gene expression was analyzed using DESeq2 1.26.0 using ~donor+treatment design.
genome build: GRCh38.p13NCBI assembly, accession :GCF_000001405.39, annotation-date 12/05/2019, annotation-source NCBI Homo sapiens Updated Annotation Release 109.20191205
processed data files format and content: merged tab delimited text file containing raw gene counts for each methods processed by featureCounts of subread package-1.6.4
processed data files format and content: gene length for all genes in raw gene counts

source_name: cultured human dermal fibroblast

growth_protocol: Human primary dermal fibroblasts were obtained using methods described in Vangipuram M etal,2013 . Cells were maintained in DMEM (Gibco, Dublin, Ireland, Item No. 11965-092) with 20% FBS (Gibco, Dublin, Ireland, Item No. 26140-079) and Pen/Strep 1:100 (Gibco, Dublin, Ireland, Item No. 15140-122)and gentamycin 25μg/mL (IBI Scientific, Dubuque, IA, Item No. IB02030), at 37℃ with 5% CO2 and were used at passage #4.

extract_protocol:
Total RNA was extracted and purified from cell cultures using RNeasy plus mini kit from QIAGEN (Hilden, Germany). For in-lysate RNA, cell cultures were washed with PBS, treated with a lysis buffer consisting of 0.1% (1mg/mL) BSA (New England Biolabs, Ipswich, MA, Item No. B9000S) / 0.3% Igepal CA 630 (Sigma-Aldrich, St. Louis, MO, Item No. I8896) for 5 minutes, and the supernatant was used for further library prep.
Extracted RNA and cell lysate were used for preparing sequencing libraries according to the Smart-3SEQ protocol (Foley et al., 2019). Illumina TruSeq libraries were prepared at the University of Iowa Genomics Facility using standard Illumina TruSeq stranded mRNA protocols. Concentration and fragment size of prepared library was measured using Qubit HS and bioanalyzer. Fragment size for Smart-3SEQ library was ~500bp which falls within the recommended 200-600bp

treatment_protocol: Samples were treated for 6 hours as indicated with DMSO,  10μM Calmidazolium chloride (Cayman Chemical Company, Ann Arbor, MI, Item No. 14442) or Fludrocortisone acetate (Sigma-Aldrich, St. Louis, MO, Item No. F6127).

value: human dermal fibroblast

value: Fludrocortisone

tag: library prep

value: TruSeq


title: donor6_truseq_calmidazolium

value: Calmidazolium


title: donor4_truseq_calmidazolium


title: donor4_truseq_fludrocortisone


title: donor5_truseq_fludrocortisone


title: donor1_truseq_fludrocortisone


title: donor1_truseq_calmidazolium


title: donor6_truseq_vehicle

value: DMSO


title: donor2_truseq_calmidazolium


title: donor3_truseq_calmidazolium


title: donor2_truseq_fludrocortisone


title: donor3_truseq_fludrocortisone


title: donor5_truseq_calmidazolium


title: HGSOC_P05 Time1 scRNA-seq

description:
scRNA-seq 10X
P05.counts.txt


title: donor3_truseq_vehicle


title: HGSOC_P04 Time1 scRNA-seq

description:
scRNA-seq 10X
P04.counts.txt


title: donor1_truseq_vehicle


title: donor6_purified_RNA_fludrocortisone


title: donor5_purified_RNA_fludrocortisone


title: donor3_purified_RNA_fludrocortisone


title: donor2_purified_RNA_fludrocortisone


title: donor1_purified_RNA_fludrocortisone


title: donor6_purified_RNA_calmidazolium


title: donor3_purified_RNA_calmidazolium


title: donor5_purified_RNA_calmidazolium


title: donor2_purified_RNA_calmidazolium


title: donor4_purified_RNA_calmidazolium


title: donor2_truseq_vehicle


title: donor5_truseq_vehicle


title: donor4_truseq_vehicle


title: donor5_purified_RNA_vehicle


title: donor4_purified_RNA_fludrocortisone


title: donor2_purified_RNA_vehicle


title: donor4_purified_RNA_vehicle


title: donor5_inlysate_fludrocortisone


title: donor6_purified_RNA_vehicle


title: donor1_purified_RNA_vehicle


title: donor6_inlysate_fludrocortisone


title: donor4_inlysate_fludrocortisone


title: donor3_purified_RNA_vehicle


title: donor3_inlysate_fludrocortisone


title: donor6_inlysate_calmidazolium


title: donor5_inlysate_calmidazolium


title: donor2_inlysate_calmidazolium


title: donor4_inlysate_calmidazolium


title: donor6_inlysate_vehicle


title: donor1_inlysate_fludrocortisone


title: donor1_inlysate_calmidazolium


title: donor5_inlysate_vehicle


title: donor3_inlysate_calmidazolium


title: donor4_inlysate_vehicle


title: donor3_inlysate_vehicle


title: donor1_purified_RNA_calmidazolium


title: infected hRPTEC [RNA_H3_PLUS]

status: Public on Jan 14 2021

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

data_processing:
Illumina HiSeq2500 sequencer
Sequenced reads were aligned to the hg19 genome using BWA
DGE profiles were generated by counting for each sample the number of unique UMIs associated with each RefSeq genes
The analysis design used to perform differential expression with Deseq2 between the infected vs non-infected conditions took into account the individual donors as a confounding variable
Genome_build: hg19
Supplementary_files_format_and_content: csv text files include Deseq2-normalized read counts

source_name: hRPTEC_with BKPyV

extract_protocol:
Total RNA was extracted using the Trizol reagent according to the manufacturer's instructions.
3′ digital gene expression (DGE) RNAseq libraries were prepared from 10 ng of total RNA. The mRNA poly(A) tails were tagged with universal adapters, specific barcodes and unique molecular identifiers (UMIs) during template switching reverse transcriptase. Barcoded cDNAs from multiple samples were  pooled, amplified and tagmented using a transposon-fragmentation. The obtained library was sequenced on an Illumina HiSeq 2500.

value: hRPTEC cells (kidney epithelial cells)

tag: type

value: primary cells

tag: source subject

value: adult

value: with BKPyV (Dunlop strain, MOI=0.1)


title: donor1_inlysate_vehicle

tag: donor


title: non infected hRPTEC [RNA_H2NEG]

source_name: hRPTEC_w/o BKPyV

value: w/o BK polyomavirus (BKPyV)


title: infected DC [RNA_DC_PLUS]

source_name: MDDC_with BKPyV

value: blood monocyte-derived dendritic cells (MDDC)


title: non infected DC [RNA_DCNEG]

source_name: MDDC_w/o BKPyV


title: infected DB [RNA_DB_PLUS]


title: donor2_inlysate_fludrocortisone


title: non infected DA [RNA_DANEG]


title: infected DA [RNA_DA_PLUS]


title: non infected D6 [RNA_D6NEG]


title: non infected DB [RNA_DBNEG]


title: infected D6 [RNA_D6_PLUS]