title: Blood mononuclear cells - cow 6 - low - heat stressed

city: Guelph

first: Alexandra

last: Livernois

state: ON

address: 50 Stone Rd East

department: Pathobiology

country: Canada

institute: University of Guelph

data_processing:
Preliminary quality control of raw reads was carried out with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Illumina raw sequences were then filtered with Trimmomatic software v.0.38 to remove adapters and low-quality bases at the sequences end using a sliding window approach.
Bismark software (version 0.203.0) was used to align each bisulfite-treated reads to the bovine reference genome (BosTau9) with the parameters “--directional’’ for targeted bisulfite sequencing libraries and “--pbat” for post-bisulfite prepared RRBS libraries.
Sequence reads that produced a unique best alignments were then compared to the normal genomic sequence, and the methylation state of all cytosine positions in the reads was inferred using the Bismark_methylation_extractor function (cov file). The same reads that aligned to the same regions of the genome were regarded as duplicated reads.
Genome_build: BosTau9
Supplementary_files_format_and_content: For each sample, a tab-delimited cov file was generated with methylation call for every single position including the following fileds: chromosome, start position, end position, methylation percentage, count methylated, count unmethylated

organism: Bos taurus

source_name: Blood mononuclear cells

growth_protocol: Blood mononuclear cells were grown in RPMI media containing fetal bovine serum and penicillin-streptomycin. Cells were plated in triplicate in 24-well flat bottom culture plates and incubated overnight at 37°C with 5% CO2.

extract_protocol:
Cells were homogenized in 1 mL of Trizol reagent and DNA was extracted following the manufacturer's instructions.
For each sample, 40-50ng of DNA was digested for 2 hours with MSP1 at 20U/sample at 37C, followed by 2 hours with TaqI/sample at 65C. Digested DNA was size selected with <300 bp DNA fragments and then bisulfite-treated with the Methylamp DNA Biulfite Conversion Kit (Epigentek Cat. # P-1001). Conversion efficiency of bisulfite treated DNA was determined by real time PCR using two primer pairs with using control DNA. A method of reduced representation bisulfite sequencing (RRBS), Enhanced MethylSeq (Epigentek, NY), was used to assess DNA methylation in control and HS samples. Libraries were prepared from 2-10ng of genomic DNA using the PBAT parameter (Post-Bisulfite Adapter Tagging. Libraries were prepared by DNA end polishing and adaptor ligation followed by library amplification using indexed primers and library purification. Libraries were sequenced on an Illumina HiSeq 4000 with single reads SR50 (Epigentec, NY (https://www.epigentek.com).

treatment_protocol: Half of the replicates were moved to an incubator set to 42°C with 5% CO2 for 4 hours.

value: Holstein

value: Blood mononuclear cells

tag: immune response genotype

value: low

tag: treatment

value: cultured at 42°C for four hours

tag: cow age (years)


title: Taf1_IAA_F

status: Public on Jun 09 2021

type: SRA

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

country: USA

institute: Oklahoma Medical Research Foundation

library_source: genomic

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: 30 degrees in rich medium to mid-log phase.

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.
OTHER: ChEC-seq

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins.

tag: genotype

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HygMX, BDF1-3xV5 IAA7::KanMX, TAF1-MNase::TRP1

tag: strain


title: 231control#4

type: RNA

city: Boston

first: Antoine

middle: Elias

last: Karnoub

state: MA

address: 3 Blackfan Circle

department: Pathology

institute: Beth Israel Deaconess Medical Center and Harvard Medical School

hyb_protocol: cRNA targets were cleaned up, fragmented, and hybridized to Affymetrix HT-HG U133 2.0 Plus Arrays (900751; Affymetrix). The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip Array Station automation platform.

scan_protocol: Scanning was performed using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The abundance values are the MAS 5.0 expression measurements, as implemented by Bioconductor's 'affy' package (version 1.68.0) and the chip design file (hgu133plus2cdf, version 2.18.0). The array platform used is GPL570.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-231 cultured alone and sorted-replicate#4

label_protocol: One micro- gram total RNA was used to prepare cDNA using the Genechip HT One-Cycle cDNA Synthesis Kit (900687; Affymetrix) and the GeneChip HT IVT Labeling Kit (900688; Affymetrix).

growth_protocol: For co-cultures, human MSCs were mixed with GFP-labeled cancer cells (at 3:1 ratio of MSC:cancer cell) and cultured in DMEM-10% FBS for 72 hrs. GFP-labeled cancer cells were subsequently recovered using FACS. Corresponding cancer cells cultured alone in DMEM-10% FBS and sorted in parallel served as controls.

extract_protocol: RNA was extracted by RNEasy Qiagen kit.

treatment_protocol:
MDA-MB-231 cells were infected with pRRL3-GFP lentiviral particles to render them GFP in >98% penetrance
Co-cultures consisted of GFP-MDA-MB-231 cells admixed to human bone marrow derived MSCs.

tag: cell type

value: MDA-MB-231 cells

value: cultured alone and sorted


title: 231plus#4

source_name: MDA-MB-231 recovered from co-cultures with human MSCs -replicate #4

value: recovered from co-cultures with MSCs


title: mature tomato fruit, line AS5, pool 3

city: Hurlingham

first: Pia

middle: Guadalupe

last: Dominguez

state: Buenos Aires

address: N. REPETTO Y LOS RESEROS S/N

department: IABIMO

country: Argentina

institute: INTA (National Institute of Agriculture Technology)

description: Gene expression data from mature fruits of line AS5

hyb_protocol: The hybridization step was done following the Expression Analysis Technical Manual, with Specific protocols for Use with the Hybridization, Wash, and Stain Kit (Affymetrix®). 15 Ug of cRNA were hibridised during 16 hs in a GeneChip Tomato Genome Array® .

scan_protocol: The scan was done using the Affymetrix® GeneChip® Scanner 3000 according to the manufacturer´s specifications (Affymetrix®).

data_processing: The data was sujected to RMA normalization and Rank Product statistical analysis using the default settings of Robin software (Lohse et al., 2010).

organism: Solanum lycopersicum

source_name: Tomato mature fruit

label_protocol: Biotin-labeled cRNA was prepared from 100 ng of total mRNA employing the MessageAmp Premier Amplification Kit (Ambion) following the manufacturer´s specifications.

growth_protocol: Plants were grown in controlled greenhouse conditions (80% relative humidity; 200 mmol PAR s-1m-2; 16 hours of light and 8 hours of darkness).

extract_protocol: RNA was extracted with phenol (TRIzol Reagent®; Gibco). RNA quantification and contamination assessment were done by spectrophotometry (NanoDrop 2000c UV-Vis Spectrophotometer). RNA integrity was analyzed with the Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: Asr1-silenced lines (AS5 and AS17) and control plants (WT).

tag: cultivar

value: cv Money Maker

tag: lines

value: line AS5, pool 3


title: Blood mononuclear cells - cow 5 - low - heat stressed

tag: breed

value: untreated


title: 231control#2

source_name: MDA-MB-231 cultured alone and sorted-replicate#2


title: TC106_input_DNA

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 TC-106 ChIP-Seq with ChIP antibody none

data_processing:
Raw sequencing data were aligned to human reference genome hg19 with bowtie2
Duplicates were eliminated with samtools
Peaks were called with MACS2, broad peak option for histone marks and narrow peak for transcription factors, and giving the respective input, mode FE
MACS2 output was converted intro bigwig with the UCSC bedGraphToBigWig tool
bigwig files were normalized cross cell-lines with the CHIPIN R tool
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format; files were generated via MACS2, UCSC bedGraphToBigWig and CHIPIN; indexed binary format indicating quantitatively ChIP signal in hg19 genome build

source_name: Ewing sarcoma cell line

growth_protocol: Cell lines were cultured in RPMI 1640 medium with stable glutamine with 10% FCS and 100 units/ml penicillin and 100µg/ml streptomycin in a fully humidified environment at 37°C and 5% CO2. Cells were subcultured every 2-4 days.

extract_protocol:
Cells were fixed with 1% formalin for 10 min, glycine at final 200 mM was added for 5 min, cell surface was washed with ice-cold PBS three thimes, cells were lysed with the lysis buffers of the Diagenode iDeal ChIP-seq kit for transcription factors, DNA was sheared with Bioruptor Plus sonication device, cell debris was separated by centrifugation, genomic sheared DNA was added to ChIP antibodies coupled to magnetic beads. The next day, beads were washed with four washing buffers of the Diagenode iDeal ChIP-seq kit, DNA was eluted with the respective buffer and cleaned up with beads.
Libraries were constructed with the Illumina TruSeq ChIP library preparation kit following the manufacturer’s protocol

tag: cell line

tag: chip antibody


title: Blood mononuclear cells - cow 4 - low - heat stressed


title: TC106_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line TC-106 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)

value: H3K27ac (Abcam, ab4729, 1 µg)


title: 231control#1

source_name: MDA-MB-231 cultured alone and sorted-replicate#1


title: mature tomato fruit, line AS17, pool 3

description: Gene expression data from mature fruits of line AS17

value: line AS17, pool 3


title: IL-1b+Wnt5A 4 h3

city: Zürich

first: TOM

last: SKARIA

address: Rämistr. 100

department: INTERNAL MEDICINE

country: Switzerland

institute: UNIVERSITY HOSPITAL ZURICH

description: Human coronary artery endothelial cells (HCAEC) treated with IL-1b+Wnt5A for 4h

hyb_protocol: After purification of amplified cRNA according to the QIAgen RNeasy purification protocol (QIAGEN) 825 ng of Cy3 and Cy5 labeled cRNA were competitively hybridized for 17 hours at 65° C in a hybridization oven (Agilent G2545A) set to 10 rpm in GEx Hybridization buffer HI-RPM according to the manufacturer's protocol (Agilent’s Two-Color Microarray-Based Gene Expression Analysis). Washing was performed according to the recommended protocol including the Stabilization and Drying Solution step.

scan_protocol: Array slides were XDR scanned at 5 mcm resolution on a Agilent Microarray High-Resolution C Scanner (G2505C) with 100% PMT and 10% for lower intensity.

data_processing:
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.7.3.1. Spot values were normalized using the default linear-lowess normalization.
We don't provide a Matrix Table as we imported the calculated and lowess-normalized log10 ratios of the Feature Extraction result text files directly into Genesrping GX 9.0 Software (Agilent Tech. Inc.) and Metacore GeneGO (Thomson Reuters, http://portal.genego.com) software without further normalization.

source_name: Human Coronary Artery Endothelial Cells

label_protocol: Fluorescently labeled cRNA was generated from 500 ng total RNA with the Quick Amp Labeling Kit (Agilent) according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7, March 2008 (Agilent publication number G4140-90050). In short, total RNA was reverse transcripted to cDNA using T7 Promotor Primer and MMLV-RT. Then cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: Human Coronary Artery Endothelial Cells (HCAEC) obtained from Lonza were cultured in EBM-2 medium (Clonetics, Lonza) supplemented with EGM-2MV Single Quots (Clonetics, Lonza) and 5% FBS.

extract_protocol: After washing and lysing the cells with Buffer RLT, total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) according to the manufacturer’s instructions, including an on-column DNA digestion step (RNase-Free DNase Set; QIAGEN). To ensure that only high quality RNA (RIN >9.0) was used for gene expression analysis, each RNA sample was checked on a RNA Nanochip with a Bioanalyzer 2100 (Agilent Technologies, Basel, Switzerland). RNA was quantified spectrophotometrically with a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: HCAEC were treated with a combination of recombinant (rec.) human (h) IL-1b (20 U/mL, PeproTech, USA) and rec.h Wnt5A (250 ng/mL) for 4 h. Treatments were performed by replacing culture medium containing 5% FBS by one with 2% FBS added with suitable stimuli.

value: no treatment

tag: incubation time

value: 4 h

source_name: HCAEC


title: Taf1_IAA_D


title: TC106_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line TC-106 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: IL-1b+Wnt5A 4 h1

source_name: Human Coronary Artery Endothelial Cells (HCAEC)


title: 231plus#3

source_name: MDA-MB-231 recovered from co-cultures with human MSCs -replicate #3


title: IL-1b+Wnt5A 4 h2


title: 231control#3

source_name: MDA-MB-231 cultured alone and sorted-replicate#3


title: Taf1_IAA_C


title: Blood mononuclear cells - cow 5 - low - control


title: TC106_ERG_ChIPSeq

description: Ewing sarcoma cell line TC-106 ChIP-Seq with ChIP antibody ERG (Abcam, ab92513, 2 µg)

value: ERG (Abcam, ab92513, 2 µg)


title: TC71_input_DNA

description: Ewing sarcoma cell line TC-71 ChIP-Seq with ChIP antibody none


title: Taf1_IAA_B


title: 231plus#2

source_name: MDA-MB-231 recovered from co-cultures with human MSCs -replicate #2


title: 231plus#1

source_name: MDA-MB-231 recovered from co-cultures with human MSCs -replicate #1


title: TC71_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line TC-71 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: Wnt5A_4 h_HCAEC2

data_processing:
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.7.3.1. Spot values were normalized using the default linear-lowess normalization.
Lowess-normalized log10 ratios of the Feature Extraction result text files were imported directly into Genesrping GX 9.0 Software (Agilent Tech. Inc.) and Metacore GeneGO (Thomson Reuters, http://portal.genego.com) software without further normalization.

label: Cy3 (green signal)

source_name: Human Coronary Artery Endothelial Cells (HCAEC), Untreated

treatment_protocol: HCAEC were treated with recombinant (rec.) human (h) Wnt5A (250 ng/mL; R&D systems) for 4 h. Treatments were performed by replacing culture medium containing 5% FBS by one with 2% FBS added with suitable stimuli.

tag: tissue

label: Cy5 (red signal)

source_name: Human coronary artery endothelial cells (HCAEC) treated with Wnt5A for 4 h

value: Wnt5A 250 ng/mL


title: TC71_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line TC-71 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: Blood mononuclear cells - cow 4 - low - control

source_name: Blood mononuclear cells

value: Holstein


title: Taf1_IAA_A

source_name: whole organism


title: TC71_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line TC-71 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: Wnt5A_4 h_HCAEC3

value: Human Coronary Artery Endothelial Cells


title: Taf1_DMSO_F


title: Blood mononuclear cells - cow 3- high - heat stressed

value: Blood mononuclear cells

value: high


title: TC71_FLI1_ChIPSeq

description: Ewing sarcoma cell line TC-71 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)

value: FLI1 (Abcam, ab15289, 2 µg)


title: Taf1_DMSO_E

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HygMX, BDF1-3xV5 IAA7::KanMX, TAF1-MNase::TRP1


title: TC32_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line TC-32 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: TC32_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line TC-32 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: TC32_input_DNA

description: Ewing sarcoma cell line TC-32 ChIP-Seq with ChIP antibody none


title: Blood mononuclear cells - cow 2- high - heat stressed


title: TC32_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line TC-32 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: Blood mononuclear cells - cow 3- high - control


title: Taf1_IAA_E


title: TC32_FLI1_ChIPSeq

description: Ewing sarcoma cell line TC-32 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: TC106_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line TC-106 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: Taf1_DMSO_D


title: SKNMC_input_DNA

description: Ewing sarcoma cell line SK-N-MC ChIP-Seq with ChIP antibody none

value: SK-N-MC


title: SKNMC_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line SK-N-MC ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: SKNMC_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line SK-N-MC ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: Taf1_DMSO_B


title: SKNMC_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line SK-N-MC ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: Taf1_DMSO_C


title: SKNMC_FLI1_ChIPSeq

description: Ewing sarcoma cell line SK-N-MC ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: Blood mononuclear cells - cow 1- high - control


title: Blood mononuclear cells - cow 1- high - heat stressed

value: cultured at 42°C for four hours


title: SKES1_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line SK-ES-1 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: Taf1_DMSO_A


title: siDCAF8+siLSH/Erastin rep2

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

country: China

institute: Peking University Health Science Center

library_source: transcriptomic

data_processing:
Raw reads were subjected to quality control
Sequence reads were pre-processed to remove adaptors and filter low-quality reads
Transcript assembly and quantification with StringTie. Analysis of RNA-seq experiments requires accurate reconstructions of all the isoforms expressed from each gene, as well as estimates of the relative abundance of those isoforms. Use parameters as stringtie –e –B -p 8 -G -o.
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Ballgown from Pertea M et al., Nature Protocols, 2016. In short, differential expression analysis proceeds using a linear model. The FPKM values attached to transcripts are typically highly skewed; thus, to stabilize the variance, Ballgown’s builtin functions apply a log transformation and then fit standard linear models that can be used to test for differential expression.
Genome_build: GRCH38
Supplementary_files_format_and_content: excel files include FPKM values for each Sample …

growth_protocol: HT-1080 cells were obtained from ATCC and maintained at 37℃ and 5% CO2 in DMEM supplemented with 10% (v/v) FBS, 100 U/mL penicillin, and 100 mg/mL streptomycin. All cell lines were tested for mycoplasma contamination and authenticated utilizing short tandem repeat profiling.

extract_protocol:
HT-1080 cells were harvested and RNA were extracted with Trizol reagent. RNA was amplified using the Smart-seq v4 (Takara) and library prep was performed using the NEBNext Ultra DNA Library prep kit (Illumina)
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols

treatment_protocol: HT-1080 cells were incubated with erastin (10μM, 24h) before harvesting for RNA extraction.

value: fibrosarcoma cells

tag: genotype/variation

value: erastin (10μM, 24h)


title: Taf11_IAA_F

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HygMX, BDF1-3xV5 IAA7::KanMX, TAF11-MNase::TRP1


title: SKES1_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line SK-ES-1 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: SKES1_FLI1_ChIPSeq

description: Ewing sarcoma cell line SK-ES-1 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: SKES1_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line SK-ES-1 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: RH1_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line Rh1 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)

value: H3K27ac (Abcam, ab4729, 1 µg)


title: RH1_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line Rh1 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: RH1_FLI1_ChIPSeq

description: Ewing sarcoma cell line Rh1 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: Taf11_IAA_E


title: Taf11_IAA_A


title: siDCAF8+siLSH rep2


title: oeWDR76 rep2


title: RH1_input_DNA

description: Ewing sarcoma cell line Rh1 ChIP-Seq with ChIP antibody none


title: Blood mononuclear cells - cow 2- high - control


title: Taf11_IAA_D


title: SKES1_input_DNA

description: Ewing sarcoma cell line SK-ES-1 ChIP-Seq with ChIP antibody none


title: RDES_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line RD-ES ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)

value: RD-ES


title: RDES_FLI1_ChIPSeq

description: Ewing sarcoma cell line RD-ES ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: RH1_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line Rh1 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: oeWDR76/Erastin rep2


title: POE_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line POE ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)

value: POE


title: siDCAF8+siLSH/Erastin rep1


title: oeWDR76 rep1


title: Taf11_DMSO_E


title: Taf11_IAA_B


title: siDCAF8/Erastin rep2


title: RDES_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line RD-ES ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: siDCAF8+siLSH rep1


title: Taf11_DMSO_D


title: oeWDR76/Erastin rep1


title: Taf11_IAA_C


title: RDES_input_DNA

description: Ewing sarcoma cell line RD-ES ChIP-Seq with ChIP antibody none


title: siDCAF8/Erastin rep1


title: RDES_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line RD-ES ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: POE_input_DNA

description: Ewing sarcoma cell line POE ChIP-Seq with ChIP antibody none


title: POE_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line POE ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: Taf11_DMSO_C


title: POE_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line POE ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: MIC_input_DNA

description: Ewing sarcoma cell line MIC ChIP-Seq with ChIP antibody none

value: MIC


title: siDCAF8 rep2


title: Taf11_DMSO_F


title: siDCAF8 rep1


title: MIC_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line MIC ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: siNS/Erastin rep2

value: siNS


title: MIC_FLI1_ChIPSeq

description: Ewing sarcoma cell line MIC ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: Spt7_Taf13deg_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, TAF13-3xV5 IAA7::KanMX, SPT7-MNase::TRP1


title: MIC_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line MIC ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: siNS/Erastin rep1


title: Taf11_DMSO_A


title: MHHES1_FLI1_ChIPSeq

description: Ewing sarcoma cell line MHH-ES-1 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: MHHES1_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line MHH-ES-1 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: MHHES1_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line MHH-ES-1 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: Spt7_Taf13deg_IAA_A


title: MHHES1_input_DNA

description: Ewing sarcoma cell line MHH-ES-1 ChIP-Seq with ChIP antibody none


title: MHHES1_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line MHH-ES-1 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: siNS rep2


title: Taf11_DMSO_B


title: Spt7_Taf13deg_DMSO_B


title: EW7_input_DNA

description: Ewing sarcoma cell line EW-7 ChIP-Seq with ChIP antibody none


title: siNS rep1


title: POE_FLI1_ChIPSeq

description: Ewing sarcoma cell line POE ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: EW7_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line EW-7 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: Spt7_Taf13deg_DMSO_A


title: EW7_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line EW-7 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: MIC_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line MIC ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: EW3_ERG_ChIPSeq

description: Ewing sarcoma cell line EW-3 ChIP-Seq with ChIP antibody ERG (Abcam, ab92513, 2 µg)

value: ERG (Abcam, ab92513, 2 µg)


title: Spt3_Med14deg_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, MED14-3xV5 IAA7::KanMX, SPT3-MNase::TRP1


title: EW3_input_DNA

description: Ewing sarcoma cell line EW-3 ChIP-Seq with ChIP antibody none


title: Spt3_Med14deg_IAA_A


title: Spt3_IAA_F

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HygMX, BDF1-3xV5 IAA7::KanMX, SPT3-MNase::TRP1


title: EW3_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line EW-3 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: Spt3_Med14deg_DMSO_A


title: EW7_FLI1_ChIPSeq

description: Ewing sarcoma cell line EW-7 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: EW3_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line EW-3 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: EW22_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line EW-22 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: EW22_input_DNA

description: Ewing sarcoma cell line EW-22 ChIP-Seq with ChIP antibody none


title: EW22_FLI1_ChIPSeq

description: Ewing sarcoma cell line EW-22 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: Spt3_Med14deg_DMSO_B


title: EW3_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line EW-3 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: EW1_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line EW-1 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: EW22_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line EW-22 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: Spt3_IAA_E


title: EW22_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line EW-22 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: Spt3_IAA_D


title: EW7_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line EW-7 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: Spt3_IAA_C


title: Spt3_IAA_A


title: CHLA25_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line CHLA-25 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: CHLA25_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line CHLA-25 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: CHLA25_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line CHLA-25 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: Spt3_DMSO_F


title: EW1_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line EW-1 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: Spt3_DMSO_D


title: Spt3_DMSO_E


title: EW1_input_DNA

description: Ewing sarcoma cell line EW-1 ChIP-Seq with ChIP antibody none


title: Spt3_DMSO_C


title: A673_input_DNA

description: Ewing sarcoma cell line A-673 ChIP-Seq with ChIP antibody none


title: CHLA10_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line CHLA-10 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: A673_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line A-673 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)


title: CHLA10_input_DNA

description: Ewing sarcoma cell line CHLA-10 ChIP-Seq with ChIP antibody none


title: CHLA10_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line CHLA-10 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: Spt3_DMSO_B


title: CHLA25_input_DNA

description: Ewing sarcoma cell line CHLA-25 ChIP-Seq with ChIP antibody none


title: EW1_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line EW-1 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: A673_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line A-673 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: A673_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line A-673 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: A673_FLI1_ChIPSeq

description: Ewing sarcoma cell line A-673 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: CHLA25_ERG_ChIPSeq

description: Ewing sarcoma cell line CHLA-25 ChIP-Seq with ChIP antibody ERG (Abcam, ab92513, 2 µg)


title: Blood mononuclear cells - cow 6 - low - control

value: Holstein

value: Blood mononuclear cells

value: low

value: untreated


title: CHLA10_FLI1_ChIPSeq

description: Ewing sarcoma cell line CHLA-10 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)

value: FLI1 (Abcam, ab15289, 2 µg)


title: CHLA10_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line CHLA-10 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: Spt3_IAA_B


title: Vector3

city: Shanghai

first: Jingzhi

last: Tang

state: Shanghai

address: The 15th floor of Building 17,No.160 Pujian Road .

institute: Ren ji Hospital,School of Medicine, Shanghai Jiao Tong University,Shanghai

data_processing:
Quality control and base calling was completed using Illumina CASAVA.
Reads were aligned to the GRCh38 reference genome using STAR and genes quantified using FeatureCounts
Raw fastq reads were adapter trimmed and quality assessed using the Trimgalore wrapper for FastQC and Cutadapt. Reads with phred scores >30 were retained.
Genome_build: GRCh38.83
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: sw480 colorectal carcinoma cell line(control 3)

growth_protocol: Cell culture medium was DMEM  (gibco#C11995500BT) supplemented with 10% FBS(gibco#10099-141) and 1% Penicillin/Streptomycin (gibco#15140) and cell cultures were maintained with 5% CO2 at 37 °C (Thermo Fisher)

extract_protocol:
Total RNA was isolated from cell lines using TRIreagent (Sigma). RNA quality and quantity were measured using a Spectrophotometer (NanoDrop2000, ThermoFisher Scientific) and samples were stored at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: control and hnRNPA2B1-KO cell lines

value: colorectal carcinoma cell line

value: control


title: Vector2

source_name: sw480 colorectal carcinoma cell line(control 2)


title: KO3

source_name: sw480 colorectal carcinoma cell line(hnRNPA2B1-KO3)


title: Spt3_DMSO_A


title: EW1_FLI1_ChIPSeq

description: Ewing sarcoma cell line EW-1 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)


title: 29-PT_S7

city: Houston

first: Michael

middle: A.

last: Curran

state: TX

address: 1515 HOLCOMBE BLVD, UNIT 901

department: Immunology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Sequencing reads were trimmed using the trimGalore software.
The trimmed reads were mapped using HISAT against the human genome build UCSC hg38, and quantified using StringTie against the Gencode gene model.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited file with FPKM values

source_name: Prostate Cancer Biopsy

extract_protocol: Qiagen All-Prep Kit

tag: biopsy sample id

value: Prostate Cancer Biopsy

value: pre-treatment


title: 21-PT_S18

source_name: Pancreatic Cancer Biopsy

value: Pancreatic Cancer Biopsy


title: Med8_Taf13deg_IAA_C

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, TAF13-3xV5 IAA7::KanMX, MED8-MNase::TRP1


title: 12-PT_S11


title: Med8_Taf13deg_DMSO_A


title: Med8_Taf13deg_IAA_B


title: Vector1

source_name: sw480 colorectal carcinoma cell line(control 1)


title: 19-C3D8_S24


title: KO1

source_name: sw480 colorectal carcinoma cell line(hnRNPA2B1-KO1)


title: Med8_Taf13deg_IAA_A


title: 24-PT_S21

source_name: Head and Neck Cancer Biopsy

value: Head and Neck Cancer Biopsy


title: Med8_Taf13deg_DMSO_C


title: KO2

source_name: sw480 colorectal carcinoma cell line(hnRNPA2B1-KO2)


title: Med8_Taf13deg_DMSO_B


title: 15-C3D8_S22


title: 28-C3D8_S16


title: 19-PT_S15


title: Med8_IAA_D

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HygMX, BDF1-3xV5 IAA7::KanMX, MED8-MNase::TRP1


title: 4-C3D8_S12


title: 15-PT_S14


title: Med8_IAA_C


title: Med8_IAA_F


title: 17-PT_S6


title: 20-PT_S25


title: 23-PT_S3


title: Med8_IAA_E


title: 24-C3D8_S23


title: 23-C3D8_S8


title: Med8_IAA_B


title: 28-PT_S9


title: Med8_IAA_A


title: 5-C3D8_S17

source_name: Melanoma Biopsy

value: Melanoma Biopsy


title: 10-PT_S19


title: 2-PT_S1


title: 4-PT_S2


title: OTX-015-treated HepG2 (OTX-3)

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

description:
HepG2 cells were treated with OTX-015.
HepG2 (ATCC HB-8065)

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33).
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the STAR (version 2.7.1) software based on reference genome sequence (Homo sapiens UCSC hg38) and the differential gene expressed values of each sample were calculated by the DESeq2 Bioconductor package.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Homo sapiens UCSC hg38 (GRCh38)
Supplementary_files_format_and_content: *.ReadsPerGene.out.tab: Tab-delimited text files including normalized read counts for each sample.

source_name: HepG2 cells

growth_protocol: HepG2 cells were grown in Minimum Essential Medium Eagle (MEM) supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 10 μg/ml streptomycin (Thermo Fisher Scientific, MA, USA).

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with DMSO, JQ1, or OTX-015.

value: Hepatocellular carcinoma cell


title: 9-PT_S13


title: 5-PT_S4


title: 25-PT_S20


title: Med8_DMSO_A


title: Med8_DMSO_C


title: Med8_DMSO_D


title: 29-C3D8_S10


title: Med8_DMSO_E


title: 25-C3D8_S5


title: Med8_DMSO_B


title: Med8_DMSO_F


title: OTX-015-treated HepG2 (OTX-2)


title: JQ1-treated HepG2 (JQ1-2)

description:
HepG2 cells were treated with JQ1.
HepG2 (ATCC HB-8065)


title: JQ1-treated HepG2 (JQ1-3)


title: JQ1-treated HepG2 (JQ1-1)


title: Control HepG2 (Con-3)

description:
HepG2 cells were treated with DMSO (control).
HepG2 (ATCC HB-8065)

value: DMSO


title: Control HepG2 (Con-2)


title: Med17_IAA_F

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0


title: Med17_IAA_D

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HygMX, BDF1-3xV5 IAA7::KanMX, MED17-MNase::TRP1


title: HepG2 trim33 shRNA-942, clone 5-17, +Dox, replicate 3

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: rRNA depleted RNA

data_processing:
Step 1: Reads were mapped to the hg19 version of the human reference genome using hisat2 (PMID: 25751142) in paired-end mode with default parameters.
Step 2: Gene-level expression quantification was performed for all RefSeq genes downloaded 7/5/2017 using htseq-count (PMID: 25260700) with parameters -i gene_id --stranded=reverse -f bam -m intersection-strict.
Step 3: Transcript-per-million (TPM) values were calculated by multiplying gene-level htseq-count read counts by 75 (read length), dividing by the total bases in all exons of all isoforms of genes with the same name, multiplying by 1000000, and dividing by the scaling factor, which was calculated by summing the following across all genes: 75 x read counts / number of bases in all exons of all isoforms of genes with the same name.
Genome_build: hg19
Supplementary_files_format_and_content: Transcript-per-million (TPM) files contain gene names and TPM values.

growth_protocol: Independent clonal cell lines of human HepG2 cells purchased from ATCC (cell line HB-8065) and stably transduced with one of two non-targeting control shRNAs (SMARTvector, Dharmacon VSC11653 and VSC11497) or one of two TIF1γ shRNAs (SMARTvector, Dharmacon, source clones V3IHSHEG_5569942 and V3IHSHEG_8321548) were propagated in MEMα containing GlutaMAX (Thermo Fisher Scientific, 32561102), 10% tetracycline-free fetal bovine serum (Clontech, 631367), 1% penicillin-streptomycin (Thermo Fisher Scientific, 15140122), and 4 µg/ml puromycin at 5% CO2, 95% air atmosphere according to seller’s protocol (ATCC).

extract_protocol:
2 x 106 cells each of induced and uninduced control and TIF1γ shRNA HepG2 cells were harvested after trypsinization with TrypLE™ Express Enzyme (ThermoFisher Scientific, 12604013), washed in PBS, and total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134). RNA samples were spiked with ERCC ExFold RNA Spike-In Mixes (Thermo Fisher Scientific, 4456739) and a second genomic DNA removal step was performed with the TURBO DNA-free Kit (Thermo Fisher Scientific, AM1907) followed by an Agencourt RNAClean XP beads clean-up (Beckman Coulter, A63987).
Ribosomal RNAs were removed with the Ribo-Zero Magnetic Gold Kit (Illumina, MRZG12324) according to the manufacturer’s protocol. Strand-specific libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420S) and NEBNext Multiplex Oligos for Illumina kit (NEB, E7335L) according to the manufacturer’s protocols. For quality control, the 24 final libraries were run on a HS D1000 chip in an Agilent 2200 TapeStation. The average library size was 311 bp. Libraries were sequenced on the Illumina HiSeq 2500.
Directional RNA-seq

treatment_protocol: Three biological replicates each of two different control and two different TIF1γ shRNA HepG2 cell clones were induced with 1 µg/ml doxycycline (Sigma, D9891) or the equivalent amount of the solvent PBS (Thermo Fisher Scientific, 14190144) for 48 hours.

value: trim33 shRNA-942, clone 5-17, +Dox


title: OTX-015-treated HepG2 (OTX-1)


title: Control HepG2 (Con-1)


title: HepG2 trim33 shRNA-942, clone 5-17, +Dox, replicate 2

description: rRNA depleted RNA


title: HepG2 trim33 shRNA-942, clone 5-17, +Dox, replicate 1

description: rRNA depleted RNA


title: HepG2 TRIM33 shRNA-942, clone 5-17, -Dox, replicate 3

description: rRNA depleted RNA

value: TRIM33 shRNA-942, clone 5-17, -Dox


title: Med17_IAA_C


title: HepG2 TRIM33 shRNA-942, clone 5-17, -Dox, replicate 1

description: rRNA depleted RNA


title: Med17_IAA_A


title: HepG2 control shRNA-1, clone 1-16, +Dox, replicate 3

description: rRNA depleted RNA

value: control shRNA-1, clone 1-16, +Dox


title: Med17_IAA_B


title: HepG2 TRIM33 shRNA-942, clone 5-17, -Dox, replicate 2

description: rRNA depleted RNA


title: HepG2 control shRNA-1, clone 1-16, +Dox, replicate 2

description: rRNA depleted RNA


title: HepG2 control shRNA-1, clone 1-16, +Dox, replicate 1

description: rRNA depleted RNA


title: HepG2 control shRNA-1, clone 1-16, -Dox, replicate 3

description: rRNA depleted RNA

value: control shRNA-1, clone 1-16, -Dox


title: Med17_DMSO_F


title: HepG2 TRIM33 shRNA-548, clone 4-7, +Dox, replicate 3

description: rRNA depleted RNA

value: TRIM33 shRNA-548, clone 4-7, +Dox


title: HepG2 control shRNA-1, clone 1-16, -Dox, replicate 2

description: rRNA depleted RNA


title: HepG2 control shRNA-1, clone 1-16, -Dox, replicate 1

description: rRNA depleted RNA


title: HepG2 TRIM33 shRNA-548, clone 4-7, -Dox, replicate 3

description: rRNA depleted RNA

value: TRIM33 shRNA-548, clone 4-7, -Dox


title: HepG2 TRIM33 shRNA-548, clone 4-7, +Dox, replicate 1

description: rRNA depleted RNA


title: HepG2 TRIM33 shRNA-548, clone 4-7, +Dox, replicate 2

description: rRNA depleted RNA


title: Med17_DMSO_D


title: Med17_DMSO_C


title: Med17_DMSO_B


title: HepG2 TRIM33 shRNA-548, clone 4-7, -Dox, replicate 2

description: rRNA depleted RNA


title: HepG2 TRIM33 shRNA-548, clone 4-7, -Dox, replicate 1

description: rRNA depleted RNA


title: Med17_IAA_E


title: HepG2 control shRNA-2, clone 2-8, +Dox, replicate 3

description: rRNA depleted RNA

value: control shRNA-2, clone 2-8, +Dox


title: Med17_DMSO_A


title: TRIM33 ChIP - 50 million cells

data_processing:
Step 1: Reads were aligned to the hg19 version of the human reference genome using bowtie (PMID: 19261174) version 1.2 with parameters -k 2 -m 2 --best and -l set to the read length.
Step 2: Wiggle files for display were created using MACS (PMID: 18798982) version 1.4.2 with parameters -w -S --space=50 --nomodel --shiftsize=200 and were normalized to reads-per-million by dividing the values in each bin by the millions of mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files contain reads-per-million normalized counts of reads in 50bp bins.

source_name: HepG2 hepatocellular carcinoma cell line

growth_protocol: Human HepG2 cells purchased from ATCC (cell line HB-8065) were propagated in MEMα containing GlutaMAX (Thermo Fisher Scientific, 32561102), 10% premium fetal bovine serum (Atlanta Biologicals, S11150), and 1% penicillin-streptomycin (Thermo Fisher Scientific, 15140122) at 5% CO2, 95% air atmosphere according to seller’s protocol (ATCC).

extract_protocol:
After lysing the cells, DNA was sonicated in a Bioruptor Plus waterbath sonicator (Diagenode) for 24 cycles of 30 sec on, 59 sec off each, medium setting at 4°C yielding largely 200-bp fragments. 10 µg of H3K27Ac (Abcam, ab4729, lot GR312651-2), RNA Pol II (Santa Cruz, sc-899 X, lot F0616), RNA Pol II-Ser2P (Abcam, ab5095, lot GR3195689-1), or TRIM33 (Bethyl Laboratories, A301-060A, lot 1) was used per immunoprecipitation reaction. After crosslink reversal, RNase and proteinase K treatment, the DNA was purified by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation.
Fragmented DNA overhangs were turned into phosphorylated blunt ends using the End-It DNA End-Repair Kit (Epicentre, ER81050), followed by a clean-up using Agencourt AMPure XP beads (Beckman Coulter, A63881) at a 1.8x bead-to-sample ratio. Next, 3’ ends were dA-tailed using Klenow Fragment (3'→5' exo-, NEB, M0212) to allow for directional adaptor ligation, and then the samples bead-purified as above (1.8x). NEBNext Adaptor oligos (1:10 dilution) were added to the DNA using the Quick Ligation Kit (NEB, M2200), linearized with USER Enzyme (NEB, E7335) and the DNA was purified as above (1.8x). Adaptor-ligated DNA fragments were then size-selected using Agencourt AMPure XP beads at a 0.9x bead-to-sample ratio, followed again by a bead clean-up at a 0.2x bead-to-sample ratio. PCR enrichment was for 18 cycles using the Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, NEB, E7335). Indexed libraries were bead-purified as above, at a 1.0x bead-to-sample ratio. Library concentration was assessed using an Invitrogen Qubit Fluorometer. For quality control and determination of library size (on average 299 bp), libraries were run on a HS D1000 chip in an Agilent 2200 TapeStation. Equimolar library mixtures were sequenced on an Illumina HiSeq2500.

treatment_protocol: 15 million (H3K27Ac) or 50 million (Pol II, Pol II-Ser2P, TRIM33) logarithmically growing HepG2 cells were crosslinked with 11% formaldehyde and cell pellets were snap-frozen at -80°C.


title: RNA Pol II ChIP - 50 million cells


title: Bdf2_IAA_F

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF1-3xV5 IAA7, BDF2-MNase::TRP1


title: HepG2 control shRNA-2, clone 2-8, +Dox, replicate 2

description: rRNA depleted RNA


title: Med17_DMSO_E


title: freeMNase_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pBDF2-Mnase::TRP1


title: freeMNase_A


title: HepG2 control shRNA-2, clone 2-8, -Dox, replicate 2

description: rRNA depleted RNA

value: control shRNA-2, clone 2-8, -Dox


title: HepG2 control shRNA-2, clone 2-8, +Dox, replicate 1

description: rRNA depleted RNA


title: RNA Pol II-Ser2P ChIP - 50 million cells


title: HepG2 control shRNA-2, clone 2-8, -Dox, replicate 1

description: rRNA depleted RNA


title: Input ChIP - 15 million cells


title: Bdf2_IAA_E


title: Bdf2_IAA_C


title: Input ChIP - 50 million cells


title: IL1b_C

city: Erlangen

first: Beate

last: Winner

address: Glückstr. 6

institute: FAU Erlangen-Nürnberg

data_processing:
Illumina RTA 1.18.66.3 software was used for base calling. Reads were trimmed for adapter sequence.
Reads were aligned to hg19 using STAR under previously published conditions (Kapeli et al. 2016)
Aligned sam-files were annotated with gencode.v19 and features counted using SubReads featureCounts.
DESeq2 was used to determine differential expression. Only genes with a mean expression greater than one RPKM throughout all samples were considered.
Genome_build: hg19
Supplementary_files_format_and_content: text-file that includes RPKM values for all 15 samples.

source_name: primary fetal

growth_protocol: according to the suppliers instruction (Cat# 1810, ScienCell Research Laboratories)

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Netherlands)
Libraries were generated using the TrueSeq Stranded mRNA kit (Illumina) according to the protocol

treatment_protocol: Parallel generation of all five groups within 72 h in culture. For senescence induction, H2O2 application within the first 2 h and rotenone application within the first 16 h. For induction of reactivity in astrocytes, TNFa+IL1a or IL1b treatment within the last 24 h. For comparability within the first 16 h the rotenone-solvent DMSO and within the last 24 h the carrier protein BSA was added to the control group and respective other groups.

value: cerebellar astrocytes

tag: passage

value: 3 ng/ml IL1b, 24h


title: H3K27Ac ChIP - 15 million cells


title: IL1b_A


title: Bdf2_IAA_D


title: IL1b_B


title: TNFa_C

value: 10 ng/ml TNFa  + 3 ng/ml IL1a, 24 h


title: Bdf2_DMSO_F


title: HepG2 control shRNA-2, clone 2-8, -Dox, replicate 3

description: rRNA depleted RNA


title: TNFa_B


title: Bdf2_IAA_B


title: H2O2_A


title: ROT_A

value: 900 nM rotenone, 16 h


title: H2O2_B


title: TNFa_A


title: Bdf2_IAA_A


title: Bdf2_DMSO_D


title: Bdf2_DMSO_E


title: ROT_B


title: Bdf1_IAA_F

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7, BDF1-MNase::TRP1


title: DMSO_B

value: control


title: DMSO_C


title: Bdf2_DMSO_C


title: Bdf2_DMSO_A


title: DMSO_A


title: H2O2_C


title: Bdf1_IAA_E


title: Mf-31

city: Bronx

first: Phillip

last: Galbo

state: New York

address: 1300 Morris Park

institute: Albert Einstein College Of medicine

data_processing:
Alignment was done using STAR
featureCounts was used to quanitfy the number of RNA-seq fragements mapped to each gene
differntial expression analysis prformed using DESeq2 (version 1.26)
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

organism: Mus musculus

source_name: cells

growth_protocol: CD138-purified GFP+ Vk*myc myeloma cells were intra-tibially injected into WT B6 mice.

extract_protocol:
We FACS-purified TAMs from tumor bearing mice that both were in contact (TAM-IC) or not in contact (TAM-NIC) with myeloma, on the basis of GFP expression as well as BM macrophages from naïve mice as controls (Naive) for comparison. In addition, Vk*MYC myeloma and polyclonal (CD138high B220low) BM PCs from naïve mice were also FACS-sorted and analyzed to investigate myeloma-macrophage interactions.
Libraries were generated with SMART-Seq® v4 Ultra™ Low Input RNA Kit for Sequencing and Prep Kit (TakaraBio 634899)

treatment_protocol: no treatment performed

value: WT

value: GFP+ TAMs in contact with myeloma cells (mouse 1)


title: Mf-1

value: GFP- TAMs cells not in contact with myeloma cells (mouse 2)


title: Mf-naive-1

value: BM Macrophages from naive mice


title: Mf-3

value: GFP- TAMs cells not in contact with myeloma cells (mouse 1)


title: PC-1

value: Plasma Cells


title: Mf-naïve-2


title: Mf-51

value: GFP+ TAMs in contact with myeloma cells (mouse 2)


title: ROT_C


title: Bdf1_IAA_C


title: PC-2


title: Bdf1_IAA_A


title: Riociguat 12h-2

city: Amsterdam

first: Wu

last: Yang

address: B7, Plesmanlaan 121 1066CX Amsterdam

country: Netherlands

institute: Netherlands Cancer Institute

description:
HSC.rio-12h-2
After Culture 12h after isolated from mouse liver, change medium, 12h later, treat with Riociguat for 12h.

data_processing:
Reads cleaning: raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files by both read quality and length (Q30 > 20, length > 36).
Alignment: clean reads were processed to pseudo-align to mouse transcriptome GRCm38 using salmon.
Quantification: transcriptional level expression was aggregated to gene level expression using tximport. Ensembl release 95 was used to annotate genes.
Quality check: sample clustering was performed with principle component analysis analysis and sample to sample distance correlation analysis.
DEGs analysis: differential expressed genes were defined by DESeq2 with foldchange > 1.5 and adjusted p-value < 0.05. DEGs based hypergeometric test and gene set enrichment analysis were produced by clusterProfiler.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv, gene expression raw counts

source_name: WT mouse HSCs

extract_protocol:
Sangon RNA extraction kit (Order NO. B511321)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rioxiguat or DMSO treat 6h-24h

value: Riociguat

tag: time point


title: Riociguat 12h-1

description:
HSC.rio-12h-1
After Culture 12h after isolated from mouse liver, change medium, 12h later, treat with Riociguat for 12h.


title: Bdf2_DMSO_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF1-3xV5 IAA7, BDF2-MNase::TRP1


title: Riociguat 24h-1

description:
HSC.rio-24h-1
After Culture 12h after isolated from mouse liver, change medium,treat with Riociguat for 24h.


title: Riociguat 24h-3

description:
HSC.rio-24h-3
After Culture 12h after isolated from mouse liver, change medium,treat with Riociguat for 24h.


title: Riociguat 24h-2

description:
HSC.rio-24h-2
After Culture 12h after isolated from mouse liver, change medium,treat with Riociguat for 24h.


title: posterior Piriform cortex viral injection [sn-seq P]

city: London

first: Andreas

last: Schaefer

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

molecule: polyA RNA

extract_protocol:
The minced tissue was gently homogenized in Nuclei PURE Lysis Buffer and 10% Triton X-100 using an ice-cold dounce and pestle, and filtered two times through a 40 μm cell strainer on ice. After centrifuging at 500 rpm for 5 min at 4 °C, the supernatant was aspirated and gently resuspended in 500 μl of cold buffer (1x of cold Hanks' Balanced Salt Solution HBSS, 1% nuclease-free BSA, RNasin Plus and 1/2000 DRAQ5). Fluorescence-activated nuclei sorting of single nuclei was performed using a BD FACSAriaTM III Cell Sorter  with a 70 μm nozzle at a sheath pressure of 70 psi.
Libraries were prepared using the 10x Library Construction Kit PN-1000190. The quality and quantity of the final libraries were assessed with TapeStation D5000 Assay (Agilent Technologies) before sequencing with an Illumina NextSeq 500 using the 10X kit version Chromium Single Cell 3 dual index" v 3.1.

treatment_protocol: A retrogradely transported Adeno Associated Virus (retroAAV-CAG-H2B-GFP) was injected stereotaxically into multiple sites of posterior piriform cortex (PCx) for the P experiment, on into anterior olfactory nucleus (AON) for the A experiment.

tag: Stage

value: adult


title: Riociguat 12h-3

description:
HSC.rio-12h-3
After Culture 12h after isolated from mouse liver, change medium, 12h later, treat with Riociguat for 12h.

tag: treatment


title: AON viral injection [sn-seq A]

source_name: AON viral injection

value: AON viral injection


title: Bdf1_IAA_B

source_name: whole organism


title: Bdf1_Esa1deg_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, esa1delta-::KanMX, BDF1-MNase::TRP1/pRD8 (LEU2 ESA1-3xV5 IAA7)


title: Bdf1_Esa1deg_DMSO_B


title: DMSO-1

description:
HSC.dmso-12h-1
After Culture 12h after isolated from mouse liver, change medium, 12h later, treat with DMSO for 12h.

value: DMSO


title: Riociguat 6h-2

description:
HSC.rio-6h-2
After Culture 12h after isolated from mouse liver, change medium, 18h later, treat with Riociguat for 6h.


title: Riociguat 6h-3

description:
HSC.rio-6h-3
After Culture 12h after isolated from mouse liver, change medium, 18h later, treat with Riociguat for 6h.


title: Bdf1_Esa1deg_DMSO_A


title: Bdf1_DMSO_F


title: DMSO-2

description:
HSC.dmso-12h-2
After Culture 12h after isolated from mouse liver, change medium, 12h later, treat with DMSO for 12h.


title: Bdf1_IAA_D


title: Bdf1_Esa1deg_IAA_A


title: Riociguat 6h-1

description:
HSC.rio-6h-1
After Culture 12h after isolated from mouse liver, change medium, 18h later, treat with Riociguat for 6h.


title: EA.hy926 Hy rep2

city: chengdu

first: Guodan

last: Zeng

state: sichuan

address: Keyuan Road 4, Gaopeng Street

department: West China Hospital

institute: 四川大学

data_processing:
Raw data (raw reads) of fastq format were firstly processed by Casava. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human umbilical vein cell line

growth_protocol: The EA.hy926 cell line was cultured in high-glucose Dulbecco’s modified Eagle’s medium (H-DMEM) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a 5% CO2 incubator. Cells were maintained in a tri-gas incubator with 1% O2 for 8 h to induce hypoxia after achieving 80%-90% confluence.

extract_protocol:
Cells were expoused to 1% O2 for 8 h, and RNA was harvested using Trizol reagent. Sequencing libraries were generated using the NEBNext UltraTM RNA Library Prep Kit for Illumina according to the manufacturer’s recommendations, and index codes were assigned to the sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: endothelial

value: hypoxia (1% O2) 8 h


title: EA.hy926 Hy rep3

treatment_protocol: Cells were maintained in a tri-gas incubator with 1% O2 for 8 h to induce hypoxia after achieving 80%-90% confluence.


title: EA.hy926 Hy rep1


title: EA.hy926 Nor rep3

value: normoxia (20% O2)


title: Bdf1_DMSO_E

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7, BDF1-MNase::TRP1


title: EA.hy926 Nor rep2


title: Bdf1_DMSO_C


title: OA117_MOI01_24hpi-Rep4 [SP066_011]

city: Berlin

first: Fabian

last: Pott

state: Berlin

address: Charitéplatz 1

department: Institute for Virology

institute: Charité - Universitaetsmedizin Berlin

description:
SP066_011_S1
processed data file: integrated_24hpi.RDS

data_processing:
https://github.com/GoffinetLab/CHIKV_scRNAseq-fibroblast
creation of CHIKV reference genome Uploaded with the data files
alignment using cellranger (Cellranger v5.0 (10X Genomics))
Creation of Seurat object, preprocessing Seurat v4.0
Genome_build: human: hg38 release 102, CHIKV: DQ443544.2
Supplementary_files_format_and_content: RDS file of integrated data from all sample of each timepoint, genome build of human and CHIKV genes

growth_protocol: Primary human fibroblasts were obtained from synovial biopsies from donors suffering from osteoarthritis or a non-arthritic background, purified, and cultured in standard cell culture flask in Dulbecco’s modified Eagle’s medium - high glucose (DMEM, Sigma-Aldrich) supplemented with 20 % heat-inactivated fetal bovine serum (FBS, Sigma-Aldrich), 2mM L-Glutamine (Gibco), and 100 units/ml penicillin-streptomycin (Gibco).

extract_protocol: Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

treatment_protocol: CHIKV particles produced by electroporation of in-vitro transcribed full-length genomic RNA into BHK-21 cells were used to infect Fibroblasts at an MOI of 0.01, 0.1, 1, or 10 or mock-infected and harvested at 6 and 24 hpi for single-cell RNA-sequencing.

value: human primary synovial fibroblasts, knee

tag: tag

value: infected

value: 24 hours post infected


title: OA117_MOI10_24hpi-Rep4 [SP066_012]

description:
SP066_012_S1
processed data file: integrated_24hpi.RDS


title: OA117_MOI01_6hpi-Rep4 [SP066_008]

description:
SP066_008_S1
processed data file: integrated_6hpi.RDS

value: 6hours post infected


title: EA.hy926 Nor rep1


title: OA117_Mock_24hpi-Rep4 [SP066_010]

description:
SP066_010_S1
processed data file: integrated_24hpi.RDS

value: mock


title: Bdf1_DMSO_D

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.
OTHER: ChEC-seq

tag: genotype


title: OA117_MOI10_6hpi-Rep4 [SP066_009]

description:
SP066_009_S1
processed data file: integrated_6hpi.RDS


title: DMSO-3

description:
HSC.dmso-12h-3
After Culture 12h after isolated from mouse liver, change medium, 12h later, treat with DMSO for 12h.


title: Bdf1_DMSO_B

tag: strain


title: OA117_Mock_6hpi-Rep4 [SP066_007]

description:
SP066_007_S1
processed data file: integrated_6hpi.RDS

tag: cell type


title: Bdf1_DMSO_A


title: RRBS_embryo_48h_control_KD_clutch8

data_processing:
Step 1: Raw reads were subjected to adapter and quality trimming using cutadapt (version 2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter), followed by Nugene diversity adapter trimming (https://github.com/nugentechnologies/NuMetRRBS).
Step 2: The trimmed reads were aligned to the zebrafish reference genome assembly GRCz11 using BSMAP (version 2.90; parameters: -v 0.1 -s 12 -q 20 -w 100 -S 1 -u -R -D C-CGG).
Step 3: Aligned reads were deduplicated based on unique molecular identifiers using NuDup (https://github.com/nugentechnologies/nudup; parameters: --start 6 --length 6). Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters). Only CpGs covered by at least 10 reads were used for further analysis.
Genome_build: Ensembl GRCz11
Supplementary_files_format_and_content: Methylation rates per CpG covered by at least 10 reads

organism: Danio rerio

source_name: AB + control KD, 48 hpf, clutch 8

growth_protocol: Zebrafish embryos were grown in embryo medium (E3) at 28.5°C water temperature as per standard protocols

extract_protocol:
15 (22 hpf) or 20 (11 hpf and 48 hpf) snap-frozen embryos were lysed in lysis buffer for 1 h at 55°C (10 mM Tris-HCl (pH=8.0), 10 mM NaCl, 10 mM EDTA, 0.5% SDS, 300 µg/ml proteinase K). Genomic DNA was isolated by phenol-chloroform extraction and quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). RRBS was performed on 100 ng of each sample using the NuGen Ovation® RRBS Methyl-Seq System (Tecan, 0353) following the manufacturer’s recommendations with the following modifications. After the final repair step, the bisulfite conversion of DNA was conducted using the EpiTect Fast Bisulfite Conversion Kit (Qiagen, 59824) following the manufacturer’s recommendations, eluting the bisulfite-converted DNA in 23 µl EB.
Libraries were amplified with 12 cycles of PCR. Amplified libraries were purified twice using RNAClean XP SPRI paramagnetic beads (Beckman Coulter, A63987) at 1x reaction volume. The purified libraries were quality-assessed with a D1000 ScreenTape (Agilent, 5067-5582) on the Agilent 4150 TapeStation System and sequenced for 100-bp single-end reads on the NovaSeq6000 (Illumina).

treatment_protocol: No treatment

value: Whole zebrafish embryos

tag: age

value: 48 hpf


title: RRBS_embryo_48h_control_KD_clutch9

source_name: AB + control KD, 48 hpf, clutch 9


title: RRBS_embryo_48h_tif1g_KD_clutch8

source_name: AB + tif1γ KD, 48 hpf, clutch 8


title: RRBS_embryo_22h_control_KD_clutch8

source_name: AB + control KD, 22 hpf, clutch 8

value: 22 hpf


title: RRBS_somites_tif1g_KD_clutch9

source_name: AB + tif1γ KD, 11 hpf, clutch 9

value: 11 hpf


title: RRBS_embryo_48h_tif1g_KD_clutch9

source_name: AB + tif1γ KD, 48 hpf, clutch 9


title: RRBS_somites_tif1g_KD_clutch8

source_name: AB + tif1γ KD, 11 hpf, clutch 8


title: RRBS_somites_control_KD_clutch8

source_name: AB + control KD, 11 hpf, clutch 8


title: RRBS_somites_control_KD_clutch9

source_name: AB + control KD, 11 hpf, clutch 9


title: RRBS_embryo_22h_control_KD_clutch9

source_name: AB + control KD, 22 hpf, clutch 9


title: RRBS_embryo_22h_tif1g_KD_clutch9

source_name: AB + tif1γ KD, 22 hpf, clutch 9


title: RRBS_embryo_22h_tif1g_KD_clutch8

source_name: AB + tif1γ KD, 22 hpf, clutch 8


title: HPCs Tnfrsf1β-/- rep2

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

data_processing:
The sequencing reads were automatically uploaded and evaluated for quality using Illumina BaseSpace Onsite Computing platform.
Fastq sequence files were generated and analysis was performed using applications available on BaseSpace Onsite Computing platform
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Clustering and correlation analysis were carried out using Metaboanalyst 3.0 software analysis package (http://www.metaboanalyst.ca).
Genome_build: Rnor6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.Matrix table with raw gene counts for every gene and every sample.

organism: Rattus norvegicus

source_name: HPCs

extract_protocol:
The total RNA of HPC  was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-2501) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: day 13.5 of gestation

value: untreated


title: HPCs Tnfrsf1α-/- rep1


title: control_1

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 lncRNA, circRNA, mRNA
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.

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 4°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 4°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 4°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 25µL~100µL 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).
Take 200ng total RNA samples (only for human or mouse) and use RNase H to remove the rRNA.   DNase I digested double-stranded and single-stranded DNA presenting in RNA samples. mRNA   molecules were fragmented into small pieces using fragmentation reagent. First-strand cDNA was   generated by First Strand Master Mix and Super Script II reverse transcription, then add Second   Strand Master Mix to synthesize the second-strand cDNA. Purify the DNA with Ampure XP Beads,   then carry out end repair. The end-repaired products were purified by magnetic beads and re-dissolved in EB Solution. The purified fragmented cDNA was combined with A-Tailing Mix, and   incubated. Then combine the Adenylate 3'Ends DNA, RNA Index Adapter and Ligation Mix,   incubate. Purify the product DNA with Ampure XP Beads. Several rounds of PCR amplification   with PCR Primer Cocktail and PCR Master Mix were performed to enrich the cDNA fragments.   Then the PCR products were purified with Ampure XP Beads. The libraries were assessed quality   and quantity 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 qualified libraries were amplified on cBot to generate the cluster on the flowcell. And the   amplified flowcell will be sequenced single end on the HiSeq X-ten paltform (BGI-Shenzhen,  China).

value: control group


title: Treat_2

value: 4-nonylphenol treated group


title: control_2


title: Treat_1


title: HPCs Tnfrsf1β-/-+TNFα rep2

value: treated with TNFα for 1 hour


title: HPCs Tnfrsf1α-/- rep2


title: HPCs Tnfrsf1α-/-+TNFα rep2


title: HPCs Tnfrsf1β-/-  rep1


title: HPCs WT+TNFα rep2

value: Wild Type


title: HPCs Tnfrsf1β-/-+TNFα rep1


title: HPCs Tnfrsf1α-/-+TNFα rep1


title: HPCs WT+TNFα rep1


title: 17d-3

city: Chicago

first: Xu

last: Han

state: Illinois

address: 303 E Chicago Avenue, Ward 3-240

institute: Northwestern University

data_processing:
The reads mapped to rRNAs were removed and rawdata was gotten.
The low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get clean reads.
Clean reads were assembled into Unigenes, followed with Unigene functional annotation and calculate the Unigene expression levels and SNPs of each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel files include FPKM values for each Sample ...

source_name: Erythroblast

growth_protocol: Total bone marrow cells were harvested after wild-type mice were sacrificed, and lineage negative cells were purified and cultured in EPO induction system.

extract_protocol:
After treatment, cells were harvested and total RNA were extracted using Trizol reagent. Total RNA sample QC was done with Agilent RNA 6000 Nano Kit.
mRNA enrichment was firstly performed based on Oligo dT in the total RNA. Then fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. Finally sequencing was performed on DNBseq platform.

treatment_protocol: Purified lineage negative cells were treated with NUP-17d or DMSO (NC) for 48 hours in the EPO induction culture system.

value: treated with NUP-17d for 48 hours


title: HPCs WT rep2


title: HPCs WT rep1


title: NC-3

value: treated with DMSO for 48 hours


title: 17d-1


title: Placenta-sample-106

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.

source_name: Placenta

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

value: Placenta

tag: fetus number

value: BtBi

value: fetus

tag: Sex

value: female


title: 17d-2


title: NC-2


title: NC-1


title: Placenta-sample-80

value: BiBt

value: male


title: Placenta-sample-97


title: Placenta-sample-78

value: BiBi


title: Placenta-sample-74


title: Placenta-sample-77


title: Placenta-sample-65


title: Placenta-sample-52

value: BtBt


title: Placenta-sample-46


title: Placenta-sample-62


title: Placenta-sample-100


title: Placenta-sample-103


title: Placenta-sample-104


title: Placenta-sample-105


title: Placenta-sample-99


title: Placenta-sample-60


title: Placenta-sample-61


title: Placenta-sample-7


title: Placenta-sample-53


title: RDES_EETS-high_rep3

type: genomic

first: Thomas

last: Grunewald

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

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

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

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

value: RD-ES

value: Ewing sarcoma cell line

value: Control


title: Placenta-sample-13


title: Placenta-sample-56


title: Placenta-sample-22


title: Placenta-sample-8


title: EW7_EETS-low_rep3

description: Ewing sarcoma cell line EW-7; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3

value: Doxycycline induced EWSR1-ETS knockdown


title: TC71_EETS-high_rep3

description: Ewing sarcoma cell line TC-71; Control sample; replicate 3


title: Muscle-sample-106

source_name: Muscle

value: Muscle


title: Muscle-sample-97


title: RDES_EETS-low_rep2

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


title: RDES_EETS-low_rep3

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


title: Muscle-sample-91


title: SKES1_EETS-low_rep2

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


title: EW7_EETS-low_rep1

description: Ewing sarcoma cell line EW-7; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


title: Muscle-sample-80


title: EW7_EETS-low_rep2

description: Ewing sarcoma cell line EW-7; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: Muscle-sample-78


title: RDES_EETS-high_rep1

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


title: SKES1_EETS-high_rep3

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


title: Muscle-sample-74


title: Muscle-sample-77


title: EW7_EETS-high_rep1

description: Ewing sarcoma cell line EW-7; Control sample; replicate 1


title: EW7_EETS-high_rep2

description: Ewing sarcoma cell line EW-7; Control sample; replicate 2


title: RH1_EETS-low_rep2

description: Ewing sarcoma cell line Rh1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


title: Muscle-sample-65


title: Muscle-sample-62


title: SKES1_EETS-low_rep3

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


title: TC71_EETS-low_rep3

description: Ewing sarcoma cell line TC-71; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


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

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

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

organism: 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).

value: Treated with spermin NONOate complex

value: Staphylococcus aureus MRSA252


title: RDES_EETS-high_rep2

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


title: SKES1_EETS-high_rep2

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


title: RDES_EETS-low_rep1

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


title: T48Is-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

institute: Gansu Agricultural University

description:
Rainbow trout
miRNAs_tpm_expression.txt

data_processing:
Raw reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides (N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5’adapters; 4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; 5) Removing reads containing polyA in small RNA fragment; 6) Removing reads shorter than 18nt (not include adapters).
Low-quality raw reads and clean tags were identified as tRNA, rRNA, snoRNA, snRNA and scRNA using GenBank and Rfam database were removed and enriched clean tags were compared with the reference genome USDA_OmykA_1.1 and the reads mapped to exons, introns and repeat sequences were removed.
The expression profiles of miRNAs were calculated and normalized to transcripts per million (TPM), and the formula was TPM = Actual miRNA counts/Total counts of clean tags ×10 ^ 6, obtained the expression profiles of all miRNA of all samples.
Genome_build: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary_files_format_and_content: miRNAs_tpm_expression.txt: Tab-delimited text file includes counts and TPM values for each Sample.

organism: Oncorhynchus mykiss

source_name: Intestine

extract_protocol:
Total RNA was extracted by Trizol reagent kit (Invitrogen, Carlsbad, CA,USA), the RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel electrophoresis (PAGE).
cDNA 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: S. aureus (MRSA) under nitrosative stress - rep2


title: Muscle-sample-7


title: TC71_EETS-low_rep2

city: Heidelberg

description: Ewing sarcoma cell line TC-71; Doxycycline induced EWSR1-ETS knockdown sample; replicate 2


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


title: TC71_EETS-high_rep2

description: Ewing sarcoma cell line TC-71; Control sample; replicate 2


title: T48Is-2

description:
Rainbow trout
miRNAs_tpm_expression.txt


title: RH1_EETS-low_rep3

description: Ewing sarcoma cell line Rh1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 3


title: EW7_EETS-high_rep3

description: Ewing sarcoma cell line EW-7; Control sample; replicate 3


title: SKES1_EETS-low_rep1

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


title: T48Is-1

description:
Rainbow trout
miRNAs_tpm_expression.txt


title: Muscle-sample-52


title: Muscle-sample-104

value: BtBi


title: RH1_EETS-low_rep1

description: Ewing sarcoma cell line Rh1; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1


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

value: Treated with removal of nutrients


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


title: Muscle-sample-100

value: fetus

value: female


title: Muscle-sample-103

value: male


title: RH1_EETS-high_rep3

description: Ewing sarcoma cell line Rh1; Control sample; replicate 3


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

value: Treated with oxygen deprivation


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


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


title: Muscle-sample-105

value: BtBt


title: wild type untagged t4 WCE

city: Vienna

first: Franz

last: Klein

address: Dr. Bohr-Gasse 9

department: Chromosome Biology

country: Austria

institute: Max Perutz Labs, University of Vienna

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

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: AGCGATAG

tag: index 2

value: CCTATCCT


title: Muscle-sample-99

tag: tissue

value: BiBi


title: C48Is-1

description:
Rainbow trout
miRNAs_tpm_expression.txt

value: Intraperitoneal injection of M199


title: Muscle-sample-61

value: Muscle


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

value: Staphylococcus aureus MRSA252


title: SKES1_EETS-high_rep1

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

value: Ewing sarcoma cell line

value: Control


title: Muscle-sample-60


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

value: Treated with 2,2-dipyridryl


title: wild type Top2-myc9 t4 WCE

value: GAATTCGT


title: C48Is-3

description:
Rainbow trout
miRNAs_tpm_expression.txt

value: Intestine

value: 48 hours after infection


title: wild type untagged t4 ChIP

description: Figure 3a

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

value: ATTCAGAA


title: C48Is-2

description:
Rainbow trout
miRNAs_tpm_expression.txt


title: RH1_EETS-high_rep2

description: Ewing sarcoma cell line Rh1; Control sample; replicate 2


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


title: wild type Top2-myc9 t2 WCE

value: ATAGAGGC


title: TC71_EETS-high_rep1

description: Ewing sarcoma cell line TC-71; Control sample; replicate 1


title: wild type Top2-myc9 t4 ChIP

description: Figure 3a, 3b, 3c, EDF4b, EDF4c, EDF4d, EDF4e

value: GAGATTCC


title: Muscle-sample-53

value: BtBt

value: fetus

value: female


title: Muscle-sample-56

value: BiBi

value: male


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

value: Untreated


title: Muscle-sample-22

value: Muscle


title: wild type Top2-myc9 t2 ChIP

description: Figure 3a

value: SK1 + CBS138


title: wild type Top2-myc9 t0 WCE

value: TATAGCCT


title: Muscle-sample-13

value: BiBt


title: TC71_EETS-low_rep1

description: Ewing sarcoma cell line TC-71; Doxycycline induced EWSR1-ETS knockdown sample; replicate 1

value: Ewing sarcoma cell line

value: Doxycycline induced EWSR1-ETS knockdown


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

value: Staphylococcus aureus MRSA252


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


title: Muscle-sample-8


title: Lung-sample-106

source_name: Lung

value: Lung

value: BtBi