title: dDSB Spo11-myc18 com1∆ t6 ChIP, S. kud.

description: Figure EDF3b, EDF3c, EDF3e

data_processing:
library strategy: Protec-seq
Unaligned bam files were converted to fastq files with the help of SamToFastq.jar (picard-tools v1.119). Adapter sequences were trimmed by cutadapt (version 1.8.1) with a maximum error rate of 0.15 and minimum clipped read length of 15 nt (options -O 1 -e 0.15 -m 15 --max-n 3). Clipped read pairs were aligned with the help of NextGenMap (version 0.5.5) to both ASMv1 and the calibration genome ZP591 in order to obtain specific S. cer. and S. kud. alignments, as well as read counts for both the ChIP and the WCE samples. Reads aligning to both genomes, typically only 0.2% of the clipped reads, were discarded. In order to map the 5-prime ends accurately and sensitively, global (end-to-end) alignments, a maximum error rate of 4%, and a kmer-size of 9 were applied. In addition, a maximal insert size of 1000nt was set (upper limit of Illumina sequencing machines), and multiple hits were discarded.
Calibration factors (see supplementary file) were calculated by multiplication of the occupancy ratio (OR), IP.asmv1 x WCE.zp591 / IP.zp591 x WCE.asmv1, with the read count normalization factor (to 10M, RP10M), 10M/IP.asmv1. Conversion of alignment data to various data formats representing dDSB fragments or their 5-prime ends were performed with custom Java scripts. dDSB fragment lengths were determined by the distance between start and ends of read pairs (see fd files). Since these fragments include the 2 nt overhangs generated by the Spo11 staggered cuts at both ends, the cleavage axis distances are obtained by subtracting 2 nt from the respective original fragment lengths.
Wiggle files were created with the help of IGVTools v. 2.3.72.
Genome_build: ASM205788v1 (GenBank accession GCA_002057885.1; "ASMv1") for S. cer.; ZP591 (GenBank accession GCA_000167075.2) for S. kud.
Supplementary_files_format_and_content: For each Protec-Seq IP sample, wiggle files of dDSB fragment 5-prime ends are provided as gz-compressed file archives containing one file each for Watson and Crick (numbers preceding the .wig file extension correspond to the RGB color code). Likewise, fragment depth (fd) files containing chromosome, start, length and depth of each dDSB fragment are listed.

organism:
Saccharomyces cerevisiae
Saccharomyces kudriavzevii

growth_protocol: Diploid SK1 strains were induced to undergo meiosis synchronously and were sampled at desired time points in sporulation medium. Diploid SK1 yeast strains from a frozen stock were grown on YPD plates for 2 days at 30°C. Single colonies were inoculated in 5ml YPD and grown over night at 30°C. For synchronous sporulation, the saturated YPD cultures were inoculated in SPS pre-sporulation medium (0.5% Yeast extract, 1% Peptone, 0.17% Yeast nitrogen base (without amino acids and without ammonium sulfate), 1% potassium acetate, 1% ammonium sulfate, 0.05 M potassium biphtalate, pH 5.5) and grown, shaking vigorously, to an OD660 of 1.0 (4x10^7cells/ml). Cells were harvested by centrifugation, washed once and resuspended in sporulation medium (SPM, 2% potassium acetate, 0.1% polypropylene glycol). The meiotic progression of the cells was monitored by DAPI staining and/or western blot analysis.

extract_protocol:
At the desired time points, cells were harvested from 100 ml meiotic cultures and collected by centrifugation (4 min, 2,000 rpm , 4°C), washed once with ice-cold 1xTBS, centrifuged again and pellets were frozen at -80°C. Cells pellets were lysed in 2.4 ml ice-cold lysis buffer (50 mM Hepes-KOH pH=7.5, 150 mM NaCl, 5 mM EDTA, 1% Trition X-100, 0.1% Na-deoxycholate, 1 protease inhibitor tablet (Roche, Complete Protease Inhibitor Cocktail)). For spike-in experiments, 20-30 % of S. kud. meiotic cells were added to S. cer. cells. All steps were carried out at 4°C unless stated. Cells were opened with glass beads 2 x 20 sec, 5.5 m/s in a FastPrep-24™ 5G Instrument (MP Biomedicals). The cell lysates were centrifuged at full speed for 10 min at 4°C and the supernatants were transferred into new Eppendorf tubes. A pre-clearing step was performed by incubating the soluble chromatin fractions with Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) for 1 hour at 4°C. After removing 40 µl of the lysate for the whole cell extract (WCE), chromatin immunoprecipitation was carried out by incubating the lysates with Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) coupled to anti-myc antibody (9E11, mouse monoclonal AB) for 3 hours at 4°C. Thereafter, the beads were washed 2 times with 1 ml lysis buffer, 2 times with 1 ml lysis buffer high salt, 3 times with 1 ml washing buffer (10 mM Tris-HCL pH=8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 5 mM EDTA) and finally 2 times with 1 ml 10 mM Tris-HCl pH=8.0. Unprotected DNA or partially protected DNA was digested with 3 µl ExonucleaseV (NEB) in NebBuffer 4 (50 mM K-acetate, 20 mM Tris-acetate, 10 mM Mg-acetate and 1 mM DTT at pH=7.9 containing 1 mM ATP) for 30 min at 37°C. In parallel, RNA was removed by incubation with 10 µl RNase (Dnase-free, Roche). The reaction was stopped by the addition of 11 mM EDTA, the beads were washed 3 times with ice-cold 1xTE and incubated at 65°C for 30min in elution buffer (50 mM Tris-HCL pH=8.0, 10 mM EDTA, 1 % SDS). Spo11-protected DNA complexes were digested over night using 12 µl Proteinase K (Sigma) at 50°C. DNA was extracted once with phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 0.5 μg/μl glycogen (Roche), 200 mM NaCl and 2.5 volumes of 96 % ethanol. The DNA was pelleted by centrifugation at 4°C for 1 hour, washed once with 1 ml of 70% ethanol and centrifuged again. After air-drying the pellet for 5 min, the DNA was resuspended in 60 µl 10 mM Tris-Cl pH=8.0. The WCE control was digested with RNase and proteinase K, followed by DNA extraction exactly as with the immunoprecipitated samples.
The immunoprecipitated DNA was digested with 3 µl hTdp2 (BPS Bioscience) in 1x hTdp2 Buffer (50 mM Tris-HCl pH7.4, 1 mM MgCl2, 50 mM KCl, 1 mM DTT, 0.1 mg/ml BSA) at 25°C for 30 min. The DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated as described above. The hTdp2 digested DNA was end-repaired, A-tailed and adapters were ligated to the DNA ends using the NEBNext Ultra II DNA Library Preparation Kit (NEB) according to the manufacturer´s instructions except that we aimed to select for fragments between 140 bp  - 1000 bp length using Agencourt AMPure XP beads (Beckman Coulter). This necessary step likely results in under-representation of the shortest inserts. For amplification, we used either the NEBNext multiplex oligos or the NEBNext dual indexes primer sets. Before library preparation of the WCE control, we fragmented the DNA using NEBNext dsDNA fragmentase (NEB) according to the manufacturer´s protocol. Briefly, we incubated 32µl of the WCE control in 1x fragmentase reaction buffer V2 (50 mM NaCl, 20 mM Tris-HCl, 0.1 mg/ml BSA, 0.15% Triton® X-100, 15 mM MgCl2, pH 7.5@25°C) with 4µl NEBNext dsDNA fragmentase at 37°C for 20 min. The reaction was stopped by the addition of 5 µl of 0.5 M EDTA and the DNA was extracted by phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated as described above. The library preparation of the WCE control was performed the same way as for the immunoprecipitated samples. The concentration and the molarity of the library were determined by NanoDrop™ 3300 Fluorospectrometer and Agilent 2100 Bioanalyzer.

value: anti-myc (9E11, mouse monoclonal) antibody

value: CTGAAGCT

value: CCTATCCT


title: S. aureus (MRSA) under bile stress - rep3

status: Public on Jun 09 2021

type: SRA

city: Umea

first: Kemal

last: Avican

address: Building 6L

department: Department of Molecular Biology

country: Sweden

institute: Umea University

description:
rRNA depleted total RNA
MRSA_processed.txt

library_source: transcriptomic

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

molecule: total RNA

organism: Staphylococcus aureus subsp. aureus MRSA252

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: Bile salts treated

tag: strain

value: Staphylococcus aureus MRSA252


title: Lung-sample-97

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were mapped using the align function in the hisat2 d package (Kim et al., 2019)) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.16.1) using the UOA_Brahman_1 and UOA_Angus _1 genomes
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.22.0, Ritchie et al. Nucleic Acids Research, 2015).
Genome_build: UOA_Brahman_1 and UOA_Angus _1
Supplementary_files_format_and_content: tab-delimited text files with columns representing chromosome number, gene symbol  and the number of reads mapping to that gene.

organism: Bos taurus

source_name: Lung

extract_protocol:
The total RNA was isolated from the tissues using the illumina kit, in accordance with the manufacturer’s recommendations (Illumina).
RNA libraries were prepared with with a KAPA Stranded RNA-Seq Library Preparation Kit following the Illumina paired-end library preparation protocol.Sequence reads were produced on an Illumina Next-Seq  platform Illumina

treatment_protocol: please see the two papers for more details:  Xiang et al., 2014 Widespread Differential Maternal and Paternal Genome Effects on Fetal Bone Phenotype at Mid-Gestation and Ghanipoor-Samami et al., 2018 Atlas of tissue-and developmental stage specific gene expression for the bovine insulin-like growth factor (IGF) system

tag: tissue

value: Lung

tag: fetus number

tag: genotype

value: BtBi

tag: age

value: fetus

tag: Sex

value: male


title: wild type Top2-myc9 t0 ChIP

city: Vienna

first: Franz

last: Klein

address: Dr. Bohr-Gasse 9

department: Chromosome Biology

country: Austria

institute: Max Perutz Labs, University of Vienna

description: Figure 3a

library_source: genomic

data_processing:
Unaligned bam files were converted to fastq files with the help of SamToFastq.jar (picard-tools v1.119). After removal of adapter sequences with cutadapt (-O 3 -e 0.15 -m 15 –max-n 3), read pairs were aligned to both the ASMv1 and the calibration genome CBS138 with NextGenMap (“local”, allowing up to 10% soft clipping and 4% error), in order to get specific alignments from either species.
Aligned read pairs were "filled up" to cover the whole insert length before calculation of the depths per position ("filled dpp") with a custom Java script. Calibration factors (see supplementary file) were calculated by multiplication of the occupancy ratio (OR), IP.asmv1 x WCE.cbs138 / IP.cbs138 x WCE.asmv1, with the read count normalization factor (to 10M, RP10M), 10M/IP.asmv1.
Wiggle files were created with the help of IGVTools v. 2.3.72.
Genome_build: ASM205788v1 (GenBank accession GCA_002057885.1; "ASMv1") for S. cer.; CBS138 genome version s02-m07-r01 for C. gla.
Supplementary_files_format_and_content: For each IP sample, filled dpp (chrom, position, depth) and corresponding wiggle files (numbers preceding the .wig file extension correspond to the RGB color code) are provided

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: meiotic yeast cells

growth_protocol: S. cer. cells (experimental strain) were sporulated in 2% potassium acetate supplemented with 0.1% (w/v) polypropylene glycol (PPG) to undergo synchronous meiosis at 30°C by the SPS pre-growth method described in Mendoza et al., Methods Mol Biol. 2009;557:267-83.  C. gla. cells (calibrating strain) were grown in YPD to reach a density of 0.6 at OD660 (Hu et al., Nucleic Acids Res. 2015).

extract_protocol:
Cells were opened by FastPrep-24™ 5G Instrument (MP Biomedicals) followed by sonication with Bioruptor® Pico instrument. After removing the cell debris, the supernatant was used for the chromatin immuno-precipitation with anti-myc 9E11 antibody. To reverse crosslink, all the samples were incubated in 65°C overnight. DNA purification was conducted by regular phenol/chloroform/isoamyl alcohol extraction.
Library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit according to the manufacturer´s protocol. Amplified library DNA was purified and subjected to ~140 bp - 800 bp size selection using Agencourt AMPure XP beads (Beckman Coulter) and quantified by NanoDrop™ 3300 Fluorospectrometer and Agilent 2100 Bioanalyzer.

treatment_protocol: All cells were crosslinked for 15 min in 1 % formaldehyde at room temperature. The formaldehyde was stopped by addition of glycine to 131 mM.  For each ChIP, 2x109 S. cerevisiae cells were mixed with 2x108 C. glabrata cells which where crosslinked separately. ChIP from meiotic cultures was performed as described in Mendoza et al., Methods Mol Biol. 2009;557:267-83.

value: SK1 + CBS138

tag: antibody

tag: index 1

value: GAGATTCC

tag: index 2

value: TATAGCCT


title: S. aureus (MRSA) under bile stress - rep2


title: dDSB spo11Y135F-myc18 rad50S t4 replicate 1 WCE

value: TCTCGCGC


title: RH1_EETS-high_rep1

type: genomic

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Ewing sarcoma cell line Rh1; Control sample; replicate 1

hyb_protocol: DNA was bisulfite converted, amplified, fragmented, and hybridised to Illumina Infinium MethylationEPIC BeadChip arrays following manufacturer's protocol

scan_protocol: Arrays were imaged using Illumina iScan system

data_processing: Data were processed using Illumina Genome Studio Software V 2011.1 Methylation 1.9.0

label: cy3, cy5

organism: Homo sapiens

source_name: Ewing sarcoma cell line stably transduced with inducible shRNA expressing construct targeting the respective EWSR1-ETS fusion oncogene

label_protocol: Illumina protocol

growth_protocol: Cell lines were cultured in RPMI 1640 medium with stable glutamine (Biochrom, Berlin, Germany), supplemented with 10% FCS tested to be dox-free (Sigma-Aldrich, Taufkirchen, Germany) and penicillin and streptomycin (final concentrations 100 units/ml and 100µg/ml, respectively; Merck, Darmstadt, Germany) in tissue culture flasks and plates (TPP, Trasadingen, Switzerland) in a fully humidified 5% CO2 atmosphere at 37°C.

extract_protocol: Samples were lysed and genomic DNA was extracted with the NucleoSpin Tissue kit (Macherey Nagel). Genomic DNA was stored at -20°C

treatment_protocol: Addition of 1 µg/ml doxycycline for 96 h, medium renewal at 48 h.

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

value: Control


title: S. aureus (MRSA) under bile stress - rep1


title: Lung-sample-80

value: BiBt


title: TC32_EETS-low_rep3

description: Ewing sarcoma cell line TC-32; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: Doxycycline induced EWSR1-ETS knockdown


title: Lung-sample-78

value: BiBi


title: S. aureus (MRSA) under acidic stress - rep3

value: Acetic acid treated


title: Lung-sample-77


title: dDSB spo11Y135F-myc18 rad50S t4 replicate 1 ChIP

description: Figure 2b

value: anti-myc (9E11, mouse monoclonal) antibody

value: TAATGCGC

value: CCTATCCT


title: S. aureus (MRSA) under low iron - rep2

value: Treated with 2,2-dipyridryl

value: Staphylococcus aureus MRSA252


title: TC32_EETS-high_rep3

description: Ewing sarcoma cell line TC-32; Control sample; replicate 3


title: dDSB spo11Y135F-myc18 rad50S t4 ChIP

description: Figure 1c, 1d, 1d, EDF2a, EDF2b, EDF4a, EDF4b, EDF6b

value: ATCACG


title: Lung-sample-74

value: Lung

value: BtBi

value: fetus

value: male


title: POE_EETS-low_rep2

description: Ewing sarcoma cell line POE; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: POE


title: POE_EETS-low_rep3

description: Ewing sarcoma cell line POE; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: Ewing sarcoma cell line


title: S. aureus (MRSA) under acidic stress - rep1


title: POE_EETS-high_rep1

description: Ewing sarcoma cell line POE; Control sample; replicate 1

value: Control


title: Lung-sample-65

value: female


title: S. aureus (MSSA) under human serum treatment - rep3

description:
rRNA depleted total RNA
MSSA_processed.txt

organism: Staphylococcus aureus subsp. aureus MSSA476

value: Treated with human serum

value: Staphylococcus aureus MSSA476


title: S. aureus (MSSA) under human serum treatment - rep2


title: Lung-sample-62

value: BiBt


title: POE_EETS-high_rep3

description: Ewing sarcoma cell line POE; Control sample; replicate 3


title: dDSB Spo11-myc18 wt t6 ChIP

value: anti-myc (9E11, mouse monoclonal) antibody

value: CTGAAGCT

value: AGGCGAAG


title: S. aureus (MRSA) under acidic stress - rep2

value: Acetic acid treated


title: S. aureus (MSSA) under human serum treatment - rep1


title: POE_EETS-low_rep1

description: Ewing sarcoma cell line POE; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

value: Doxycycline induced EWSR1-ETS knockdown


title: dDSB Spo11-myc18 wt t5 replicate 1 WCE

value: TCCGCGAA

value: CAGGACGT


title: dDSB Spo11-myc18 wt t5 replicate 1 ChIP

value: TAATGCGC

value: TATAGCCT


title: Lung-sample-7

value: Lung

value: BtBt

value: fetus


title: POE_EETS-high_rep2

description: Ewing sarcoma cell line POE; Control sample; replicate 2

value: POE

value: Ewing sarcoma cell line

value: Control


title: dDSB Spo11-myc18 wt t6 WCE


title: TC32_EETS-high_rep2

description: Ewing sarcoma cell line TC-32; Control sample; replicate 2


title: dDSB Spo11-myc18 wt t5 WCE

value: GTACTGAC


title: S. aureus (MSSA) under high temperature - rep3

value: Treated with 41C

value: Staphylococcus aureus MSSA476


title: MIC_EETS-low_rep3

description: Ewing sarcoma cell line MIC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: MIC


title: S. aureus (MSSA) under high temperature - rep2


title: MIC_EETS-high_rep2

description: Ewing sarcoma cell line MIC; Control sample; replicate 2


title: Lung-sample-105

value: male


title: TC32_EETS-low_rep2

description: Ewing sarcoma cell line TC-32; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: Lung-sample-104

value: BtBi

value: female


title: S. aureus (MSSA) under high temperature - rep1


title: dDSB Spo11-myc18 wt t4 replicate 2 WCE

value: CGGCTATG


title: MIC_EETS-high_rep3

description: Ewing sarcoma cell line MIC; Control sample; replicate 3


title: MIC_EETS-low_rep2

description: Ewing sarcoma cell line MIC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: Doxycycline induced EWSR1-ETS knockdown


title: MIC_EETS-high_rep1

description: Ewing sarcoma cell line MIC; Control sample; replicate 1


title: Lung-sample-52


title: Lung-sample-100


title: S. aureus (MSSA) at stationary phase - rep2

value: Grown until stationary phase


title: dDSB Spo11-myc18 wt t4 replicate 1 WCE

value: TCCGCGAA

value: AGGCGAAG


title: Lung-sample-99

value: Lung

value: BiBi


title: S. aureus (MSSA) at stationary phase - rep1


title: dDSB Spo11-myc18 wt t4 replicate 1 ChIP

description: Figure EDF2a

value: anti-myc (9E11, mouse monoclonal) antibody

value: CTGAAGCT

value: CAGGACGT


title: dDSB Spo11-myc18 wt t4 replicate 2 ChIP

value: CCTATCCT


title: Lung-sample-61

value: fetus


title: dDSB spo11Y135F-myc18 rad50S t4 WCE

value: ATCACG


title: dDSB Spo11-myc18 wt t4 WCE

value: TAATCTTA


title: MIC_EETS-low_rep1

description: Ewing sarcoma cell line MIC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

value: MIC

value: Ewing sarcoma cell line


title: Lung-sample-60

value: BtBt

value: female


title: S. aureus (MSSA) under oxidative stress - rep2

value: Treated with H2O2

value: Staphylococcus aureus MSSA476


title: dDSB Spo11-myc18 wt t5 ChIP

description: Figure 2b, EDF1d, EDF2a, EDF2c

value: TAATGCGC

value: ATAGAGGC


title: dDSB Spo11-myc18 wt t4 ChIP

description: Figure 1c, 1d, 2a, 2b, 2c, 3a, 3b, 3c, 4f, 4g, EDF1d, EDF1e, EDF1f, EDF2a, EDF2b, EDF2c, EDF2d, EDF3a, EDF3g, EDF4a, EDF6b, EDF6c, EDT1

value: GTACTGAC


title: Lung-sample-56

value: Lung

value: BiBi

value: male


title: Lung-sample-103


title: MHHES1_EETS-low_rep2

description: Ewing sarcoma cell line MHH-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: Doxycycline induced EWSR1-ETS knockdown


title: dDSB Spo11-myc18 wt t3.5 replicate 1 WCE

value: TCCGCGAA

value: GGCTCTGA


title: Lung-sample-22

value: fetus


title: S. aureus (MSSA) under osmotic stress - rep2

value: Treated with NaCl


title: MHHES1_EETS-low_rep1

description: Ewing sarcoma cell line MHH-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: S. aureus (MSSA) under osmotic stress - rep3


title: dDSB Spo11-myc18 wt t3.5 WCE

value: CCTATCCT


title: S. aureus (MSSA) under oxidative stress - rep1


title: dDSB Spo11-myc18 wt t3.5 replicate 1 ChIP

value: anti-myc (9E11, mouse monoclonal) antibody

value: CTGAAGCT

value: TAATCTTA


title: TC106_EETS-high_rep3

description: Ewing sarcoma cell line TC-106; Control sample; replicate 3

value: Ewing sarcoma cell line

value: Control


title: TC32_EETS-low_rep1

description: Ewing sarcoma cell line TC-32; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: S. aureus (MSSA) under oxidative stress - rep3

description:
rRNA depleted total RNA
MSSA_processed.txt

value: Treated with H2O2

value: Staphylococcus aureus MSSA476


title: Lung-sample-53

value: BtBt

value: female


title: MHHES1_EETS-high_rep2

description: Ewing sarcoma cell line MHH-ES-1; Control sample; replicate 2


title: S. aureus (MSSA) under osmotic stress - rep1


title: S. aureus (MSSA) under nitrosative stress - rep2

value: Treated with spermin NONOate complex


title: dDSB Spo11-myc18 tel1∆ t4 replicate 1 WCE

value: TCTCGCGC


title: TC32_EETS-high_rep1

description: Ewing sarcoma cell line TC-32; Control sample; replicate 1


title: MHHES1_EETS-high_rep3

description: Ewing sarcoma cell line MHH-ES-1; Control sample; replicate 3


title: Liver-sample-106

source_name: Liver

value: Liver

value: BtBi


title: Lung-sample-13

value: Lung

value: BiBt


title: Lung-sample-8

value: fetus


title: MHHES1_EETS-low_rep3

description: Ewing sarcoma cell line MHH-ES-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: Doxycycline induced EWSR1-ETS knockdown


title: Liver-sample-97

value: male


title: dDSB Spo11-myc18 tel1∆ t4 replicate 1 ChIP

description: Figure 2c

value: anti-myc (9E11, mouse monoclonal) antibody

value: TAATGCGC


title: S. aureus (MSSA) under nitrosative stress - rep1


title: TC106_EETS-low_rep2

description: Ewing sarcoma cell line TC-106; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: Ewing sarcoma cell line


title: TC106_EETS-low_rep3

description: Ewing sarcoma cell line TC-106; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: Liver-sample-80


title: S. aureus (MSSA) under nutritional downshift - rep3

value: Treated with removal of nutrients


title: dDSB Spo11-myc18 tel1∆ t4 WCE

value: GTGGCC


title: dDSB Spo11-myc18 tel1∆ t4 ChIP

description: Figure EDF1d, EDF1f

value: CAGATC


title: S. aureus (MSSA) under nutritional downshift - rep2

value: Staphylococcus aureus MSSA476


title: dDSB Spo11-myc18 rec114-8A tel1∆ t4 WCE

value: GTTTCG


title: Liver-sample-78

value: BiBi


title: EW3_EETS-low_rep2

description: Ewing sarcoma cell line EW-3; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: S. aureus (MSSA) at stationary phase - rep3

value: Grown until stationary phase


title: EW3_EETS-high_rep2

description: Ewing sarcoma cell line EW-3; Control sample; replicate 2

value: Control


title: EW3_EETS-low_rep1

description: Ewing sarcoma cell line EW-3; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: dDSB Spo11-myc18 wt t3.5 ChIP

description: Figure 2b

value: CTGAAGCT

value: AGGCGAAG


title: dDSB Spo11-myc18 rec114-8A rad50S t4 replicate 1 WCE

value: AGCGATAG

value: GGCTCTGA


title: Liver-sample-91

value: Liver

value: BiBt

value: fetus


title: TC106_EETS-high_rep2

description: Ewing sarcoma cell line TC-106; Control sample; replicate 2


title: EW3_EETS-high_rep3

description: Ewing sarcoma cell line EW-3; Control sample; replicate 3


title: S. aureus (MSSA) under hypoxia - rep3

value: Treated with oxygen deprivation


title: EW3_EETS-low_rep3

description: Ewing sarcoma cell line EW-3; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: Ewing sarcoma cell line

value: Doxycycline induced EWSR1-ETS knockdown


title: S. aureus (MSSA) under hypoxia - rep2


title: Liver-sample-74

value: BtBi

value: male


title: Liver-sample-77


title: dDSB Spo11-myc18 rec114-8A rad50S t4 replicate 1 ChIP

value: anti-myc (9E11, mouse monoclonal) antibody

value: CGGCTATG

value: TAATCTTA


title: MHHES1_EETS-high_rep1

description: Ewing sarcoma cell line MHH-ES-1; Control sample; replicate 1


title: dDSB Spo11-myc18 rec114-8A rad50S t4 ChIP

description: Figure EDF1d

value: CTTGTA


title: dDSB Spo11-myc18 rec114-8A tel1∆ t4 ChIP

description: Figure EDF1e, EDF3d

value: ACTTGA


title: S. aureus (MSSA) under low iron - rep2

value: Treated with 2,2-dipyridryl

value: Staphylococcus aureus MSSA476


title: S. aureus (MSSA) under nitrosative stress - rep3

value: Treated with spermin NONOate complex


title: dDSB Spo11-myc18 Rec104-FRB-HA3 t4.5 + Rapamycin t4 WCE

value: GAATTCGT

value: TATAGCCT


title: Liver-sample-65

value: Liver

value: BiBi

value: female


title: Liver-sample-46

value: fetus


title: EW3_EETS-high_rep1

description: Ewing sarcoma cell line EW-3; Control sample; replicate 1

value: Ewing sarcoma cell line

value: Control


title: S. aureus (MSSA) under nutritional downshift - rep1

value: Treated with removal of nutrients


title: S. aureus (MSSA) under low iron - rep1


title: dDSB Spo11-myc18 Rec104-FRB-HA3 t4.5 + Rapamycin t4 ChIP

description: Figure 4d, 4e, EDF5c

value: anti-myc (9E11, mouse monoclonal) antibody

value: CGCTCATT


title: Liver-sample-7

value: BtBt


title: S. aureus (MSSA) untreated (control) - rep3

value: Untreated


title: dDSB Spo11-myc18 Rec104-FRB-HA3 t4 WCE

value: ATTCAGAA

value: GTACTGAC


title: S. aureus (MSSA) under hypoxia - rep1

value: Treated with oxygen deprivation

value: Staphylococcus aureus MSSA476


title: dDSB Spo11-myc18 rec114-8A rad50S t4 WCE

value: CTTGTA


title: Liver-sample-105

value: male


title: S. aureus (MSSA) untreated (control) - rep2


title: dDSB Spo11-myc18 Rec104-FRB-HA3 t4 ChIP

description: Figure 4d, 4e, EDF5c

value: AGGCGAAG


title: Liver-sample-104

value: Liver

value: BtBi


title: Liver-sample-52

value: fetus


title: S. aureus (MSSA) under low iron - rep3

value: Treated with 2,2-dipyridryl


title: EW22_EETS-low_rep1

description: Ewing sarcoma cell line EW-22; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

value: Ewing sarcoma cell line

value: Doxycycline induced EWSR1-ETS knockdown


title: EW22_EETS-low_rep2

description: Ewing sarcoma cell line EW-22; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: Liver-sample-62

value: BiBt

value: female


title: TC106_EETS-high_rep1

description: Ewing sarcoma cell line TC-106; Control sample; replicate 1

value: Control


title: S. aureus (MSSA) untreated (control) - rep1

description:
rRNA depleted total RNA
MSSA_processed.txt

value: Untreated


title: S. aureus (MSSA) under bile stress - rep3

value: Bile salts treated


title: Liver-sample-103

value: BtBt


title: dDSB Spo11-myc18 rad50S tel1∆ t4 replicate 1 ChIP

description: Figure EDF1d, EDF1f

value: anti-myc (9E11, mouse monoclonal) antibody

value: GCCAAT


title: Liver-sample-100


title: dDSB Spo11-myc18 rad50S tel1∆ t4 WCE

value: TCTCGCGC

value: CAGGACGT


title: dDSB Spo11-myc18 rad50S tel1∆ t4 ChIP

description: Figure 2d

value: CGGCTATG

value: TATAGCCT


title: EW22_EETS-high_rep3

description: Ewing sarcoma cell line EW-22; Control sample; replicate 3


title: S. aureus (MSSA) under acidic stress - rep3

value: Acetic acid treated

value: Staphylococcus aureus MSSA476


title: Liver-sample-99

value: Liver

value: BiBi

value: fetus


title: dDSB Spo11-myc18 rad50S t6 WCE

value: ATTCAGAA


title: Liver-sample-61

value: BtBi

value: male


title: dDSB Spo11-myc18 rad50S tel1∆ t4 replicate 1 WCE

value: GTGAAA


title: Liver-sample-60

value: female


title: S. aureus (MSSA) under acidic stress - rep2


title: TC106_EETS-low_rep1

description: Ewing sarcoma cell line TC-106; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

value: Ewing sarcoma cell line

value: Doxycycline induced EWSR1-ETS knockdown


title: EW22_EETS-high_rep2

description: Ewing sarcoma cell line EW-22; Control sample; replicate 2

value: Control


title: dDSB Spo11-myc18 rad50S t6 ChIP

description: Figure 4f, 4g, EDF6b, EDF6c

value: anti-myc (9E11, mouse monoclonal) antibody

value: TCCGGAGA

value: TAATCTTA


title: Liver-sample-56


title: S. aureus (MSSA) under acidic stress - rep1


title: EW22_EETS-high_rep1

description: Ewing sarcoma cell line EW-22; Control sample; replicate 1


title: dDSB Spo11-myc18 rad50S t4 replicate 1 WCE

value: AGCGATAG

value: ATAGAGGC


title: S. aureus (MSSA) under bile stress - rep1

value: Bile salts treated

value: Staphylococcus aureus MSSA476


title: S. epidermidis under human serum treatment - rep3

description:
rRNA depleted total RNA
SEPI_processed.txt

organism: Staphylococcus epidermidis

value: Treated with human serum

value: Staphylococcus epidermidis 1457


title: EW1_EETS-low_rep3

description: Ewing sarcoma cell line EW-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: dDSB Spo11-myc18 rad50S t4 replicate 1 ChIP

description: Figure EDF2a, EDT1

value: CGGCTATG

value: GGCTCTGA


title: SKNMC_EETS-low_rep3

description: Ewing sarcoma cell line SK-N-MC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: SK-N-MC


title: Liver-sample-22

value: Liver

value: BiBi

value: fetus


title: S. epidermidis under human serum treatment - rep2


title: dDSB Spo11-myc18 rad50S t4 WCE

value: CCTATCCT


title: Liver-sample-13

value: BiBt

value: female


title: EW1_EETS-low_rep1

description: Ewing sarcoma cell line EW-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

value: Ewing sarcoma cell line

value: Doxycycline induced EWSR1-ETS knockdown


title: EW22_EETS-low_rep3

description: Ewing sarcoma cell line EW-22; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: SKNMC_EETS-high_rep3

description: Ewing sarcoma cell line SK-N-MC; Control sample; replicate 3

value: Control


title: EW1_EETS-high_rep3

description: Ewing sarcoma cell line EW-1; Control sample; replicate 3


title: Liver-sample-53

value: BtBt


title: dDSB Spo11-myc18 rad50S t4 ChIP

description: Figure 1c, 1d, 1d, 2d, EDF1d, EDF1e, EDF1f, EDF2a, EDF2b, EDF2c, EDF2d, EDF4a, EDF4b, EDT1

value: anti-myc (9E11, mouse monoclonal) antibody

value: AGGCGAAG


title: Liver-sample-8


title: S. epidermidis under high temperature - rep3

value: Treated with 41C


title: S. epidermidis under high temperature - rep2

value: Staphylococcus epidermidis 1457


title: dDSB Spo11-myc18 mre11S t4 replicate 1 WCE

value: AGTTCC


title: dDSB Spo11-myc18 mre11S t4 replicate 1 ChIP

value: TGACCA


title: Brain-sample-97

source_name: Brain

value: Brain

value: BtBi

value: male


title: SKNMC_EETS-low_rep2

description: Ewing sarcoma cell line SK-N-MC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: SK-N-MC


title: Brain-sample-106

value: fetus


title: S. epidermidis under high temperature - rep1


title: S. aureus (MSSA) under bile stress - rep2

value: Bile salts treated

value: Staphylococcus aureus MSSA476


title: S. epidermidis at stationary phase - rep3

value: Grown until stationary phase


title: EW1_EETS-high_rep2

description: Ewing sarcoma cell line EW-1; Control sample; replicate 2

value: Ewing sarcoma cell line


title: Brain-sample-91

value: BiBt


title: Brain-sample-80


title: dDSB Spo11-myc18 mre11S t4 ChIP

description: Figure EDF1d, EDF1e, EDF1f, EDF2a, EDF2b

value: CGGCTATG

value: CCTATCCT


title: dDSB Spo11-myc18 com1∆ t4 WCE

value: TCTCGCGC

value: TAATCTTA


title: EW1_EETS-low_rep2

description: Ewing sarcoma cell line EW-1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: Doxycycline induced EWSR1-ETS knockdown


title: Brain-sample-77


title: S. epidermidis at stationary phase - rep1

value: Staphylococcus epidermidis 1457


title: S. epidermidis under oxidative stress - rep3

value: Treated with H2O2


title: S. epidermidis at stationary phase - rep2


title: dDSB Spo11-myc18 com1∆ t4 ChIP

description: Figure 1c, EDF1d, EDF1e, EDF2a, EDF2b, EDT1

value: anti-myc (9E11, mouse monoclonal) antibody

value: TAATGCGC

value: GTACTGAC


title: SKNMC_EETS-high_rep2

description: Ewing sarcoma cell line SK-N-MC; Control sample; replicate 2

value: SK-N-MC

value: Control


title: S. epidermidis under human serum treatment - rep1

value: Treated with human serum


title: S. epidermidis under oxidative stress - rep2


title: dDSB spo11∆ rad50S t4 ChIP

description: Figure 4f

value: CTGAAGCT

value: TATAGCCT


title: Brain-sample-74

value: Brain

value: BtBi

value: fetus

value: male


title: CHLA25_EETS-low_rep3

description: Ewing sarcoma cell line CHLA-25; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: Ewing sarcoma cell line


title: EW1_EETS-high_rep1

description: Ewing sarcoma cell line EW-1; Control sample; replicate 1


title: Brain-sample-62

value: BiBt

value: female


title: Reinke´s edema sample 7

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

description: Biological replicate 7 of 8

hyb_protocol: Standard Agilent protocol. Labeled test and control samples were mixed and hybridized into a 4 x 180K slide (Agilent - G4449A)

scan_protocol: The slides were scanned on na Agilent G2565B scanner

data_processing:
Data were extracted using the Agilent Feature Extraction software (v 8.5.1.1) and analyzed using the Agilent CytoGenomics software (v 5.1) with the following parameters: ADM-2 algorithm, threshold of 6.0, at least four altered probes, log2 ratio > 0.25 for gains and < -0.25 for losses. The fuzzy zero correction was applied, with a detailed visual analysis being performed for all alterations, excluding regions with poor data quality.
Normalized and processed log2 ratio (Cy3/Cy5) representing test/reference

source_name: Laryngeal tissue

label_protocol: Standard Agilent protocol. Test samples have been labeled with Cy3 and controls with Cy5

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted using the standard phenol-chloroform method

tag: gender

value: Female

source_name: Comercial reference DNA


title: S. epidermidis under oxidative stress - rep1

value: Treated with H2O2

value: Staphylococcus epidermidis 1457


title: dDSB spo11∆ rad50S t4 WCE

value: CGGCTATG

value: AGGCGAAG


title: CHLA25_EETS-high_rep3

description: Ewing sarcoma cell line CHLA-25; Control sample; replicate 3


title: S. epidermidis under osmotic stress - rep3

description:
rRNA depleted total RNA
SEPI_processed.txt

value: Treated with NaCl


title: CHLA25_EETS-high_rep2

description: Ewing sarcoma cell line CHLA-25; Control sample; replicate 2

value: Control


title: CHLA25_EETS-high_rep1

description: Ewing sarcoma cell line CHLA-25; Control sample; replicate 1


title: dDSB Spo11-myc18 mre11S t4 WCE

value: AGCGATAG


title: Brain-sample-52

value: BtBt


title: Brain-sample-46

value: BiBi


title: S. epidermidis under osmotic stress - rep1


title: Reinke´s edema sample 5

description: Biological replicate 5 of 8


title: Brain-sample-65

value: Brain


title: Reinke´s edema sample 8

description: Biological replicate 8 of 8

value: Male


title: SKNMC_EETS-high_rep1

description: Ewing sarcoma cell line SK-N-MC; Control sample; replicate 1

value: SK-N-MC


title: SKNMC_EETS-low_rep1

description: Ewing sarcoma cell line SK-N-MC; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

value: Doxycycline induced EWSR1-ETS knockdown


title: Brain-sample-78

value: fetus

value: male


title: Reinke´s edema sample 4

description: Biological replicate 4 of 8


title: S. epidermidis under nitrosative stress - rep2

value: Treated with spermin NONOate complex


title: Brain-sample-105


title: Brain-sample-7

value: female


title: S. epidermidis under osmotic stress - rep2


title: Brain-sample-104

value: BtBi


title: CHLA25_EETS-low_rep2

description: Ewing sarcoma cell line CHLA-25; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: Ewing sarcoma cell line


title: S. epidermidis under nitrosative stress - rep1

value: Staphylococcus epidermidis 1457


title: CHLA25_EETS-low_rep1

description: Ewing sarcoma cell line CHLA-25; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: Brain-sample-103


title: S. epidermidis under nitrosative stress - rep3


title: EW24_EETS-low_rep2

description: Ewing sarcoma cell line EW-24; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: Reinke´s edema sample 6

description: Biological replicate 6 of 8


title: S. epidermidis under nutritional downshift - rep3

value: Treated with removal of nutrients


title: A673_EETS-low_rep1

description: Ewing sarcoma cell line A-673; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: S48lm-3

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

country: China

institute: Gansu Agricultural University

description:
Rainbow trout
genes_fpkm_expression.txt

data_processing:
Use fastp for quality control of raw reads, and remove reads containing adapters, N ratios greater than 10%, all A bases, and low-quality reads (the number of bases with a quality value Q≤20 accounts for more than 50% of the entire read).
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
Compare the obtained Clean reads with the reference genome USDA_OmykA_1.1 of rainbow trout and the corresponding gene annotation model file. Eliminate reads with multiple matching sites and only use reads with unique matching sites to measure gene transcription levels.
The expression level of each gene is expressed by FPKM, which is the number of fragments from a gene per-kilobase length per million fragments. The differentially expressed genes between the control and virus infection groups were analyzed using the DESeq2. The adjusted P-value < 0.05 was used to identify differentially expressed genes (DEGs).
Genome_build: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary_files_format_and_content: genes_fpkm_expression.txt: Tab-delimited text file includes counts and FPKM values for each Sample.

organism: Oncorhynchus mykiss

source_name: Intestine

extract_protocol:
The samples were homogenized and total RNA was extracted by using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The experimental and control groups were treated with IHNV and M199 for 48 hours, respectively.

value: Intestine

value: Intraperitoneal injection of IHNV

tag: time

value: 48 hours after infection


title: Reinke´s edema sample 1

description: Biological replicate 1 of 8


title: Brain-sample-99


title: A673_EETS-low_rep2

description: Ewing sarcoma cell line A-673; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: A673_EETS-high_rep3

description: Ewing sarcoma cell line A-673; Control sample; replicate 3

value: Control


title: A673_EETS-low_rep3

description: Ewing sarcoma cell line A-673; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: S48lm-2

description:
Rainbow trout
genes_fpkm_expression.txt


title: EW24_EETS-high_rep3

description: Ewing sarcoma cell line EW-24; Control sample; replicate 3


title: S. epidermidis under hypoxia - rep3

value: Treated with oxygen deprivation


title: S. epidermidis under nutritional downshift - rep1


title: Brain-sample-100

value: Brain


title: wild type FLT3+Cxcl12 rep2

type: RNA

city: Izumo

first: Seiji

last: Fukuda

state: Shimane

address: 89-1 Enya

department: Pediatrics

country: Japan

institute: Shimane University

description: gene expression after 4 hour incubation with 100ng/ml Cxcl12

hyb_protocol: The hybridization procedure was performed according to the Agilent microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, Cy3 labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x40K using Agilent’s recommended hybridization chamber and oven. Finally, the microarray was washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities and ratios (including background subtraction and normalization), rejects outliers and calculates statistical confidences (p-values). For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).
normalized intensity

organism: Mus musculus

source_name: Ba/F3 cells expressing wild type FLT3 and incubated with 100ng/ml of Cxcl12

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the Agilent 2100 Bioanalyzer.

growth_protocol: cells were maintained in 10% FBS, RPMI1640 supplemented with 0.1ng/ml of remombinant mouse IL3.

extract_protocol: total RNA was harvested from the collected cells using the standard protocol using commercially available total RNA extraction kit.

treatment_protocol: cells were washed three time with plain RPMI160 and incubated for 4 hours at 37oC in 0.5% BSA RPMI1640 in the presence or absence of 100ng/ml of recombinant murine Cxcl12

value: Ba/F3 cells

tag: sample type

value: wild type FLT3+Cxcl12


title: FLT3/ITD N78+Cxcl12

source_name: Ba/F3 cells expressing N78 FLT3/ITD and incubated with 100ng/ml of Cxcl12

value: FLT3/ITD N78+Cxcl12


title: Reinke´s edema sample 2

description: Biological replicate 2 of 8

value: Female


title: EW24_EETS-low_rep1

description: Ewing sarcoma cell line EW-24; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

value: Doxycycline induced EWSR1-ETS knockdown


title: S48lm-1

description:
Rainbow trout
genes_fpkm_expression.txt


title: Brain-sample-60

value: BtBt

value: fetus


title: Reinke´s edema sample 3

description: Biological replicate 3 of 8

value: Male


title: S. epidermidis under hypoxia - rep2


title: C48lm-3

description:
Rainbow trout
genes_fpkm_expression.txt

value: Intraperitoneal injection of M199


title: Brain-sample-56

value: BiBi

value: male


title: S. epidermidis under hypoxia - rep1

value: Staphylococcus epidermidis 1457


title: EW24_EETS-high_rep1

description: Ewing sarcoma cell line EW-24; Control sample; replicate 1

value: Ewing sarcoma cell line


title: FLT3/ITD N78

description: gene expression after 4 hour incubation without Cxcl12

source_name: Ba/F3 cells expressing N78 FLT3/ITD

value: FLT3/ITD N78


title: S. epidermidis under low iron - rep3

description:
rRNA depleted total RNA
SEPI_processed.txt

value: Treated with 2,2-dipyridryl


title: EW24_EETS-high_rep2

description: Ewing sarcoma cell line EW-24; Control sample; replicate 2

value: Control


title: wild type FLT3 rep2

source_name: Ba/F3 cells expressing wild type FLT3

value: wild type FLT3


title: Brain-sample-61

value: Brain

value: BtBi


title: C48lm-1

description:
Rainbow trout
genes_fpkm_expression.txt

value: Intestine

value: 48 hours after infection


title: S. epidermidis under low iron - rep2


title: Brain-sample-22

value: female


title: C48lm-2

description:
Rainbow trout
genes_fpkm_expression.txt


title: A673_EETS-high_rep1

description: Ewing sarcoma cell line A-673; Control sample; replicate 1


title: Brain-sample-13

value: BiBt


title: Brain-sample-8

value: fetus


title: wild type FLT3+Cxcl12 rep1

value: Ba/F3 cells

value: wild type FLT3+Cxcl12


title: ILL6002

city: Nathan

first: Ido

last: Bar

state: QLD

address: 170 Kessels Road

department: School of Environment and Science

institute: Griffith University

description:
Parent
Unimelb_parents_2.vcf

data_processing:
Read trimming performed using custom perl script and Cutadapt v1.4.1 software. Reads were filtered by removing adaptor sequences along with reads and bases of low quality. Reads which had three consecutive N's and >3 consecutive nucleotides with Phred scores ≤ 20 were trimmed. Finally, any reads that were shorter than 50 bp were removed from the final set.
Parental read alignment to reference performed using BWA-MEM. SAM files were converted into binary format (BAM) files, sorted and indexed using SAMtools (version 1.9) sort and view options.
Variant calling performed through SAMtools mpileup and bcftools (version 1.9), and filtered using vcftools (v0.1.16).
RILs read alignment to reference performed using BWA-MEM. SAM files were converted into binary format (BAM) files, sorted and indexed using SAMtools (version 1.9) sort and view options.
Variant calling in RILs performed using SAMtools mpileup and bcftools (version 1.9), and filtered using vcftools (v0.1.16) with the SNP list identified from the parents.
Genome_build: Cassab reference transcriptome (Sudheesh et al., 2016).
Supplementary_files_format_and_content: vcf files include SNPs.

organism: Lens culinaris

source_name: leaf

extract_protocol:
Total RNA was extracted from selected young leaves of 14-day-old seedlings of parents and 140 RILs using the RNeasy® 96 kit (Qiagen Inc., Hilden, Germany) following the manufacturer’s instructions.
cDNA libraries were prepared for sequencing using standard Illumina protocols.

tag: line

value: Leaf tissue

value: 14 days


title: CHLA10_EETS-low_rep2

description: Ewing sarcoma cell line CHLA-10; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2

value: Doxycycline induced EWSR1-ETS knockdown


title: S. epidermidis under low iron - rep1

value: Staphylococcus epidermidis 1457


title: CHLA10_EETS-low_rep3

description: Ewing sarcoma cell line CHLA-10; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: Ewing sarcoma cell line


title: Tilwa Tween40 Rep-4

city: West Lafayette

first: Teeratas

last: Kijpornyongpan

state: IN

address: 915 W State St

department: Botany and Plant Pathology

country: USA

institute: Purdue University

description:
MCA4186_T-R5
processed data file: Tilwa_RawReadCount.txt
processed data file: Tilwa_NormReadCount.csv

data_processing:
Adapter and low base-quality bases trimming by Cutadapt version 1.13 and Trimmomatics version 0.36 using default parameters.
Clean reads were mapped to the reference genomic sequence of each species (T. washingtonensis MCA 4186 v 1.0 and M. miltonrushii MCA 3882 v 1.0) through TopHat version 2.1.1 using default parameters.
BAM alignments were transformed into raw gene counts using htseq version 0.7.0 with default parameters and using proteinId as a feature.
Genome_build: JGI MycoCosm genome portal
Supplementary_files_format_and_content: *_RawReadCount.txt: Raw gene count in tab-delimited txt file.
Supplementary_files_format_and_content: *_NormReadCount.csv: Normalized gene count, using DESeq2 version 1.20.0, in comma-separated txt file.

organism: Tilletiopsis washingtonensis

source_name: fungal biomass

growth_protocol: Fungal cultures were grown in Potato Dextrose Broth (PDB) for 7 days. After that, fungal biomasses were centrifuged and resuspended in sterile water.

extract_protocol:
The fungal biomasses were centrifuged, rinsed in sterile water three times and ground-frozen in liquid nitrogen. Total RNA of each sample was extracted using the Omega BioTek E.Z.N.A.® Fungal RNA Mini Kit (R6840-01).
Poly A+ libraries were prepared using Illumina’s TruSeq mRNA Library Prep Kit followed by manufacturer's protocol.

treatment_protocol: About 5 x 10^6 cells were inoculated into each experimental unit. We used Holliday's minimal media with 1% glucose or 1% Tween40 as a carbon source. The cultures were incubated at room temperature (25 C) for three days before RNA harvest.

tag: phenotype

value: Filamentous growth

value: Fungal biomass


title: genomic DNA from PT2016-172-CORE

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Within-sample normalization and QC performed using seSAMe in R.
value definition: noob-normalized average Beta

label: Cy5 and Cy3

source_name: normal lung sample

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

tag: race

value: white

value: male

tag: ethnicity

value: non-hispanic

tag: diagnosis

value: normal

tag: smoking

value: Never

tag: tissue type

value: control


title: wild type FLT3 rep1

value: wild type FLT3


title: WT TCR-activated

city: Cambridge

first: Alexander

last: Poltorak

state: MA

address: 150 Harrison avenue, J529

institute: tufts

description:
Sample 3
Naïve total CD3+, CD4+, and CD8+ T cells were isolated from mouse spleens and pLN using STEMCELL Technologies (Vancouver, BC) EasySep Mouse T cell isolation kits according to manufacturer’s instructions. Expanded T cells were prepared using Mouse T activator CD3/CD28 DynaBeads (ThermoFisher Scientific) in complete RPMI with 10% FBS and 50 U/ml recombinant IL-2. Cells were rested overnight in complete media without IL-2 before experiments.
Seven to fifteen week old mice were used for each experiment. Wild type C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor Maine). STING-/- mice obtained from Dr. Glen Barber (University of Miami) and IFNAR-/- mice provided by Dr. Katherine Fitzgerald

data_processing:
The resulted data were demultiplexed using Illumina CASAVA 1.8 and fastq files for each initial sample were generated
Tophat2 alignment of raw paired reads to UCSC mm10 genome
Cuffdids using the outputs from two previous steps with mm10 annotation
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: T cells

extract_protocol:
RNA was prepared according to manufacture's instructions
Library was prepared using Truseq pair-end Illumina kit. Briefly, 10-100 ng of total RNA was reconstituted in water, mixed with Ribosomal removal Buffer containing RNAClean XP beads, and depleted from rRNA. First strand was synthesized using RT, followed by a second strand synthesis, 3' ends were adenylated and ligated to the adaptors, followed by ligateion of the 5' adaptors; the library was purified and measured on DNA-concentration

treatment_protocol: Naïve or expanded T cells were stimulated with 10 μg/ml DMXAA (Invivogen) unless otherwise indicated; for experiments involving TCR activation, tissue culture plates were coated overnight with anti-CD3 and anti-CD28 antibodies (BD Bioscience; Biolegend) at 5 μg/ml.

tag: genotype

value: WT

tag: developmental treatment

value: TCR-activated

tag: strain


title: STING-KO TCR-activated

description:
Sample 4
Naïve total CD3+, CD4+, and CD8+ T cells were isolated from mouse spleens and pLN using STEMCELL Technologies (Vancouver, BC) EasySep Mouse T cell isolation kits according to manufacturer’s instructions. Expanded T cells were prepared using Mouse T activator CD3/CD28 DynaBeads (ThermoFisher Scientific) in complete RPMI with 10% FBS and 50 U/ml recombinant IL-2. Cells were rested overnight in complete media without IL-2 before experiments.
Seven to fifteen week old mice were used for each experiment. Wild type C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor Maine). STING-/- mice obtained from Dr. Glen Barber (University of Miami) and IFNAR-/- mice provided by Dr. Katherine Fitzgerald

value: STING-KO


title: FLT3/ITD N51

source_name: Ba/F3 cells expressing N51 FLT3/ITD

value: Ba/F3 cells

value: FLT3/ITD N51


title: genomic DNA from PT2016-168-CORE

tag: age

tag: Sex

value: Ever


title: S. epidermidis untreated (control) - rep2

source_name: in vitro bacterial culture

tag: treatment

value: Untreated

value: Staphylococcus epidermidis 1457


title: S. epidermidis untreated (control) - rep1


title: Tilwa Tween40 Rep-3

description:
MCA4186_T-R4
processed data file: Tilwa_RawReadCount.txt
processed data file: Tilwa_NormReadCount.csv

value: Filamentous growth

tag: tissue


title: STING-KO Unstimulated

description:
Sample 2
Naïve total CD3+, CD4+, and CD8+ T cells were isolated from mouse spleens and pLN using STEMCELL Technologies (Vancouver, BC) EasySep Mouse T cell isolation kits according to manufacturer’s instructions. Expanded T cells were prepared using Mouse T activator CD3/CD28 DynaBeads (ThermoFisher Scientific) in complete RPMI with 10% FBS and 50 U/ml recombinant IL-2. Cells were rested overnight in complete media without IL-2 before experiments.
Seven to fifteen week old mice were used for each experiment. Wild type C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor Maine). STING-/- mice obtained from Dr. Glen Barber (University of Miami) and IFNAR-/- mice provided by Dr. Katherine Fitzgerald

value: Unstimulated


title: CHLA10_EETS-high_rep2

description: Ewing sarcoma cell line CHLA-10; Control sample; replicate 2

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

value: Control


title: genomic DNA from PT2016-155-CORE

value: white

value: male

value: non-hispanic


title: Tilwa Tween40 Rep-2

description:
MCA4186_T-R3
processed data file: Tilwa_RawReadCount.txt
processed data file: Tilwa_NormReadCount.csv

value: Fungal biomass


title: S. epidermidis under bile stress - rep2

value: Bile salts treated


title: Tilwa Tween40 Rep-1

description:
MCA4186_T-R2
processed data file: Tilwa_RawReadCount.txt
processed data file: Tilwa_NormReadCount.csv


title: invitro, 100cell, lineage

city: Philadelphia

first: Kamen

middle: P

last: Simeonov

state: PA

address: 3800 Spruce St

institute: University of Pennsylvania

data_processing:
Demultiplexed fastq files are obtained either by illumina basespace or 10x Cell Ranger v3
10x Cell Ranger v3 was used to align transcriptomes and a custom pipeline was used to align barcodes (https://github.com/mckennalab/SingleCellLineage/)
Sparse expression matrices for transcriptomes were produced using 10x Cell Ranger v3
Clonal and subclonal annotation was produced from barcode data using custom scripts (https://github.com/ksimeono/macsGESTALT)
Genome_build: mm10
Supplementary_files_format_and_content: .tsv files are tab seperated txt files and .mtx files are sparse expression matrices

molecule: polyA RNA

source_name: cancer cells

growth_protocol: PDAC cells were cultured in complete media (DMEM, 10% FBS, 1% glutamine with penicillin and streptomycin).

extract_protocol:
Tissues were collected, single-cell dissociated, GFP+ cells were FACS isolated, samples were then loaded for 10x encapsulation (Chromium Single Cell 3’ Reagent Kits v3)
Single cell RNA-seq libraries were prepared as in the 10x Chromium Single Cell 3' v3 user guide (Rev A) until Step 2.3. After cDNA amplification, the 100 µL cDNA PCR was split 50:50 for separate barcode and transcriptome library preparation. Transcriptome library construction continued as in the 10x user guide instructions. Barcode libraries were prepared using a custom targeted PCR, followed by an indexing PCR, barcode libraries were then size-selected using SPRI beads.
scRNAseq; sc transcriptome libraries were sequenced on the Illumina NovaSeq 6000 System with 100-cycle S2 Reagent Kits with the following run parameters: Read 1 - 28 cycles, i7 index - 8 cycles, Read 2 - 91; sc barcode libraries were sequenced on the Illumina MiSeq with 600-cycle v3 Reagent Kits with the following run parameters: Read 1 - 28 cycles, i7 index - 8 cycles, Read 2 - 500.

treatment_protocol: macsGESTALT PDAC cells were thawed and expanded for 2-4 d prior to dissociation and orthotopic injection into 10 week old NOD/SCID male mice (Jackson Laboratory). Approximately 30,000 PDAC cells were injected into the surgically-exposed tail of the pancreas. Cells were allowed to engraft; then doxycycline was initiated 1 week post-injection and given continuously in the drinking water at 1 mg/mL. Mice were harvested at approximately 5 weeks post injection, once reaching morbidity.

tag: harvest-site

value: Cultured cells

tag: experiment

value: invitro

tag: info-type

value: lineage


title: S. epidermidis untreated (control) - rep3


title: Tilwa Glucose Rep-4

description:
MCA4186_G-R5
processed data file: Tilwa_RawReadCount.txt
processed data file: Tilwa_NormReadCount.csv

tag: phenotype

value: Yeast growth


title: WT Unstimulated

description:
Sample 1
Naïve total CD3+, CD4+, and CD8+ T cells were isolated from mouse spleens and pLN using STEMCELL Technologies (Vancouver, BC) EasySep Mouse T cell isolation kits according to manufacturer’s instructions. Expanded T cells were prepared using Mouse T activator CD3/CD28 DynaBeads (ThermoFisher Scientific) in complete RPMI with 10% FBS and 50 U/ml recombinant IL-2. Cells were rested overnight in complete media without IL-2 before experiments.
Seven to fifteen week old mice were used for each experiment. Wild type C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor Maine). STING-/- mice obtained from Dr. Glen Barber (University of Miami) and IFNAR-/- mice provided by Dr. Katherine Fitzgerald

value: WT


title: CHLA10_EETS-low_rep1

description: Ewing sarcoma cell line CHLA-10; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

source_name: Ewing sarcoma cell line stably transduced with inducible shRNA expressing construct targeting the respective EWSR1-ETS fusion oncogene

value: Doxycycline induced EWSR1-ETS knockdown


title: S. epidermidis under bile stress - rep3


title: genomic DNA from PT2016-167-CORE

tag: race

tag: ethnicity

value: normal

value: Ever

value: control


title: invitro, 5cell, lineage


title: Brain-sample-53

value: Brain

tag: fetus number

value: BtBt

value: fetus

value: female


title: CHLA10_EETS-high_rep1

description: Ewing sarcoma cell line CHLA-10; Control sample; replicate 1

value: Ewing sarcoma cell line

value: Control


title: Tilwa Glucose Rep-3

description:
MCA4186_G-R4
processed data file: Tilwa_RawReadCount.txt
processed data file: Tilwa_NormReadCount.csv

value: Fungal biomass


title: S. epidermidis under acidic stress - rep3

description:
rRNA depleted total RNA
SEPI_processed.txt

value: Acetic acid treated

value: Staphylococcus epidermidis 1457


title: S. epidermidis under bile stress - rep1

value: Bile salts treated


title: Mouse2, Lung, lineage

value: Lung

value: lineage


title: genomic DNA from PT2016-151-CORE

value: white

value: male

value: non-hispanic

tag: diagnosis

tag: smoking

tag: tissue type


title: genomic DNA from PT2016-131-CORE

value: normal

value: Ever


title: A673_EETS-high_rep2

description: Ewing sarcoma cell line A-673; Control sample; replicate 2

tag: genotype


title: Tilwa Glucose Rep-2

description:
MCA4186_G-R3
processed data file: Tilwa_RawReadCount.txt
processed data file: Tilwa_NormReadCount.csv

tag: strain

value: Yeast growth


title: Mouse2, Liver, lineage

value: Liver


title: EW24_EETS-low_rep3

description: Ewing sarcoma cell line EW-24; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: Doxycycline induced EWSR1-ETS knockdown


title: genomic DNA from PT2016-144-CORE

tag: age

tag: Sex

value: control


title: genomic DNA from PT2016-098-CORE


title: Tilwa Glucose Rep-1

description:
MCA4186_G-R2
processed data file: Tilwa_RawReadCount.txt
processed data file: Tilwa_NormReadCount.csv

tag: tissue


title: genomic DNA from PT2016-072-CORE

value: female

value: Never


title: S. aureus (MRSA) under human serum treatment - rep2

description:
rRNA depleted total RNA
MRSA_processed.txt

tag: treatment

value: Treated with human serum

value: Staphylococcus aureus MRSA252


title: S. epidermidis under acidic stress - rep1

value: Acetic acid treated

value: Staphylococcus epidermidis 1457


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population E D5, buffer ("QS")

city: Seattle

first: Nicole

middle: E

last: Smalley

state: Washington

address: 1705 NE Pacific St Health Sci Bldg  K-359

department: Pulmonary, Critical Care and Sleep Medicine

institute: University of Washington

description: Population E D5, buffer

data_processing:
Fastq.gz files were trimmed to remove adapters using Trim Galore!; trim_galore --paired --quality 20 --phred33
Reads were mapped to transcriptome and genome using StrandNGS version 3.3.1 RNA alignment workflow using default parameters
Transcripts were quantified in StrandNGS 3.3.1 using the RNA-Seq workflow. Using the DESeq2 script function within StrandNGS, differential expression analysis was performed using the Benjamini-Hochberg adjustment for multiple comparisons and a false-discovery rate α = 0.05.
DESeq2 matrices for differential expression analyses compared transcript abundance under the 3 growth conditions described above for each day 5 and each day 160 population separately.
Genome_build: NC_002516
Supplementary_files_format_and_content: tab-delimited text file containing raw transcript counts

organism: Pseudomonas aeruginosa

source_name: cell culture

growth_protocol: Evolved PAO1-derived populations were obtained by daily passaging in CAM medium for 160 days. Evolving populations were collected at regular timepoints, including days 5 and 160. Experiments with evolved populations were initiated by taking scrapings from frozen glycerol stock and inoculated directly into buffered LB and grown overnight. Overnight cultures were backdiluted to OD600 0.01 in fresh buffered LB and grown to logarithmic phase OD600 0.1-0.4 for use as starter culture in RNA-Seq experiments.

extract_protocol:
Thawed cell pellets were resuspended in QIAzol reagent and mechanically lysed by bead beating. RNA was extracted using the Qiagen RNeasy kit. Isolated RNA was then treated with Ambion Turbo DNase and purified using the Qiagen MinElute cleanup kit.
Illumina Ribo-Zero bacteria TruSeq Stranded Libraries were constructed according to manufacturer's guidelines. Paired-end libraries for each sample were used to generate 150 bp reads with the Illumina HiSeq.

treatment_protocol: We grew each casein and adenosine medium (CAM)-evolved PAO1 populations from days 5 and 160 in buffered LB under three treatment regimes: (i) “plus AiiA lactonase” with added AiiA in 250 ul protein buffer (100 ug/ml final AiiA concentration), (ii) “natural AHL accumulation” with 250 ul of protein purification buffer, and (iii) “plus AHLs” with added 2 uM 3OC12-HSL and 10 uM C4-HSL plus 250 ul of protein purification buffer.  2-ml samples were collected at OD 2.0 for RNA extraction and stored in Qiagen RNAprotect. Two biological replicates were prepared for each sample condition.

tag: population

value: CAM evolved Population D D5

value: buffer


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population D D5, +AiiA ("QS-Off")

description: Population D D5, +AiiA

value: +AiiA lactonase


title: Mouse2, Peritoneal mets, lineage

tag: harvest-site

value: Peritoneal mets

value: lineage


title: S. epidermidis under acidic stress - rep2


title: S. aureus (MRSA) under human serum treatment - rep3


title: Mouse2, Primary tumor, lineage

value: Primary tumor

tag: experiment


title: genomic DNA from PT2016-065-CORE

value: white

value: male

value: non-hispanic

value: normal

value: Ever


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population E D160, +AiiA ("QS-Off")

description: Population E D160, +AiiA

value: CAM evolved Population E D160


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population D D5, buffer ("QS")

description: Population D D5, buffer


title: S. aureus (MRSA) under high temperature - rep3

value: Treated with 41C


title: Mouse1, Lung, lineage

value: Lung

tag: info-type


title: Mouse1, Liver, lineage

value: Liver


title: genomic DNA from PT2016-050-CORE

value: Never

value: control


title: Mouse1, CTCs, lineage

value: Blood


title: genomic DNA from PT2016-045-CORE

value: female


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population E D160, buffer ("QS")

description: Population E D160, buffer

value: buffer


title: genomic DNA from LTRC_XX274606

source_name: IPF lung sample

value: ipf

value: biopsy


title: S. aureus (MRSA) under high temperature - rep2

value: Staphylococcus aureus MRSA252


title: genomic DNA from LTRC_XX293881

value: white

value: explant


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population D D160, +AiiA ("QS-Off")

description: Population D D160, +AiiA

value: CAM evolved Population D D160

value: +AiiA lactonase


title: S. aureus (MRSA) under high temperature - rep1


title: S. aureus (MRSA) under human serum treatment - rep1

value: Treated with human serum


title: genomic DNA from LTRC_XX266525

value: male

value: non-hispanic

value: Ever


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population D D160, buffer ("QS")

description: Population D D160, buffer


title: S. aureus (MRSA) at stationary phase - rep3

value: Grown until stationary phase


title: genomic DNA from LTRC_XX264609


title: genomic DNA from LTRC_XX233433


title: Mouse1, Primary tumor, lineage

value: Primary tumor

value: lineage


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population E D5, +AiiA ("QS-Off")

description: Population E D5, +AiiA

value: CAM evolved Population E D5


title: genomic DNA from LTRC_XX223383


title: S. aureus (MRSA) at stationary phase - rep2


title: Mouse1, Peritoneal mets, lineage

value: Peritoneal mets


title: S. epidermidis under nutritional downshift - rep2

value: Treated with removal of nutrients

value: Staphylococcus epidermidis 1457


title: S. aureus (MRSA) at stationary phase - rep1


title: S. aureus (MRSA) under oxidative stress - rep3

value: Treated with H2O2


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population E D5, +AHL ("QS")

description: Population E D5, +AHL

value: +AHL


title: genomic DNA from LTRC_XX220877

value: white

value: ipf


title: S. aureus (MRSA) under oxidative stress - rep2

value: Staphylococcus aureus MRSA252


title: genomic DNA from LTRC_XX204089

value: female

value: Never

value: biopsy


title: KO_1

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
Library strategy: iCLIP
Fastq files were uploaded to the Genialis iMaps platform (without first demultiplexing), and demultiplexed based on the constant sequence in their 5' barcode.
Reads were trimmed with cutadapt (v2.4) and mapped to the GRCm38 genome using STAR (v2.7.0f).
Reads were deduplicated using the random portion of their 5' barcodes, and crosslink sites for individual replicates were determined as described in PMID:20601959 with iCOUNT (v2.0.1.dev): https://icount.readthedocs.io/en/latest/cite.html. In the provided fastq files, the random, constant and biased portions of the 5' barcodes are tagged to the end of the header lines; these 5' barcodes have been removed from the reads themselves.
Significant crosslink binding sites (FDR<0.05) were identified with iCOUNT (https://icount.readthedocs.io/en/latest/cite.html), for each replicate independently.
Genome_build: GRCm38
Supplementary_files_format_and_content: Bedgraphs for each replicate showing significant xlink-binding sites (FDR<0.05)  identified with iCOUNT (https://icount.readthedocs.io/en/latest/index.html)

source_name: OT-I cytotoxic T lymphocytes, re-stimulated 3h

extract_protocol:
Cell extracts were prepared after UV crosslinking by lysing the cells in 50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS lysis buffer
iCLIP libraries were constructed essentially as described in PMID: 27111506 with the 3′ infrared adaptor L3-IR-phos: /5Phos/AG ATC GGA AGA GCG GTT CAG AAA AAA AAA AAA /iAzideN/AA AAA AAA AAA A/3Bio/ and RT primers/5'barcodes shown for each sample, and using the ZFP36L1 rabbit polyclonal antibody ABN192 (Merk), except that non-ligated primers were removed by 5' end digestion prior to library preparation
OTHER: iCLIP

treatment_protocol: For the in vitro generation of CTLs 1*10^6 cells per ml of total splenocytes/LN cells from OT-I mice were activated with 10^-7M (N4) SIINFEKL peptide in the presence of 20nM IL-2 and 2nM IL-12 for two days. After 2 days of stimulation, cells were maintained in 20nM IL-2 for five further days. On day 7, cells were restimulated for 3h with 10^-7M N4 peptide

value: Spleen + LN

value: OT-I+; CD4-Cre; Zfp36 fl/fl; Zfp36l1 fl/fl

tag: 5' barcode

value: NNNNCCTGCWWW

tag: molecular weight


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population D D160, +AHL ("QS")

description: Population D D160, +AHL

value: CAM evolved PAO1 Population D D160


title: Mouse1, Surgical site, lineage

value: Surgical site

value: lineage


title: KO_2

value: NNNNCATACWWW


title: WT_3

value: OT-I+; CD4+; Zfp36 fl/fl; Zfp36l1 fl/fl

value: NNNNCAAGTWWW


title: WT_2

value: NNNNCAGGGWWW


title: genomic DNA from LTRC_XX195360

tag: race

tag: ethnicity

value: non-hispanic

value: Ever

value: explant


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population D D5, +AHL ("QS")

description: Population D D5, +AHL

value: CAM evolved Population D D5

value: +AHL


title: KO_3

value: NNNNATACGWWW


title: CHLA10_EETS-high_rep3

description: Ewing sarcoma cell line CHLA-10; Control sample; replicate 3

tag: cell line

tag: cell type

value: Ewing sarcoma cell line

value: Control


title: S. aureus (MRSA) under osmotic stress - rep3

value: Treated with NaCl

value: Staphylococcus aureus MRSA252


title: WT_1

value: Spleen + LN

value: NNNNTCCACWWW


title: LOAL_102

description:
Len orientalis is used as the male parent and Lens culinaris is used as the female (egg) parent.
hari_filtered_V1.recode.vcf

organism: Lens culinaris x Lens orientalis

tag: line

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue

value: 14 days


title: LOAL_56


title: genomic DNA from LTRC_XX189243

value: white

value: male

tag: diagnosis

value: ipf

tag: smoking

value: Never

tag: tissue type


title: RNA-Seq of P. aeruginosa PAO1 CAM evolved Population E D160, +AHL ("QS")

description: Population E D160, +AHL

value: CAM evolved Population E D160


title: S. aureus (MRSA) under osmotic stress - rep1

tag: strain


title: S. aureus (MRSA) under osmotic stress - rep2


title: LOAL_33

tag: tissue

tag: age


title: genomic DNA from LTRC_XX123969

tag: Sex

value: non-hispanic

value: explant


title: WT65_LPS

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
Illumina bcl2fastq version 2.17.1.14: basecalling
Bowtie2 version 2.3.0: alignment of reads to Mus musculus GRCm38 genome (options –very-sensitive –X2000 -m1)
Picard MarkDuplicates version 2.10.5: PCR duplicates removal
Read start sites adjustment (+4bp if + strand, -5bp if -strand)
macs2 version 2.1.1: peak calling (options –f BAMPE –q 0.05 –nomodel –extsize 150)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bed files with peak coordinates from macs2 software

source_name: Wild Type, LPS treated, replicate 2

growth_protocol: BMDM were generated by culturing bone marrow cell suspensions from wild-type and NFAT5-deficient mice in 25% (vol/vol) conditioned medium from M-CSF-producing L929 cells for 7 days.

extract_protocol:
Preparation of nuclei for transposase reaction followed the protocol described in Buenrostro et al., Current Protocols in Molecular Biology, 2015, was followed (DOI: 10.1002/0471142727.mb2129s109)
The protocol described in Buenrostro et al., Current Protocols in Molecular Biology, 2015, was followed (DOI: 10.1002/0471142727.mb2129s109)

treatment_protocol: BMDM were left unstimulated (steady state BMDM) or stimulated with E. coli lipopolysaccharide (LPS, 0.3 ng/ml, 2h)

tag: genotype

value: Wild Type

tag: treatment

value: Lipopolysaccharide

value: macrophages derived from bone marrow


title: WT15_LPS

source_name: Wild Type, LPS treated, replicate 1


title: S. aureus (MRSA) under oxidative stress - rep1

value: Treated with H2O2


title: small RNA Treat_3

city: xiamen

first: wenjie

last: liu

address: xiangan strict xiamen university

institute: xiamen university

data_processing:
BBMAP used for triming reads. It can binning reads based on mapping to multiple references at once
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
DEseq2 used to analyze the difference expression of small RNA
Supplementary_files_format_and_content: tab-delimited text files include the number of reads relative RPKM values, and P-values for control and experimental group Sample.

organism: Rattus norvegicus

source_name: Sertoli cells

extract_protocol:
Total RNA was extracted from the Sertoli cells using Trizol (Invitrogen, Carllsbad, CA, USA) according to the manual instructions . The mix was centrifuge at 12000xg for 5min at 4Â°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000xg for 10min at 4Â°C, the aqueous phase was transferred to a new 1.5 ml tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000 xg for 20min at 4Â°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25ÂµL-100ÂµL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop (NanoDrop, Madison, USA)and Agilent 2100 bioanalyzer (Agilent, Santa Clara, USA).
Library was prepared with 1 µg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18-30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18-30 nt small RNAs were ligated to adenylated 3' adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5' adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by Superscript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the DNBSEQ platform (BGI- Shenzhen, China).

value: 4-nonylphenol treated group


title: LOAL_142


title: LOAL_143


title: KO62_LPS

source_name: Nfat5 KO, LPS treated, replicate 2

value: Nfat5 KO


title: genomic DNA from LTRC_XX118079

value: female


title: small RNA Treat_1


title: LOAL_141

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis


title: KO22_LPS

source_name: Nfat5 KO, LPS treated, replicate 1


title: genomic DNA from LTRC_XX112291


title: small RNA Treat_2


title: WT65

source_name: Wild Type, replicate 2

value: not treated


title: small RNA control_3

value: control group


title: genomic DNA from PT2016-176-CORE

value: white

value: normal

value: control


title: genomic DNA from LTRC_XX105331

value: male

value: ipf

value: Ever


title: LOAL_140

source_name: leaf

value: Leaf tissue

value: 14 days


title: genomic DNA from LTRC_XX174555

value: non-hispanic

value: explant


title: WT15

source_name: Wild Type, replicate 1

value: Wild Type

value: macrophages derived from bone marrow


title: LOAL_139


title: KO62

source_name: Nfat5 KO, replicate 2

value: Nfat5 KO


title: small RNA control_2


title: genomic DNA from LTRC_XX123624


title: FLT3/ITD N51+Cxcl12

description: gene expression after 4 hour incubation with 100ng/ml Cxcl12

source_name: Ba/F3 cells expressing N51 FLT3/ITD and incubated with 100ng/ml of Cxcl12

value: Ba/F3 cells

tag: sample type

value: FLT3/ITD N51+Cxcl12


title: genomic DNA from LTRC_XX096521

value: female

value: biopsy


title: small RNA control_1

value: control group


title: genomic DNA from LTRC_XX066548

value: white


title: LOAL_138

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis


title: KO22

source_name: Nfat5 KO, replicate 1

value: not treated


title: AA rep3

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample ...

source_name: plasmacytoid dendritic cell

growth_protocol: Cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of mRNA-seq were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Mouse plasmacytoid dendritic cells were stimulated with R848 for 12 hours.

tag: allele

value: AA allele

value: spleen

tag: agent

value: R848 stimulated


title: LOAL_136

value: Leaf tissue

value: 14 days


title: LOAL_137


title: genomic DNA from LTRC_XX048508

tag: race

value: male

value: non-hispanic

value: ipf

value: Ever

value: explant


title: genomic DNA from LTRC_XX064909

tag: ethnicity


title: AA rep2


title: AA rep1


title: LOAL_134


title: YAP1_ChIP

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human/mouse genome (hg38) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS2 algorithm (v2.1.0) with a cutoff of pvalue = 1e-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg38
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

source_name: N/TERT2G keratinocytes

growth_protocol: Cells were cultured at 37°C in the presence of 5% CO2 and cultured in EPILIFE medium (Life Technologies) with Human Keratinocyte Growth Supplement (HKGS, Life Technologies).

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A or G agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: Cells were transduced one day after plating with a multiplicity of infection (MOI) of 25 with adeno-GFP

value: Skin

value: N/TERT2G keratinocytes

tag: chip antibody

value: YAP1 (US Biological Y1200-01D)


title: LOAL_135


title: input_2

city: LYON

first: Jean-Marc

last: Vanacker

address: 32-34 avenue Tony Garnier

country: France

institute: IGFL, ENS de Lyon, CNRS UMR 5242

data_processing:
Quality control and adapter trimming were performed with TrimGalore! Version 0.6.5. Input parameters were: phred quality score threshold = 30 and minimum read length = 77 (95% of the expected read length).
Trimmed reads were aligned on the hg38 human genome with Bowtie2 version 2.3.5.
Duplicated reads were removed with MarkDuplicates from Picard.
The 2 inputs were merged using merge from Samtools.
Peak calling was done with Macs2 version 2.2.6 using the following options: --gsize 2.91e9 --qvalue 0.05
Reproducible peaks across the 2 replicates were identified with IDR version 2.0.4.2 using global IDR-value < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage from Deeptools, using option --binSize 10.
Peak text files were narrowPeak files from MACS2 or IDR.
MACS2 output files were BED 6+4 files (columns 7 to 10 = signalValue, pValue, qValue and peak point-source).
IDR peak file contains 20 columns: 1.chrom, 2.chromStart, 3.chromEnd, 4.name, 5.score, 6.strand, 7.signalValue, 8.p-value, 9.q-value, 10.summit, 11.localIDR (-log10), 12.globalIDR (-log10), 13.rep1_chromStart, 14.rep1_chromEnd, 15.rep1_signalValue, 16.rep1_summit, 17.rep2_chromStart, 18.rep2_chromEnd, 19.rep2_signalValue, 20.rep2_summit

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% FCS, 10U/ml penicillin and 10µg/ml streptomycin.

extract_protocol:
10x10e6 cells were cross-linked with 1% formaldehyde and quenched for 5 min in 1 M Glycine. After centrifugation, cell pellets were resuspended in lysis buffer (1% SDS, 50 mM Tris-HCl pH8, 10 mM EDTA). Sonication was performed with Ultrasonicator (Covaris). Lysates from 2.5 x106 cells were processed with the iDEAL ChIP kit (Diagenode) according to the manufacturer’s recommendations using 5 μg of antibody (ERRα: GTX108166, Genetex).
Quality of samples was assessed on the Agilent TapeStation 4150 using D5000 ScreenTape and Agilent TapeStation Software 3.2. Libraries were prepared according to Illumina's instructions. The ChIP DNA libraries were sequenced as paired-ended 81bp reads with an Illumina Next Seq 500 sequencer following the manufacturer's protocols. Sequencing gave 29.106 and 10.106 reads for ERRα and input samples respectively.

tag: cell line

value: MDA-MB-231 breast cancer cells

value: breast cancer


title: AG rep3

value: AG allele


title: genomic DNA from LTRC_XX038185

value: white


title: input_1


title: TEAD1_ChIP

tag: cell type


title: LOAL_133

tag: line

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis


title: input DNA


title: genomic DNA from LTRC_XX021054

tag: diagnosis

tag: smoking

value: Never


title: LOAL_132


title: genomic DNA from LTRC_XX005390

tag: tissue type


title: ERRa_ChIPseq_2

tag: tissue

value: ERRα:GTX108166, Genetex


title: AG rep2

tag: strain

value: spleen

value: R848 stimulated


title: LOAL_131

value: Leaf tissue

tag: age

value: 14 days


title: ERRa_ChIPseq_1


title: LOAL_130


title: AG rep1


title: GG rep3

value: GG allele


title: GG rep2


title: LOAL_129


title: genomic DNA from LTRC_XX022285

tag: Sex

value: male

value: non-hispanic

value: ipf

value: Ever


title: GG rep1


title: TIGK PgSg Infected Sample 4

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

data_processing:
Fastq files were downloaded from sequencing center for analysis.
The GRCh38.p12 Homo sapiens genome was used for read alignment with STAR to generate bam format alignment files.
Samtools was used to merge the bam files for each sample and the pre- and post-alignment quaility was assesed for each sample using Picard tools.
Raw gene counts were generated and annotated with genome features using featureCounts.
DESeq2 was used to perform differential gene expression analysis using the recommened guidelines.
Performed a regularized log transformation on raw count data as outlined in Love et al. 2014 (DOI: 10.1186/s13059-014-0550-8) for principal component analysis.
Genome_build: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

growth_protocol: TIGK cells were grown at 37℃ with 5% carbon dioxide. Porphyromonas gingivalis ATCC 33277 and Streptococcus gordonii DL1 were cultured anaerobically at 37℃.

extract_protocol:
RNA was extracted using RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher).
Library construction was performed using the TruSeq Stranded Total RNA with RiboZero Plus Kit (Illumina) from 1 µg of total RNA.

treatment_protocol: TIGK cells were grown to ~80% confluence and challenged with bacteria at an MOI of 100 for 1 hr, followed by 23 hr in fresh medium.

value: TIGK


title: Meimi Tween40 Rep-3

description:
MCA3882_T-R6
processed data file: Meimi_RawReadCount.txt
processed data file: Meimi_NormReadCount.csv

organism: Meira miltonrushii

source_name: fungal biomass

tag: phenotype

value: Filamentous growth

value: Fungal biomass


title: TIGK PgSg Infected Sample 2


title: TIGK PgSg Infected Sample 3


title: pCEC

city: Wenzhou

first: ShaoHui

last: Pan

state: Zhejiang

address: Xueyuan road #270

institute: Wenzhou Medical University

description: primary corneal endothelial cells

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Corneal endothelia

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Trizol

value: Corneal endothelia

value: post natal day 30


title: Senescent cell, GCDC

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: Total RNA was extracted and analyzed

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: biliary epithelial cell

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Biliary epithelial cells are cultured in DMEM/F-12 with 10%Nu-serum, EGF, insulin, forskolin and antibiotics

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

treatment_protocol: Cellular senescence was induced in BECs cultured in vitro incubation in serum depleted media or treatment with media containing 200 μM GCDC for 4-7 days

value: biliary epithelial cell

tag: treatment

value: GCDC treatment


title: TIGK PgSg Infected Sample 5