title: HeLa dataset A

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 1.2.1
Mapping to rRNA reference sequence using Bowtie2 v. 2.1.0
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: gi|555853|gb|U13369.1|HSU13369 Human ribosomal DNA complete repeating unit with the following changes G1639-del, C1646-del and gi|555853|gb|U13369.1|HSU13369 Human ribosomal DNA complete repeating unit with the following changes A60G, C253G, G870C, G3192C, C3215G, G3216C, C4113G, G4454A
Supplementary_files_format_and_content: MS Excel files. Contains 5' and 3' read count over the rRNA sequence and the calculated RiboMeth-seq score

source_name: Cell culture

extract_protocol:
Whole cell total RNA was extracted using QIAZOL (QIAGEN), according to the manufacturers instructions, after which 15µg of total RNA per sample was subjected to native agarose gel electrophoresis and the LSU and SSU rRNA subsequently isolated and gel purified, using the NucleoSpin Gel and PCR Clean-up kit (MACHEREY-NAGEL) according to the manufacturers instructions.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2â€™,3â€™ cyclic phosphate and 5â€™- phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description.

value: S3 (ATCC CCL-2.2)


title: HTC116

status: Public on Jun 02 2016

type: SRA

city: Copenhagen

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Whole cell total RNA was extracted using QIAZOL (QIAGEN), according to the manufacturers instructions, after which 15µg of total RNA per sample was subjected to native agarose gel electrophoresis and the LSU and SSU rRNA subsequently isolated and gel purified, using the NucleoSpin Gel and PCR Clean-up kit (MACHEREY-NAGEL) according to the manufacturers instructions.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5'- phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description.

tag: cell line

tag: strain

value: ATCC CCL-247


title: HeLa dataset B

value: HeLa


title: FG-PGN rep1 at 4 hr

city: Frederiksberg C

first: Stefan

last: Olsson

address: 40 thorvaldsensvej

department: Plant and Environmental Sciences

data_processing:
Illumina casava 1.8 used for base calling. The reads are filtered on instrument using the Illumina chastity filter.
FASTQC was used to assess the quality of the read sequences
FASTQ files were processed with FASTQ Groomer for compatibility with downstream softwares
Tophat for illumina (version 1.5.0) was used to map the sequenced reads to the Fusarium graminearum genome sequence v3 (BROAD website)
Cuffdiff (version 0.0.6) was used to identify genes that were differentially expressed
Genome_build: ASM24013v3; genome information and sequences downloaded from the BROAD website.
Supplementary_files_format_and_content: For each analysis, two tab-delimited text files as produced by cuffdiff is provided. The "gene read group tracking" file provide the reading for each of the triplicate samples (test and control), and the "differential expression testing" file provide information regarding the differential expression analysis. Gene expression level reading are in FPKM.

organism: Fusarium graminearum PH-1

source_name: 4 days liquid culture

growth_protocol: Fungal mycelia were cultured in 250 ml Erlenmeyer baffled flask with 50 ml of DFM (Yoder and Christianson, 1998, Fungal Genet Biol 23: 68-80) that was inoculated with 10 fungal plugs (approximately 8 mm x 8 mm). The flasks were shaken at 150 rpm for 3 days in the dark at 21oC. The resulting  fungal biomass was filtered through Miracloth and transferred into DFM without a nitrogen source for an overnight nitrogen depletion to recreate the nitrogen limiting environment of the soil. Three milliliters of the resulting culture was filtered through Miracloth, rinsed with sterile MilliQ water prior to treatment

extract_protocol:
Freeze dried cultures of Fusarium graminearum was crushed in mortar and pestle under liquid nitrogen. The pulverised culture was processed according to manufacturer's instructions using a QIAGEN RNeasy plant mini kit with on-column Dnase digestion to remove contaminated genomic DNA.
TruSeq RNA Sample Preparation Kit v2 was used and manufacturers instruction was followed using 1ug of total RNA. Libraries were size selected to 320 bp total size (giving ~200 bp insert after subtraction of adapter length).

treatment_protocol: Fungal culture was treated with 3 ml MAMPs (100 ng/ml flagellin [containing 100µg/ml sucrose] (tlrl-pstfla; Invivogen, CA, USA); 50 µg/ml LOS that was isolated from Xanthomonas campestris pv campestris strain 8004  (LPS without the O-antigen) (Silipo et al., 2005, J Biol Chem 280: 33660-33668), 50 µg/ml PGN that was isolated from Xanthomonas campestris pv campestris strain 8004)  (Erbs et al., 2008, Chem Biol 15: 438-448) that was dissolved in sterile MilliQ water or 3 ml sterile MilliQ water as the control. The treatments were performed in 13 ml Sarstedt tubes (Germany) with shaking in the dark at 21oC for 1, 2 and 4 hours.

tag: mamp treatment

value: PGN

tag: additional info


title: H2217-MSN2-GLU.2.XYL.5-4-2-03.20.14-1169_redo-5-84

status: Public on Jun 03 2016

city: Saint Louis

first: Ezekiel

middle: John

last: Maier

state: MO

address: 4444 Forest Park Ave

department: Computer Science

country: USA

institute: Washington University

description: MSN2(YMR037C) in 2% Glucose and 5% Xylose for 4 hours

data_processing:
Sequenced reads were aligned to the S. cerevisiae S288C reference sequence genome release R63 (Engel et al. 2013) using TopHat version 2.0.4 (Trapnell et al. 2009) and Bowtie version 0.12.8 (Langmead et al. 2009).
Reads that aligned uniquely to the reference sequence were considered for gene expression quantification with Cufflinks version 2.0.2 (Trapnell et al. 2010). Gene expression was quantitated against known gene boundaries from the gene annotations provided by the SGD S288C reference genome release R63. Gene expression was normalized using the Cufflinks upper-quartile normalization option.
After gene expression quantification, samples not passing the following quality control filters were removed from consideration. Each sample was required to be sequenced at a depth of at least 750,000 reads. The expression of the deleted gene in mutant expression profiles was required to be less than 10% of its expression in WT. The mean and median expression of the deleted genes were 1.3% and 0% of the WT levels respectively. The low levels of expression that remained for some samples were likely the result of errors in the sequencing process itself, either due to contamination between samples or a low level of error in matching barcodes for multiplexed samples to reads. In addition, within each replicate set containing 3 biological replicates outlier gene expression profiles were detected and removed if the outlier caused the median of all genes’ coefficients of variation (CoV -- the standard deviation divided by the mean) to be greater than 0.5 for the replicate set or if the outlier caused the Pearson Correlation Coefficient between replicate gene expression profiles to be less than 0.8.
Counts of reads mapping to each gene were quantitated using the htseq-count tool in version 0.5.3 of the HTSeq Python package (Anders et al. 2014).
Batch effects were removed from RNA-seq read counts using Remove Unwanted Variation (RUV) (Risso et al. 2014).  Unwanted variation due to technical batch effects was identified and removed, using RUVg, through factor analysis on a set of negative control genes that were not expected to respond to the biological treatments. The set of 192 negative control genes used to identify batch effects are not predicted to be regulated by any of the deleted regulators in the top 100,000 network predicted interactions, and their expression did not change significantly (log2 fold change < 1.3 and adjusted p-value > 0.1) between any pair of expression profiled single carbon growth conditions. Dropping the first factor of unwanted variation, by using RUVg with the parameter k set to 1, was sufficient to remove the majority of the batch effect.
Differential expression analysis comparing expression profiles sets was performed by using LIMMA(Smyth 2004) with the voom transformation applied to read counts (Law et al. 2014).
Genome_build: S. cerevisiae S288C reference sequence genome release R63 (Engel et al. 2013)
Supplementary_files_format_and_content: cuff: Gene expression was quantified by processing tophat produced bam alignments with Cufflinks v2.0.2 with S. cerevisiae S288c reference sequence genome release R63 (Engel et al. 2013). Expression was normalized by applying the Cufflinks supplied upper-quartile normalization routine. counts: Counts of reads mapping to each gene were quantitated using the htseq-count tool in version 0.5.3 of the HTSeq Python package (Anders et al. 2014).The expression.mtr file is a matrix of fully processed gene expression values (upper-quartile normalized Cufflinks reported FPKM values). The matrix is of size: number of S. cerevisiae genes (rows) BY number of expression profiles (columns). Each column in the expression.mtr file lists gene FPKM values from the matching .cuff file.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells put into aerobic fermentations of SC medium with 2% glucose and 5% xylose

growth_protocol: All strains were constructed in the S. cerevisiae H2217-7 background. Cells were cultured overnight in synthetic complete medium with 2% glucose to a density of 1-2 OD600.

extract_protocol:
Total mRNA was isolated using the yeast RiboPure kit (Life Technologies, Carlsbad CA).
Libraries for RNA-Seq were prepared as in (Haynes, et al., 2011) except that the selection of poly(A) RNA from the total RNA isolated was accomplished using an mRNA Catcher Plus Kit (Life Technologies) and the resulting poly(A) RNA was subsequently sheared by incubating in TURBO DNA-free buffer at 75°C for 10 minutes and purified with a QIAquick PCR Purification Kit (Qiagen).

treatment_protocol: All S. cerevisiae strains were grown aerobically in 60 mL of synthetic complete at 30°C in 250 mL baffled Erlenmeyer flasks shaken at 225 RPM. Cultures of cells for evaluating the impact of transcriptional interventions were performed in triplicate and initiated by inoculating overnight cultures into 60 mL of synthetic complete media supplemented with 20 g/L glucose and 50 g/L xylose resulting in a density of OD600=1.0+/- 0.2. Samples taken for RNA-seq were aliquoted from the primary culture, spun down at 3000 x g and frozen in liquid nitrogen. Cultures for identification of differential expression associated with carbon sources were grown in triplicate in either 50 g/L glucose, 50 g/L xylose or 1.3 g/L ethanol for 8 hours prior to collection of biomass for RNA sequencing.

tag: condition description

value: aerobic batch fermentation of SC + 2% gluocse and 5% xylose for 4 hours


title: shCDK8, hypoxia, replicate 2

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: polyA RNA from HCT116 cells harboring CDK8 shRNA 24hrs hypoxic condition

data_processing:
Signal processing, base calling and removal of barcode and adapter sequences was carried out automatically by the Torrent Suite Software (Life Technologies).
Data quality was assessed using custom scripts and the Fastx toolkit (version 0.0.13.2, hannonlab.cshl.fastx_toolkit.html). Reads shorter than 30 nt were removed and long reads trimmed to 150nt
Alignment to the human genome (hg19/GRCh37) was carried out using GSNAP (version 2013-10-28) with a mismatch setting of 3%.
Gene level counts were obtained using htseq-count (version 0.5.4p5) with a custom modified GTF annotation file based on an hg19 RefSeq gene list obtained from UCSC table browser (Karolchik et al., 2004).
Differential gene expression was assessed using DESeq (version 1.14.0) in R (version 3.0.3)
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Gene level count data; tab-delimited text

molecule: polyA RNA

growth_protocol: HCT116 cells were plated in McCoy's 5A medium supplemented with 10%FBS 24hrs prior to treatment

extract_protocol:
Total RNA was extracted using TRI reagent according to manufacturer's instructions and quality assessed using Bioanalyzer RNA Pico chips (Agilent). PolyA RNA was purified using the Dynabeads mRNA Direct micro kit (Life Technologies) according to manufacturer's instructions and ribosomal RNA contamination assessed using Bioanalyzer RNA Pico chips.
Libraries for Ion Torrent sequencing were prepared using the Ion Total RNAseq v2 kit (Life Technologies), according to manufactorer's instructions. Yeild and insert-size distribution were measured using Bioanalyzer High Sensitivity DNA chips (Agilent). The final Ion Torrent RNAseq libraries were subjected to an additional size-selection for 120-200bp on a Blue Pippin (Sage Science). Ion Torrent template preparation was carried out using the Ion PI Template OT2 200 Kit v2 and library sequencing carried out on an Ion Torrent Proton sequencer using the Ion PI Sequencing 200 Kit v2 (Life Technologies) according to manufacturer's instructions.

treatment_protocol: untreated/normoxia: normal growth conditions; hypoxia: 24hrs 1% O2

tag: cell type

value: colorectal carcinoma cell line

tag: shRNA

tag: culture condition

value: 24 hrs hypoxia (1% O2)


title: shTIP60, hypoxia, replicate 1

description: polyA RNA from HCT116 cells harboring TIP60 shRNA 24hrs hypoxic condition


title: shTIP60, hypoxia, replicate 2


title: HIF1A-/-, hypoxia, replicate 1

description: polyA RNA from HCT116 HIF1A-/- cells in 24hrs hypoxic condition

value: HIF1A null


title: HIF1A-/-, normoxia, replicate 2

description: polyA RNA from HCT116 HIF1A-/- cells in untreated/normoxic condition

value: normoxia


title: shNT, hypoxia, replicate 1

description: polyA RNA from HCT116 cells harboring non-targeting shRNA in 24hrs hypoxic condition

value: non-targeting


title: shTIP60, normoxia, replicate 1

description: polyA RNA from HCT116 cells harboring TIP60 shRNA in untreated/normoxic condition


title: shCDK8, normoxia, replicate 1

description: polyA RNA from HCT116 cells harboring CDK8 shRNA in untreated/normoxic condition


title: HIF1A-/-, normoxia, replicate 1


title: shTIP60, normoxia, replicate 2


title: shNT, normoxia, replicate 2

description: polyA RNA from HCT116 cells harboring non-targeting shRNA in untreated/normoxic condition


title: shCDK8, hypoxia, replicate 1


title: control

status: Public on Jun 01 2016

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

institute: Aarhus University

data_processing:
Torrent Suite Software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, and short reads (length < 30nt) were filtered out. Then clean reads were mapped to the hg19 UCSC RefSeq using tmap 3.4.1 with parameters mapall -a 2 -n 8 -v -Y -u -o 1 stage1 map4.
Gene level expression was performed by transforming uniquely mapped transcript reads to TPM (transcript per million).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: human embryonic kidney

growth_protocol: HEK293T cells were cultured in DMEM medium, 10%FBS, 1%P/S, 1%GlutaMAX. 37 celsius degrees, 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (QIAGEN)
After DNase I treatment, mRNA were isolated by magnetic beads with Oligo (dT). Mixed with the fragmentation buffer, mRNA were fragmented into short fragments. cDNA was synthesized using the mRNA fragments as templates, resolved with EB buffer for end reparation and ligated with adapters. After size selected and purified by agarose gel electrophoresis, cDNA with sizes about 240 bp were selected for PCR amplification (12 cycles) and library construction.

treatment_protocol: Cells were transfected with a total of 1 ug plasmid DNA using X-tremeGENE 9. Total RNA were extracted from the FACS-sorted BFP positive cells 48 hours after transfection

tag: transfection

value: X-TremeGENE 9

tag: hours after transfection

value: 48 hours


title: dCas9-BFP-EGFP


title: HIF1A-/-, hypoxia, replicate 2


title: dCas9-BFP-DNMT3B


title: dCas9-BFP-DNMT3A


title: S. cerevisiae swr1 htz1 rep2

city: San Francisco

first: Yulia

last: Mostovoy

state: CA

address: 555 Mission Bay Blvd South

institute: University of California, San Francisco

data_processing:
Basecalling with Illumina CASAVA version 1.8
Reads were mapped to the Saccharomyces cerevisiae S288C genome using Bowtie version 0.12.7 with default settings and flags -m1 -X1000.
Filtering: To ensure that poly-A tails did not originate from stretches of As or Ts encoded endogenously in the genome, we discarded reads whose stretch of As or Ts contained more than 50% matches to the reference genome. In order to filter for potential oligo-dT mispriming during cDNA synthesis, we also discarded reads that contained 10 or more As in the 20 nucleotides upstream of their transcription termination site.
GC correction: For each lane of sequencing, we grouped sets of overlapping reads and normalized abundance according to GC content of the overlapping region using full-quantile normalization as implemented in the package EDASeq. Normalized abundance was divided by raw abundance to generate a weight that was assigned to every read in the group. These weights were used in place of raw read counts in all downstream analyses.
Genome_build: R57
Supplementary_files_format_and_content: Abundance measurements were calculated as follows: for each gene, we searched for reads that had mapped to either its sense or antisense region, and obtained GC-normalized read counts for each such feature by summing the weighted abundance of the reads.

source_name: yeast cells

growth_protocol: Cultures were grown at 30°C in YPD medium to log phase (between 0.65-0.75 OD at 600 nm).

extract_protocol: Total RNA was isolated by the hot acid phenol method' and treated with Turbo DNA-free (Ambion) according to the manufacturer's instructions.  Libraries for 3’end RNA-seq were generated according to the published protocol (Yoon and Brem, RNA 2010) with the following modifications: 1) AmpureXP beads (Beckman) were used to clean up enzymatic reactions; 2) the gel purification and size-selection step was removed; 3) the oligo-dT primer used for cDNA synthesis was phosphorothioated at position ten (TTTTTTTTTT*TTTTTTTTTTVN, V=A,C,G, N=A,C,G,T, *=phosphorothioate linkage, Integrated DNA Technologies); and 4) 12 PCR cycles were performed.

tag: genotype

value: swr1 htz1


title: S. cerevisiae wild-type rep2

value: wild type


title: S. cerevisiae swr1 htz1 rep1


title: dCas9-BFP-DNMT1


title: shNT, hypoxia, replicate 2


title: shCDK8, normoxia, replicate 2


title: IgG MeDIP-Seq

city: beijing

first: liu

last: di

address: No.18, Shuangqing road, Haidian district

country: China

institute: rcees, cas

library_source: genomic

data_processing:
MeDIP-seq reads were aligned to the Dm6 genome assembly using Torrent mapper (tmap) version 3.6.40 with the following configurations -i fastq -o 0 -v -Y -u --prefix-exclude 5 stage1 map4
peaks were called using macs14 with the following setting: -f bed -g 137567484 -w --mold 10,30
Genome_build: Dm6
Supplementary_files_format_and_content: wig files were generated using macs14; Scores represent relative methylated mesurements

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Fly stocks used in this study were maintained under standard culture conditions

extract_protocol:
Tissue genomic DNA was extracted and purified with genomic DNA purification Kit (Promega) following the manufacturer’s instructions. To avoid RNA contaminations all samples were treated with RNase A two times. Purified genomic DNA was sonicated to 200 base pairs(bp). 5ug of fragmented genomic DNA was immunoprecipitated with 5 ug of rabbit m6A Antibody(millipore) or rabbit IgG overnight at 4°C in a final volume of 500uL of immunoprecipitation buffer (10 mM sodium phosphate at pH 7.0, 140mM NaCl, 0.05% Triton X-100). Then the mixture was incubated with 50uL of protein A/G Agarose beads for 2 h at 4°C and washed three times with 1 mL of immunoprecipitation buffer.The beads were then treated with proteinase K for 3 h at 50°C in 250μL proteinase K digestion buffer (50mM Tris–HCl, pH 8.0,10mM EDTA, 0.5% SDS), and the methylated DNA was purified by phenol-chloroform extraction followed by ethanol precipitation
DNA libraries were prepared using the NEBNext® Fast DNA Library Prep Set For Ion Torrent(New England BioLabs) according to the instruction manual except that the input adaptor was reduced to 8µL and the adaptor ligated DNA was directly used in size selection without cleanup. Final libraries were purified with 12% native PAGE gel at 200 V for 40 min.

tag: medip antibody

value: rabbit IgG

tag: tissue

value: ovary

tag: age

value: adult 1-2day

value: w1118 wild-type


title: w1118 MeDIP-Seq


title: SU654-Leuk-141115

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

institute: Broad Institute

description: library strategy: ATAC-seq

data_processing:
ATAC-seq data was processed as previously described (Buenrostro et al., 2015a) with notable exceptions. In brief, reads were trimmed using a custom script and aligned using Bowtie2. To call peaks, data was aggregated by each unique cell type, peak summits were called using MACS2 and filtered using a custom blacklist, as previously described (Buenrostro et al., 2015a).
Genome_build: hg19
Supplementary_files_format_and_content: Count file is a tab-delimited text file where rows represent unique genes and columns represent unique samples.

source_name: Blast

extract_protocol:
ATAC-seq was performed directly from FACS-purified cells
5,000 sorted cells in FACS Buffer were pelleted by centrifugation at 500 RCF for 5 minutes at 4C in a pre-cooled fixed-angle centrifuge. 50 ul transposase mixture (25 ul of 2x TD, 2.5 ul of TDE1, 0.5 ul of 1% digitonin, 22 ul of nuclease-free water) (Cat# FC-121-1030, Illumina; Cat# G9441, Promega) was added to the cells and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37C for 30 minutes in an Eppendorf ThermoMixer with agitation at 300 RPM. Transposed fragments were purified and amplified as described previously (Buenrostro et al., 2015).

value: acute myeloid leukemia, blast cell

tag: donorid

tag: sample type

value: primary human leukemia cell from cryopreserved sample


title: SU623-Leuk

description: library strategy: ATAC-seq


title: SU654-LSC-150120

description: library strategy: ATAC-seq

source_name: LSC

value: acute myeloid leukemia, leukmeia stem cell


title: SU623-Leuk-Rep1-150212

description: library strategy: ATAC-seq


title: SU623-Leuk-Rep2-150212

description: library strategy: ATAC-seq


title: dALKB/Tet1/2 MeDIP-Seq


title: SU623-pHSC

description: library strategy: ATAC-seq

source_name: pHSC

value: acute myeloid leukemia, pre-leukemic hematopoietic stem cell


title: SU583-pHSC-150627

description: library strategy: ATAC-seq


title: SU575-LSC-150120

description: library strategy: ATAC-seq


title: SU575 pHSC

description: library strategy: ATAC-seq


title: SU583-LSC-150120

description: library strategy: ATAC-seq


title: SU583-pHSC-141115

description: library strategy: ATAC-seq


title: shNT, normoxia, replicate 1

value: colorectal carcinoma cell line


title: S. cerevisiae wild-type rep1


title: SU654-pHSC-141115

description: library strategy: ATAC-seq


title: SU501-pHSC-141118

description: library strategy: ATAC-seq


title: SU496-LSC-012015

description: library strategy: ATAC-seq


title: SU575-Leuk

description: library strategy: ATAC-seq


title: SU496-pHSC-140814

description: library strategy: ATAC-seq


title: SU501-Leuk-141118

description: library strategy: ATAC-seq


title: SU496-Leuk-140814

description: library strategy: ATAC-seq


title: SU444-pHSC-141118

description: library strategy: ATAC-seq


title: SU484-Leuk-140812

description: library strategy: ATAC-seq


title: SU484-pHSC-140812

description: library strategy: ATAC-seq


title: SU444-LSC-012015

description: library strategy: ATAC-seq


title: SU353-Leuk-140923

description: library strategy: ATAC-seq


title: SU444-Leuk-141118

description: library strategy: ATAC-seq


title: SU306-pHSC-141121

description: library strategy: ATAC-seq


title: SU336-pHSC-141119

description: library strategy: ATAC-seq


title: SU353-LSC-150120

description: library strategy: ATAC-seq


title: G2 phase (T=6 hour) TG003 treated sample , duplicate a

city: Shanghai

first: Zefeng

last: Wang

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

data_processing:
RNA-Seq reads were mapped to the human genome (build hg19) using the MapSplice informatics tool with default parameters
The mapped reads were further analyzed with Cufflinks to calculate the level of gene expression with FPKM
The levels of alternatively spliced isoforms were quantified with MISO (Mixture-of-Isoforms) probabilistic framework (Katz et al., 2010) using the annotated AS events for human hg19version 2.
The levels of alternatively spliced isoforms were also quantified with VAST-TOOLS using the event annotation as previously described
Genome_build: hg19

growth_protocol: Cells were cultured in humidified incubators with 5% CO2. Cell cycle synchronization was adapted from the protocol of Whitfield et al. (Whitfield et al., 2002); ~ 750,000 log phase HeLa cells were plated in 15 cm dishes in complete media and allowed to attach for 16 hrs, reaching < 30% confluence.

extract_protocol:
For RNA-Seq, cells (both adherent and detached) were harvested every 1.5 hrs for 30 hrs and frozen immediately for purification of total RNA.
RNA from synchronized cells was extracted with TRIZOL (Invitrogen), treated with DNAse I (Qiagen), and purified on RNAeasy columns. (Qiagen) according to the manufacturer’s protocol. RNA-seq libraries were robotically prepared with Illumina TruSeq Total RNA Sample Prep kits according to the manufacturer’s protocol

treatment_protocol: Cells were subsequently treated with 2 mM thymidine (Sigma) for a total of 18 hrs, washed 2 times with 1xPBS, and supplemented with fresh complete media for 10 hrs. 2 mM thymidine was subsequently added for a second block of 18 hrs and washed as described previously. Mitotic block was performed by double thymidine arrest (as above) and release in fresh media for 3.5 hrs followed by addition of nocodazole 100 μM (Sigma) for 10 hrs. G1 block was performed by serum starvation for 72 hrs in DMEM containing 0.05% FBS.

value: HeLa

tag: cell cycle

tag: treatment


title: SU336-Leuk-141119

description: library strategy: ATAC-seq


title: SU351-Leuk-140814

description: library strategy: ATAC-seq


title: SU209-LSC-012015

description: library strategy: ATAC-seq


title: SU209-Leuk-140911

description: library strategy: ATAC-seq


title: SU209-pHSC-B-150627

description: library strategy: ATAC-seq


title: SU209-pHSC-A-150627

description: library strategy: ATAC-seq


title: SU048-pHSC

description: library strategy: ATAC-seq


title: SU070-pHSC-Rep2-140805

description: library strategy: ATAC-seq


title: SU583-Leuk-141115

description: library strategy: ATAC-seq


title: SU048-Leuk-Rep2-140813

description: library strategy: ATAC-seq


title: SU048-Leuk-Rep1-150212

description: library strategy: ATAC-seq


title: SU048-Leuk

description: library strategy: ATAC-seq


title: SU070-Leuk-Rep2-140805

description: library strategy: ATAC-seq


title: SU048-Leuk-Rep1-140813

description: library strategy: ATAC-seq


title: SU353-pHSC-140923

description: library strategy: ATAC-seq


title: SU048-Leuk-Rep2-150212

description: library strategy: ATAC-seq


title: SU351-pHSC-140814

description: library strategy: ATAC-seq


title: SU209-pHSC-140911

description: library strategy: ATAC-seq


title: Donor7256-7B-141106

description: library strategy: ATAC-seq

source_name: Mono

value: CD14+ monocyte cell

value: primary human blood cell from fresh sample


title: Donor5483-Bcell-13B-150305

description: library strategy: ATAC-seq

source_name: Bcell

value: CD19+CD20+ B cell


title: SU306-Leuk-141121

description: library strategy: ATAC-seq


title: Donor7256-7A-141106

description: library strategy: ATAC-seq


title: Donor7256-6B-141106

description: library strategy: ATAC-seq

source_name: MEP

value: megakaryocyte erythroid progenitor cell


title: Donor7256-5B-141106

description: library strategy: ATAC-seq

source_name: GMP

value: granulocyte macrophage progenitor cell


title: Donor7256-4B-141106

description: library strategy: ATAC-seq

source_name: CMP

value: common myeloid progenitor cell


title: Donor7256-4A-110614

description: library strategy: ATAC-seq


title: Donor7256-3A-141106

description: library strategy: ATAC-seq

source_name: LMPP

value: lymphoid-primed multipotent progenitor cell


title: Donor7256-2A-110614

description: library strategy: ATAC-seq

source_name: MPP

value: multipotent progenitor cell


title: Donor7256-2B-110614

description: library strategy: ATAC-seq


title: Donor7256-5A-141106

description: library strategy: ATAC-seq


title: Donor7256-1B-110614

description: library strategy: ATAC-seq

source_name: HSC

value: hematopoietic stem cell


title: Donor7256-1A-110614

description: library strategy: ATAC-seq


title: SU048-Leuk-Rep3-140813

description: library strategy: ATAC-seq


title: Donor7256-6A-141106

description: library strategy: ATAC-seq


title: Donor6926-CLP-14A-150318

description: library strategy: ATAC-seq

source_name: CLP

value: common lymphoid progenitor cell


title: Donor5483-Nkcell-11B-150305

description: library strategy: ATAC-seq

source_name: NKcell

value: CD56+ natural killer cell


title: Donor5483-Erythroblast-15C-150305

description: library strategy: ATAC-seq

source_name: Ery

value: CD71+GPA+ erythroblast cell


title: Donor5483-NK-11A-150305

description: library strategy: ATAC-seq


title: Donor6926-Erythroblast-15B-150318

description: library strategy: ATAC-seq


title: Donor5483-Erythroblast-15A-150305

description: library strategy: ATAC-seq


title: Donor5483-CD8-10B-150305

description: library strategy: ATAC-seq

value: CD8+ T cell


title: Donor5483-CLP-14A-150305

description: library strategy: ATAC-seq


title: Donor5483-CD4-9B-150305

description: library strategy: ATAC-seq

value: CD4+ T cell


title: Donor5483-CD4-9A-150305

description: library strategy: ATAC-seq


title: Donor6926-Erythroblast-15A-150318

description: library strategy: ATAC-seq


title: Donor5483-Bcell-13A-150305

description: library strategy: ATAC-seq


title: Donor4983-Bcell-13A-150120

description: library strategy: ATAC-seq


title: Donor4983-CD4-9A-150120

description: library strategy: ATAC-seq


title: Donor2596-Nkcell-11A-150303

description: library strategy: ATAC-seq


title: Donor2596-MEP-6A-150303

description: library strategy: ATAC-seq


title: Donor2596-MPP-2B-150303

description: library strategy: ATAC-seq


title: Donor2596-MPP-2A-150303

description: library strategy: ATAC-seq


title: Donor6926-CLP-14B-150318

description: library strategy: ATAC-seq


title: Donor2596-Erythroblast-15C-150303

description: library strategy: ATAC-seq


title: Donor2596-Erythroblast-15A-150303

description: library strategy: ATAC-seq


title: Donor2596-GMP-5A-150303

description: library strategy: ATAC-seq


title: Donor5483-Erythroblast-15B-150305

description: library strategy: ATAC-seq


title: Donor4983-CD8-10A-150120

description: library strategy: ATAC-seq


title: Donor2596-HSC-1A-150303

description: library strategy: ATAC-seq


title: Donor2596-Erythroblast-15B-150303

description: library strategy: ATAC-seq


title: Donor2596-CMP-4A-150303

description: library strategy: ATAC-seq


title: Donor2596-CMP-4B-150303

description: library strategy: ATAC-seq


title: Donor4983-Nkcell-11A-150120

description: library strategy: ATAC-seq


title: Donor5483-CD8-10A-150305

description: library strategy: ATAC-seq


title: Donor2596-CLP-14A-150303

description: library strategy: ATAC-seq


title: Donor2596-CLP-14B-150303

description: library strategy: ATAC-seq


title: Donor2596-CD4-9A-150303

description: library strategy: ATAC-seq


title: Donor1022-Nkcell-11-150120

description: library strategy: ATAC-seq


title: Donor1022-CD4-9-150120

description: library strategy: ATAC-seq


title: Donor1022-CD8-10-150120

description: library strategy: ATAC-seq


title: CB102-CD34-150627

description: library strategy: ATAC-seq

source_name: CD34 Cord Blood

value: CD34+ cord blood


title: BM-CD34-2

description: library strategy: ATAC-seq

source_name: CD34 Bone Marrow

value: CD34+ bone marrow


title: Donor2596-HSC-1B-150303

description: library strategy: ATAC-seq


title: BM-CD34-1

description: library strategy: ATAC-seq


title: 6792-7B

description: library strategy: ATAC-seq


title: 6792-7A

description: library strategy: ATAC-seq


title: 6792-6B

description: library strategy: ATAC-seq


title: Donor2596-CD8-10B-150303

description: library strategy: ATAC-seq


title: 7dpa mRNA

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

description:
PsenD7
Polypterus_mRNA_assembly.fa.gz
Polypterus_mRNA_logCPM.txt

data_processing:
Reads were adapter clipped and quality filtered using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) for small RNA, and Trimmomatic (Bolger et al. Bioinformatics (2010)) for mRNA.
Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner (Wheeler et al. Evol. Dev. (2009)) and miRBase v. 21 (Kozomara et al. Nucleic Acids Res (2014)).
MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR (Robinson et al. Bioinformatics (2010)).
Trimmed mRNA reads were digitally normalized using khmer (http://khmer-protocols.readthedocs.org/en/v0.8.4/).
Digitally normalized mRNA reads were assembled using Trinity (Haas et al. Nat Protoc. (2013)).
Reads counts per transcript were generated using RSEM (Li and Dewey BMC Bioinformatics (2011)).
Differentially expressed transcripts were determined using R/edgeR.
Genome_build: The de novo transcriptome assembly is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: Tab-delimited text file with read counts per transcript per sample.

organism: Polypterus senegalus

source_name: pectoral fin

growth_protocol: FIsh from the Maine Pet and Aquarium (Ellsworth, ME) were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.

extract_protocol:
Total RNA was isolated using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) following manufacturer’s protocol.
Illumina TruSeq small RNA and PolyA+ mRNA libraries.

treatment_protocol: Pectoral fins were amputated with scalpels following anesthesia (0.6mM MS222).

tag: days post amputation

tag: library type

value: mRNA

tag: amputation site

value: pectoral fin


title: 14dpa mRNA

description:
PsenD14
Polypterus_mRNA_assembly.fa.gz
Polypterus_mRNA_logCPM.txt


title: 6792-4A

description: library strategy: ATAC-seq

value: primary human blood cell from fresh sample


title: 6792-5A

description: library strategy: ATAC-seq


title: 3dpa mRNA

description:
PsenD3
Polypterus_mRNA_assembly.fa.gz
Polypterus_mRNA_logCPM.txt


title: 14dpa small RNA

description:
PsenD14
Polypterus_microRNA.fa.gz
Polypterus_microRNA_logCPM.txt

data_processing:
Reads were adapter clipped and quality filtered using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) for small RNA, and Trimmomatic (Bolger et al. Bioinformatics (2010)) for mRNA.
Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner (Wheeler et al. Evol. Dev. (2009)) and miRBase v. 21 (Kozomara et al. Nucleic Acids Res (2014)).
MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR (Robinson et al. Bioinformatics (2010)).
Trimmed mRNA reads were digitally normalized using khmer (http://khmer-protocols.readthedocs.org/en/v0.8.4/).
Digitally normalized mRNA reads were assembled using Trinity (Haas et al. Nat Protoc. (2013)).
Reads counts per transcript were generated using RSEM (Li and Dewey BMC Bioinformatics (2011)).
Differentially expressed transcripts were determined using R/edgeR.
Genome_build: The de novo transcriptome assembly is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: Tab-delimited text file with read counts per miRNA per sample.

value: small RNA


title: 6792-4B

description: library strategy: ATAC-seq


title: 0dpa mRNA

description:
PsenD0
Polypterus_mRNA_assembly.fa.gz
Polypterus_mRNA_logCPM.txt


title: 6792-1A

description: library strategy: ATAC-seq


title: 6792-3A

description: library strategy: ATAC-seq


title: Donor1022-Bcell-13-150120

description: library strategy: ATAC-seq

value: CD19+CD20+ B cell


title: 6792-1B

description: library strategy: ATAC-seq


title: 6792-2A

description: library strategy: ATAC-seq


title: 3dpa small RNA

description:
PsenD3
Polypterus_microRNA.fa.gz
Polypterus_microRNA_logCPM.txt


title: 4983-7A

description: library strategy: ATAC-seq

value: CD14+ monocyte cell


title: 4983-6A

description: library strategy: ATAC-seq

value: megakaryocyte erythroid progenitor cell


title: 7dpa small RNA

description:
PsenD7
Polypterus_microRNA.fa.gz
Polypterus_microRNA_logCPM.txt


title: 4983-6B

description: library strategy: ATAC-seq


title: 4983-7B

description: library strategy: ATAC-seq


title: 4983-4B

description: library strategy: ATAC-seq

value: common myeloid progenitor cell


title: 4983-4A

description: library strategy: ATAC-seq


title: 6792-6A

description: library strategy: ATAC-seq


title: 4983-5A

description: library strategy: ATAC-seq

value: granulocyte macrophage progenitor cell


title: 0dpa small RNA

description:
PsenD0
Polypterus_microRNA.fa.gz
Polypterus_microRNA_logCPM.txt


title: 6792-5B

description: library strategy: ATAC-seq


title: 4983-3A

description: library strategy: ATAC-seq

value: lymphoid-primed multipotent progenitor cell


title: 4983-2A

description: library strategy: ATAC-seq

value: multipotent progenitor cell


title: 4983-5B

description: library strategy: ATAC-seq


title: 4983-1A

description: library strategy: ATAC-seq

value: hematopoietic stem cell


title: singles-SU070-LSC-96

description: library strategy: scATAC-seq

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
Genome_build: hg19

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

value: acute myeloid leukemia, leukmeia stem cell

tag: donor id


title: singles-SU070-LSC-92

description: library strategy: scATAC-seq

tag: cell type


title: singles-SU070-LSC-94

description: library strategy: scATAC-seq


title: singles-SU070-LSC-90

description: library strategy: scATAC-seq


title: singles-SU070-LSC-86

description: library strategy: scATAC-seq


title: singles-SU070-LSC-89

description: library strategy: scATAC-seq


title: singles-SU070-LSC-93

description: library strategy: scATAC-seq


title: singles-SU070-LSC-95

description: library strategy: scATAC-seq


title: singles-SU070-LSC-88

description: library strategy: scATAC-seq


title: singles-SU070-LSC-91

description: library strategy: scATAC-seq


title: singles-SU070-LSC-82

description: library strategy: scATAC-seq


title: singles-SU070-LSC-83

description: library strategy: scATAC-seq


title: singles-SU070-LSC-87

description: library strategy: scATAC-seq


title: singles-SU070-LSC-85

description: library strategy: scATAC-seq


title: singles-SU070-LSC-84

description: library strategy: scATAC-seq


title: singles-SU070-LSC-81

description: library strategy: scATAC-seq


title: singles-SU070-LSC-78

description: library strategy: scATAC-seq


title: singles-SU070-LSC-80

description: library strategy: scATAC-seq


title: singles-SU070-LSC-76

description: library strategy: scATAC-seq


title: singles-SU070-LSC-79

description: library strategy: scATAC-seq


title: singles-SU070-LSC-74

description: library strategy: scATAC-seq


title: singles-SU070-LSC-73

description: library strategy: scATAC-seq


title: singles-SU070-LSC-72

description: library strategy: scATAC-seq


title: singles-SU070-LSC-75

description: library strategy: scATAC-seq


title: singles-SU070-LSC-71

description: library strategy: scATAC-seq


title: singles-SU070-LSC-70

description: library strategy: scATAC-seq


title: singles-SU070-LSC-68

description: library strategy: scATAC-seq


title: singles-SU070-LSC-69

description: library strategy: scATAC-seq


title: singles-SU070-LSC-65

description: library strategy: scATAC-seq


title: singles-SU070-LSC-66

description: library strategy: scATAC-seq


title: singles-SU070-LSC-67

description: library strategy: scATAC-seq


title: singles-SU070-LSC-64

description: library strategy: scATAC-seq


title: singles-SU070-LSC-61

description: library strategy: scATAC-seq


title: singles-SU070-LSC-60

description: library strategy: scATAC-seq


title: singles-SU070-LSC-59

description: library strategy: scATAC-seq


title: singles-SU070-LSC-57

description: library strategy: scATAC-seq


title: singles-SU070-LSC-63

description: library strategy: scATAC-seq


title: singles-SU070-LSC-55

description: library strategy: scATAC-seq


title: singles-SU070-LSC-54

description: library strategy: scATAC-seq


title: singles-SU070-LSC-77

description: library strategy: scATAC-seq


title: singles-SU070-LSC-53

description: library strategy: scATAC-seq


title: singles-SU070-LSC-50

description: library strategy: scATAC-seq


title: singles-SU070-LSC-58

description: library strategy: scATAC-seq


title: singles-SU070-LSC-51

description: library strategy: scATAC-seq


title: singles-SU070-LSC-56

description: library strategy: scATAC-seq


title: singles-SU070-LSC-49

description: library strategy: scATAC-seq


title: Donor2596-NK-11B-150303

description: library strategy: ATAC-seq

value: CD56+ natural killer cell


title: singles-SU070-LSC-48

description: library strategy: scATAC-seq


title: singles-SU070-LSC-46

description: library strategy: scATAC-seq


title: singles-SU070-LSC-47

description: library strategy: scATAC-seq


title: singles-SU070-LSC-44

description: library strategy: scATAC-seq


title: singles-SU070-LSC-43

description: library strategy: scATAC-seq


title: singles-SU070-LSC-45

description: library strategy: scATAC-seq


title: singles-SU070-LSC-40

description: library strategy: scATAC-seq


title: singles-SU070-LSC-42

description: library strategy: scATAC-seq


title: singles-SU070-LSC-62

description: library strategy: scATAC-seq


title: singles-SU070-LSC-41

description: library strategy: scATAC-seq


title: singles-SU070-LSC-52

description: library strategy: scATAC-seq


title: singles-SU070-LSC-37

description: library strategy: scATAC-seq


title: singles-SU070-LSC-38

description: library strategy: scATAC-seq


title: singles-SU070-LSC-39

description: library strategy: scATAC-seq


title: singles-SU070-LSC-29

description: library strategy: scATAC-seq


title: singles-SU070-LSC-32

description: library strategy: scATAC-seq


title: singles-SU070-LSC-31

description: library strategy: scATAC-seq


title: singles-SU070-LSC-33

description: library strategy: scATAC-seq


title: singles-SU070-LSC-23

description: library strategy: scATAC-seq


title: singles-SU070-LSC-25

description: library strategy: scATAC-seq


title: singles-SU070-LSC-34

description: library strategy: scATAC-seq


title: singles-SU070-LSC-30

description: library strategy: scATAC-seq


title: singles-SU070-LSC-22

description: library strategy: scATAC-seq


title: singles-SU070-LSC-27

description: library strategy: scATAC-seq


title: singles-SU070-LSC-28

description: library strategy: scATAC-seq


title: singles-SU070-LSC-26

description: library strategy: scATAC-seq


title: singles-SU070-LSC-24

description: library strategy: scATAC-seq


title: singles-SU070-LSC-35

description: library strategy: scATAC-seq


title: singles-SU070-LSC-19

description: library strategy: scATAC-seq


title: singles-SU070-LSC-17

description: library strategy: scATAC-seq


title: singles-SU070-LSC-21

description: library strategy: scATAC-seq


title: singles-SU070-LSC-15

description: library strategy: scATAC-seq


title: singles-SU070-LSC-18

description: library strategy: scATAC-seq


title: singles-SU070-LSC-16

description: library strategy: scATAC-seq


title: singles-SU070-LSC-12

description: library strategy: scATAC-seq


title: singles-SU070-LSC-11

description: library strategy: scATAC-seq


title: singles-SU070-LSC-14

description: library strategy: scATAC-seq


title: singles-SU070-LSC-36

description: library strategy: scATAC-seq


title: singles-SU070-LSC-10

description: library strategy: scATAC-seq


title: singles-SU070-LSC-9

description: library strategy: scATAC-seq


title: singles-SU070-LSC-8

description: library strategy: scATAC-seq


title: singles-SU070-LSC-20

description: library strategy: scATAC-seq


title: singles-SU070-LSC-6

description: library strategy: scATAC-seq


title: singles-SU070-LSC-7

description: library strategy: scATAC-seq


title: matched sample_L831N

city: Solna

first: Björn

middle: M

last: Hallström

state: Stockholm

address: Tomtebodavägen 23A

department: Science for Life Laboratory

country: Sweden

institute: Royal Institute of Technology, Stockholm

data_processing:
Mapping of reads to GRCh37 reference genome using TopHat 2.0.8b with Bowtie 2.1.0. Default settings
Abundance estiamtion (FPKM) using Cufflinks 2.1.1 with transcript annotation from Ensembl v73, Homo_sapiens.GRCh37.73.gtf Non-default settings: --max-bundle-frags 10000000 --max-bundle-length 10000000
Raw read count estimation using featureCounts 1.4.0p1 with same GTF as above, Settings: -g gene_id -t exon
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-separated matrices with FPKM and read counts, respectively

source_name: Human non-malignant tissue

extract_protocol:
Tissue was cut in sections (10uM) using a cryostat. five sections (10 µm) were cut and used for RNA extraction. The five sections were transferred to RLT buffer using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Samples were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit v2, using polyA selection. The sequencing was performed multiplexed with five samples per lane on Illumina HiSeq2500 machines (Illumina, San Diego, CA, USA) using the standard Illumina RNAseq protocol with a read length of 2 x 100 bases.
Libraries were prepared according to Illumina´s TruSeq strand-specific RNA kit.

treatment_protocol: Freshly frozen tumor tissues were embedded in Optimal Cutting Temperature compound and stored at -80°C.

tag: tumor (t) or normal (n)


title: singles-SU070-LSC-5

description: library strategy: scATAC-seq

source_name: LSC


title: matched sample_L809N


title: singles-SU070-LSC-4

description: library strategy: scATAC-seq


title: matched sample_L738N


title: singles-SU070-LSC-2

description: library strategy: scATAC-seq


title: singles-SU070-LSC-3

description: library strategy: scATAC-seq


title: matched sample_L724N


title: matched sample_L723N


title: matched sample_L682N


title: matched sample_L736N


title: matched sample_L661N


title: singles-SU070-LSC-1

description: library strategy: scATAC-seq


title: singles-SU070-LSC-13

description: library strategy: scATAC-seq


title: matched sample_L656N


title: singles-SU070-Leuk-96

description: library strategy: scATAC-seq

source_name: Blast

value: acute myeloid leukemia, blast cell


title: matched sample_L644N


title: singles-SU070-Leuk-94

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-95

description: library strategy: scATAC-seq


title: matched sample_L616N


title: matched sample_L572N


title: singles-SU070-Leuk-93

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-89

description: library strategy: scATAC-seq


title: matched sample_L566N


title: matched sample_L881N


title: singles-SU070-Leuk-91

description: library strategy: scATAC-seq


title: matched sample_L563N


title: singles-SU070-Leuk-90

description: library strategy: scATAC-seq


title: matched sample_L561N


title: singles-SU070-Leuk-87

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-88

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-84

description: library strategy: scATAC-seq


title: matched sample_L532N


title: L886T

source_name: Human NSCLC tissue

tag: stage tnm

tag: histology

tag: surgery date

tag: gender

value: male

tag: vital date

tag: dead

tag: smoking

tag: ps who


title: L890T

tag: age

value: female


title: matched sample_L606N


title: singles-SU070-Leuk-82

description: library strategy: scATAC-seq


title: L887T


title: singles-SU070-Leuk-81

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-83

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-85

description: library strategy: scATAC-seq


title: L879T


title: L885T


title: L881T


title: singles-SU070-Leuk-79

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-78

description: library strategy: scATAC-seq


title: L880T


title: matched sample_L511N


title: L877T


title: L876T


title: L874T


title: L873T


title: singles-SU070-Leuk-75

description: library strategy: scATAC-seq


title: L884T


title: singles-SU070-Leuk-76

description: library strategy: scATAC-seq


title: L872T


title: singles-SU070-Leuk-73

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-70

description: library strategy: scATAC-seq


title: L865T


title: singles-SU070-Leuk-77

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-80

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-71

description: library strategy: scATAC-seq


title: L871T


title: singles-SU070-Leuk-72

description: library strategy: scATAC-seq


title: L867T


title: L863T


title: singles-SU070-Leuk-68

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-86

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-69

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-67

description: library strategy: scATAC-seq


title: L860T


title: L875T


title: singles-SU070-Leuk-74

description: library strategy: scATAC-seq


title: L858T


title: singles-SU070-Leuk-65

description: library strategy: scATAC-seq


title: L857T


title: singles-SU070-Leuk-64

description: library strategy: scATAC-seq


title: L856T


title: singles-SU070-Leuk-66

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-63

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-62

description: library strategy: scATAC-seq


title: L854T


title: L864T


title: singles-SU070-Leuk-61

description: library strategy: scATAC-seq


title: L851T


title: L850T


title: singles-SU070-Leuk-59

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-60

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-58

description: library strategy: scATAC-seq


title: L834T


title: L838T


title: singles-SU070-Leuk-57

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-56

description: library strategy: scATAC-seq


title: L848T


title: singles-SU070-Leuk-53

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-54

description: library strategy: scATAC-seq


title: L829T


title: L831T


title: L828T


title: singles-SU070-Leuk-52

description: library strategy: scATAC-seq


title: L852T


title: singles-SU070-Leuk-55

description: library strategy: scATAC-seq


title: L827T


title: L826T


title: L824T


title: singles-SU070-Leuk-50

description: library strategy: scATAC-seq


title: L820T


title: singles-SU070-Leuk-48

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-47

description: library strategy: scATAC-seq


title: L817T


title: singles-SU070-Leuk-45

description: library strategy: scATAC-seq


title: L842T


title: singles-SU070-Leuk-46

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-42

description: library strategy: scATAC-seq


title: L816T


title: singles-SU070-Leuk-44

description: library strategy: scATAC-seq


title: L815T


title: singles-SU070-Leuk-43

description: library strategy: scATAC-seq


title: L809T


title: L810T


title: L802T


title: singles-SU070-Leuk-49

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-51

description: library strategy: scATAC-seq


title: L814T


title: singles-SU070-Leuk-41

description: library strategy: scATAC-seq


title: L808T


title: singles-SU070-Leuk-35

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-39

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-40

description: library strategy: scATAC-seq


title: L788T


title: singles-SU070-Leuk-38

description: library strategy: scATAC-seq


title: L800T


title: L818T


title: singles-SU070-Leuk-37

description: library strategy: scATAC-seq


title: L791T


title: singles-SU070-Leuk-30

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-31

description: library strategy: scATAC-seq


title: L790T


title: singles-SU070-Leuk-29

description: library strategy: scATAC-seq


title: L782T


title: singles-SU070-Leuk-33

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-36

description: library strategy: scATAC-seq


title: L778T


title: singles-SU070-Leuk-32

description: library strategy: scATAC-seq


title: L768T


title: L781T


title: L766T


title: singles-SU070-Leuk-28

description: library strategy: scATAC-seq


title: L773T


title: singles-SU070-Leuk-34

description: library strategy: scATAC-seq


title: L764T


title: singles-SU070-Leuk-24

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-26

description: library strategy: scATAC-seq


title: L767T


title: singles-SU070-Leuk-27

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-25

description: library strategy: scATAC-seq


title: L771T


title: L758T


title: L760T


title: L756T


title: singles-SU070-Leuk-92

description: library strategy: scATAC-seq


title: L755T


title: L752T


title: singles-SU070-Leuk-23

description: library strategy: scATAC-seq


title: L744T


title: singles-SU070-Leuk-20

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-22

description: library strategy: scATAC-seq


title: L753T


title: L749T


title: L751T


title: L747T


title: singles-SU070-Leuk-19

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-16

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-17

description: library strategy: scATAC-seq


title: L736T


title: L731T


title: L735T


title: singles-SU070-Leuk-15

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-9

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-10

description: library strategy: scATAC-seq


title: L741T


title: L739T


title: singles-SU070-Leuk-14

description: library strategy: scATAC-seq


title: L738T


title: singles-SU070-Leuk-12

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-13

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-11

description: library strategy: scATAC-seq


title: L725T


title: singles-SU070-Leuk-21

description: library strategy: scATAC-seq


title: L723T


title: singles-SU070-Leuk-18

description: library strategy: scATAC-seq


title: L719T


title: singles-SU070-Leuk-3

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-4

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-8

description: library strategy: scATAC-seq


title: singles-SU070-Leuk-6

description: library strategy: scATAC-seq


title: L728T


title: L746T


title: L712T


title: L710T


title: singles-SU070-Leuk-5

description: library strategy: scATAC-seq


title: SU654-LSC

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard input parameters. Aligned reads were filtered for those reads that map uniquely to non-mitochondrial regions.
Duplicate reads (artifacts from amplification) were removed using PICARD MarkDuplicates.
Processed BAM files were analyzed for transcript counts using HTseq against the UCSC refGene transcriptome. Transcript counts were processed using DESeq2, normalizing for both library size and transcript GC content using Conditional Quantile Normalization (Hansen et al., 2012).
Genome_build: hg19
Supplementary_files_format_and_content: Count file is a tab-delimited text file where rows represent unique genes and columns represent unique samples.

extract_protocol:
RNA was isolated from 1,000-100,000 FACS-purified cells using the Qiagen RNeasy Plus Micro Kit
5 ul of total RNA (300 pg – 80 ng) was used as input into the NuGen Ovation V2 cDNA synthesis kit. SPIA-amplified cDNA was sheared using a Covaris S2 sonicator as follows: 10% duty cycle, 5 intensity, 100 cycles/burst, 5 minutes, 120 ul volume. Sheared cDNA was purified and size selected using Ampure XP beads at a 0.9:1 beads:sample ratio. After cleanup, Illumina TruSeq adapters were ligated onto the cDNA using the NEB Next Ultra library prep kit per manufacturer instructions

tag: donorid

tag: sample type

value: primary human leukemia cell from cryopreserved sample


title: SU583-pHSC

source_name: pHSC

value: acute myeloid leukemia, pre-leukemic hematopoietic stem cell


title: singles-SU070-Leuk-2

description: library strategy: scATAC-seq


title: SU583-LSC


title: L703T


title: singles-SU070-Leuk-7

description: library strategy: scATAC-seq


title: SU654-pHSC


title: singles-SU070-Leuk-1

description: library strategy: scATAC-seq


title: L688T


title: L695T


title: L724T


title: SU654-Blast


title: L689T


title: L683T


title: L682T


title: L673T


title: SU496-pHSC


title: L678T


title: L662T


title: L685T


title: L715T


title: SU583-Blast


title: SU575-pHSC


title: SU575-LSC


title: SU575-Blast


title: SU496-LSC


title: L656T


title: L655T


title: SU501-pHSC


title: L668T


title: SU501-Blast


title: L663T


title: L661T


title: L635T


title: L658T


title: 7653-MPP

value: primary human blood cell from fresh sample


title: SU444-pHSC


title: SU444-LSC


title: SU444-Blast


title: L628T


title: L652T


title: SU353-pHSC


title: 7653-MEP

source_name: MEP


title: L650T


title: L626T


title: L621T


title: L638T


title: 7653-HSC


title: SU353-LSC


title: SU353-Blast


title: L644T


title: L832T


title: L642T


title: 7653-GMP

source_name: GMP


title: L619T


title: 7653-CMP

source_name: CMP


title: L617T


title: L616T


title: SU496-Blast


title: 7653-Bcell

source_name: Bcell


title: 7653-CD4Tcell

value: CD4+ T cell


title: L633T


title: 7653-NKcell


title: 7256-MPP

source_name: MPP


title: L606T


title: L608T


title: 7256-MEP


title: L605T


title: 7256-HSC

source_name: HSC


title: L612T


title: L604T


title: 7256-GMP


title: 7653-Mono

source_name: Mono


title: L630T


title: L602T


title: 6926-Ery

value: CD71+GPA+ erythroblast cell


title: 6926-CLP

source_name: CLP

value: common lymphoid progenitor cell


title: L601T


title: 7653-LMPP

source_name: LMPP


title: L596T


title: 6792-Mono

value: CD14+ monocyte cell


title: SU209-LSC


title: SU070-LSC


title: L592T


title: L620T


title: 6792-CMP

value: common myeloid progenitor cell


title: 7653-CD8Tcell

value: CD8+ T cell


title: L613T


title: 7256-Mono


title: L585T


title: L599T


title: L584T


title: 5852-MPP


title: L607T


title: 7256-LMPP

value: lymphoid-primed multipotent progenitor cell


title: 5852-Mono


title: 7256-CMP


title: L582T


title: 6792-MPP

value: multipotent progenitor cell


title: 5852-HSC

value: hematopoietic stem cell


title: L572T


title: 5852-GMP

value: granulocyte macrophage progenitor cell


title: L598T


title: L569T


title: 5852-CMP


title: 6792-MEP

value: megakaryocyte erythroid progenitor cell


title: L568T


title: L567T


title: L593T


title: 6792-HSC


title: L583T


title: L566T


title: 6792-GMP


title: L603T


title: L586T


title: L563T


title: L559T


title: 5483-Ery

source_name: Ery


title: L551T


title: 5852-MEP


title: 2596-CLP


title: L545T


title: 5852-CD4Tcell


title: 5852-CD8Tcell


title: L543T


title: 2596-CD8Tcell


title: L565T


title: 5852-Bcell

value: CD19+CD20+ B cell


title: Treated_2_muscle

description:
Zebrafish mRNA.
Processed data file: muscle_CPM.txt

data_processing:
Sequence quality was assessed using Fastqc QC (v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were trimmed using Trimmomatic (v 0.3; Bolger et al., 2014).
Trimmed reads were aligned to the zebrafish (Danio rerio) transcriptome annotated by Ensembl (version 83) of the GRCz10 genome assembly using RSEM version 1.2.25 (Li and Dewey, 2011) and Bowtie 1.1.2 (Langmead et al., 2009).
Differentially expressed transcripts were determined using R/edgeR version 3.10.2 (Robinson et al., 2010).
Genome_build: Danio rerio GRCz10
Supplementary_files_format_and_content: Tab-delimited text files with read counts (counts per million) per sample.

organism: Danio rerio

source_name: muscle, cortisol

growth_protocol: AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.

extract_protocol:
RNA-EZplus kit from Qiagen.
Illumina TruSeq PolyA+ mRNA libraries.

treatment_protocol: DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development, and then maintained to 4.5 months under normal conditions.

tag: strain/background

value: AB

tag: tissue

value: muscle

value: adult

tag: embryonic treatment

value: cortisol


title: 5483-NKcell

source_name: NKcell

value: CD56+ natural killer cell

value: primary human blood cell from fresh sample


title: 2596-Bcell


title: L561T

value: female


title: 5483-CLP

value: common lymphoid progenitor cell


title: L557T


title: 5483-LMPP


title: 1022-CD8Tcell


title: 2596-NKcell


title: 2596-Ery

value: CD71+GPA+ erythroblast cell


title: Treated_3_blood

description:
Zebrafish mRNA.
Processed data file: blood_CPM.txt

source_name: whole blood, cortisol

value: whole blood


title: Treated_1_muscle


title: L534T

value: male


title: L541T


title: L546T


title: 2596-CD4Tcell

value: CD4+ T cell


title: Control_3_blood

source_name: whole blood, DMSO control

value: DMSO


title: Control_3_muscle

source_name: muscle, DMSO control


title: L529T

source_name: Human NSCLC tissue


title: Control_1_blood


title: Control_2_muscle


title: L511T


title: L539T


title: 1022-NKcell


title: L538T


title: L530T


title: Control_1_muscle


title: L504T


title: Treated_2 caudal_fin_4dpa

description:
Zebrafish mRNA.
Processed data file: fin_CPM.txt

source_name: caudal fin, cortisol, 4dpa

value: caudal fin

tag: days post amputation


title: L535T


title: 1022-CD4Tcell

tag: cell type


title: 1022-Bcell


title: Treated_2_blood


title: L532T

tag: tumor (t) or normal (n)


title: L531T

tag: stage tnm


title: Treated_3_muscle


title: Control_2_blood


title: Control_2 caudal_fin_4dpa

source_name: caudal fin, DMSO control, 4dpa


title: Treated_3 caudal_fin_4dpa


title: Ce

city: Gainesville

first: Eric

middle: T

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Base-calling: Illumina RTA v2
Alignment: Spliced transcripts alignment to a reference (STAR) was used to map reads to the mouse mm9 genome
Mixture-of-isoforms (MISO) was used to quantify splicing regulation.
Genome_build: mm9
Supplementary_files_format_and_content: monotonicTotal.txt: Tab-delimited file summarizing WT1-3 and KO1-3 splicing regulation. Includes chromosomal location of regulated exon (Event), gene symbol (Symb), Number of significant comparisons, Mean number of significant shuffled comparisons, Standard deviation of number of significant shuffled comparisons, WT_psi, KO_psi, difference between WT and KO psi values (delta_psi), and monotonicity score (Z-score).
Supplementary_files_format_and_content: nonUTRevents_819_consolidated.txt:  Tab-delimited file including chromosomal location of regulated exon (event), low confidence interval, mean psi, and high confidence interval of psi for all samples, Bayes Factors for all pair-wise comparisons between samples, name of the gene (gene), gene symbol (symb), and description of gene (desc).

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts (MEF)

growth_protocol: MEF cells were maintained in DMEM supplemented with 20% FBS 5% penicillin/streptomycin, and puromycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from  MEFs using Direct-zol RNA columns (Zymo Research) according to manufacturer's instructions. cDNA libraries were generated starting with 1ug RNA.
RNA was fragmented, depleted of ribosomal RNA using Ribo-Zero-Gold kit (Epicentre), and reverse transcribed followed by end-repair, adenylation, and adapter ligation. Unique barcodes were used for each library to allow for multiplexing all samples in a single lane (80+80 bases, paired-end, NextSeq).

tag: tag

value: Mouse embryonic fibroblasts

tag: genotype/variation

value: lacking MBNL1 and MBNL2 and stably expressing EF1alpha-driven GFP-C. Elegans MBNL1


title: Treated_3 caudal_fin_2dpa

source_name: caudal fin, cortisol, 2dpa


title: L484T

tag: histology

tag: surgery date

tag: gender


title: Hs

value: lacking MBNL1 and MBNL2 and stably expressing EF1alpha-driven GFP-Human MBNL1


title: Treated_2 caudal_fin_2dpa

value: AB


title: L496T

tag: vital date

tag: dead

tag: smoking


title: Treated_1_blood

tag: age


title: Control_3 caudal_fin_4dpa


title: L493T

tag: ps who


title: Treated_1 caudal_fin_4dpa

tag: strain/background


title: Treated_1 caudal_fin_2dpa

tag: tissue


title: L490T


title: DKO Clone 3

description: monotonicTotal.txt

value: lacking MBNL1 and MBNL2


title: Control_3 caudal_fin_2dpa

source_name: caudal fin, DMSO control, 2dpa

value: adult

tag: embryonic treatment


title: Control_1 caudal_fin_4dpa

tag: days post amputation


title: Ci

value: lacking MBNL1 and MBNL2 and stably expressing EF1alpha-driven GFP-C. intestinalis MBNL1


title: Dm

value: lacking MBNL1 and MBNL2 and stably expressing EF1alpha-driven GFP-D. melanogaster MBNL1


title: L483T


title: L488T


title: WT Clone 3

description: monotonicTotal.txt

value: wildtype


title: GFP

value: lacking MBNL1 and MBNL2 and stably expressing EF1alpha-driven GFP


title: L480T

value: female


title: Ta

value: lacking MBNL1 and MBNL2 and stably expressing EF1alpha-driven GFP-Trichoplax MBNL1


title: Treated_3 caudal_fin_0dpa

source_name: caudal fin, cortisol, 0dpa

value: cortisol


title: L468T

value: male


title: Treated_1 caudal_fin_0dpa


title: Treated_2 caudal_fin_0dpa


title: DKO Clone 2

description: monotonicTotal.txt


title: L473T


title: Control_2 caudal_fin_2dpa


title: L472T


title: L466T


title: Lockd promoter Capture, Rep 2

city: Philadelphia

first: Vikram

last: Paralkar

state: PA

address: 3400 Civic Center Boulevard, Perelman Center, 7th Floor, South Pavilion Extension

institute: University of Pennsylvania

description: Capture-C sequencing dataset obtained by Capture of restriction fragment corresponding to Cdkn1b promoter

data_processing:
Library strategy: Capture-C
see Davies et al, Nat Methods 2015, doi:10.1038/nmeth.3664
Genome_build: Mouse mm9
Supplementary_files_format_and_content: bedgraph files - contain Capture-C tracks

source_name: G1E mouse cell line

growth_protocol: G1E cells were grown in regular culture media as published

extract_protocol:
see Davies et al, Nat Methods 2015, doi:10.1038/nmeth.3664
see Davies et al, Nat Methods 2015, doi:10.1038/nmeth.3664

tag: cell line

tag: targeted promoter

value: Lockd


title: DKO Clone 1

description: monotonicTotal.txt


title: Control_1 caudal_fin_2dpa

value: DMSO


title: L471T

tag: tumor (t) or normal (n)

tag: stage tnm


title: Control_2 caudal_fin_0dpa

source_name: caudal fin, DMSO control, 0dpa

value: caudal fin


title: L481T


title: WT Clone 1

description: monotonicTotal.txt

tag: tag

value: Mouse embryonic fibroblasts

tag: genotype/variation


title: L458T

tag: histology

tag: surgery date


title: Cortisol_3

description:
Zebrafish mRNA
Processed data file: larvae_CPM.txt

data_processing:
Sequence quality was assessed using Fastqc QC (v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were trimmed using Trimmomatic (v 0.3; Bolger et al., 2014).
Trimmed reads were aligned to the zebrafish (Danio rerio) genome assembly version Zv9 using TopHat version 2.0.11 (Trapnell et al., 2009).
Read counts per gene generated using HTSeq version 0.6.1 (Anders et al., 2015).
Differentially expressed transcripts were determined using R/edgeR version 3.10.2 (Robinson et al., 2010).
Genome_build: Danio rerio Zv9
Supplementary_files_format_and_content: Tab-delimited text file with read counts (counts per million) per sample.

source_name: whole larvae, cortisol

growth_protocol: Embryos were bred from AB stocks at MDI Biological Laboratory Animal Core and maintained at 28 degrees Celsius.

treatment_protocol: DMSO or cortisol was added to larval medium for first 5 days of development.

value: whole larvae


title: Cortisol_2


title: Cortisol_1


title: DMSO_control_3

source_name: whole larvae, DMSO control


title: Control_3 caudal_fin_0dpa


title: Lockd promoter Capture, Rep 1


title: L464T

tag: gender

tag: vital date


title: Cdkn1b promoter Capture, Rep 2


title: Cdkn1b promoter Capture, Rep 1


title: L462T

tag: dead

tag: smoking


title: Control_1 caudal_fin_0dpa

tag: age


title: L459T

tag: ps who


title: 4dpa mRNA, rep 1

data_processing:
Reads were adapter clipped and quality filtered using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) for small RNA, and Trimmomatic (Bolger et al. Bioinformatics (2010)) for mRNA.
Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner (Wheeler et al. Evol. Dev. (2009)) and miRBase v. 21 (Kozomara et al. Nucleic Acids Res (2014)).
MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR (Robinson et al. Bioinformatics (2010)).
mRNA reads were mapped to the zebrafish transcriptome (Ensembl v. 76 annotation of zebrafish Zv9 assembly) using RSEM (Li and Dewey BMC Bioinformatics (2011)).
Differentially expressed transcripts were determined using R/edgeR.
Genome_build: zv9
Supplementary_files_format_and_content: Tab-delimited text file with read counts per transcript per sample.

source_name: caudal fin

growth_protocol: Adult Ekkwill (EK) zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.

extract_protocol:
Total RNA was isolated using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) following manufacturer’s protocol.
Illumina TruSeq small RNA and strand-specific PolyA+ mRNA libraries.

treatment_protocol: Caudal fins were amputated with scalpels following anesthesia (0.6mM MS222).

tag: tissue

tag: library type

value: mRNA


title: WT Clone 2

description: monotonicTotal.txt


title: DMSO_control_1

tag: strain/background

value: AB

tag: embryonic treatment


title: L470T


title: 0dpa mRNA, rep 3

tag: days post amputation


title: L457T

tag: tumor (t) or normal (n)


title: L441T

tag: stage tnm


title: L455T


title: 0dpa mRNA, rep 2


title: L452T


title: L439T


title: DMSO_control_2


title: L447T


title: 4dpa mRNA, rep 3


title: 4dpa mRNA, rep 2


title: L444T


title: L446T


title: DPZcjESC4, passage 33

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: cell line derived from expanded blastocyst

data_processing:
Fluorescence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with CASAVA (version 1.8.2)
Sequences were aligned to the genome reference sequence of Callithrix jacchus (Ensembl genome assembly 3.2.1). Alignment was performed using the STAR alignment software (version 2.3.0e) allowing for 2 mismatches within 50 bases
Conversion of resulting SAM files to sorted BAM files, filtering of unique hits and counting was conducted with SAMtools (version 0.1.18) and HTSeq (version 0.6.1p1).
Genome_build: C_jacchus3.2.1, INSDC Assembly GCA_000004665.1, Jan 2010
Supplementary_files_format_and_content: Raw Htseq count files using Ensembl genebuild from 2014

organism: Callithrix jacchus

source_name: Preimplantation embryo-derived embryonic stem cells

growth_protocol: Cells were cultured under hypoxic conditions (37°C, 8 % CO2, 5% O2) in ESM [KO-DMEM (Gibco), 20% (v/v) KnockOut™ Serum Replacement (Gibco), 1% (v/v) Penicilline/Streptomycine (Gibco), 0.1% (v/v) Amphotericin B (Gibco), 1% (v/v) MEM Non-Essential Amino Acids Solution (Gibco), 2 mM GlutaMAX (Gibco), 50 µM 2-mercaptoethanol (Gibco)], and medium was changed every two to three days. For passaging of the cells, StemPro® Accutase® (Life Technologies, #A11105-01) was used. Briefly, cells of one well in a six-well plate were washed with PBS and incubated with 1 mL Accutase at 37°C for 4 min. The cell suspension was transferred to 5 mL of pre-warmed ESM and the remaining feeder layer was washed with 3 mL ESM. Cells were pelleted (5 min, 200 x g, RT), resuspended in ESM and seeded onto fresh MEFs.

extract_protocol:
RNA was isolated using Trizol Reagent according to instructions
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

tag: cell type

value: Embryonic stem cells

tag: passage


title: L442T

tag: histology


title: DPZcjESC3, passage 37

description: cell line derived from compacted morula


title: DPZcjESC3, passage 41

description: cell line derived from compacted morula


title: 0dpa mRNA, rep 1


title: L413T

tag: surgery date


title: DPZcjESC4, passage 30


title: DPZcjESC1, passage 51

description: cell line derived from non-compacted morula


title: L417T

tag: gender


title: DPZcjESC2, passage 37


title: L414T

tag: vital date


title: DPZcjESC1, passage 46


title: L406T

tag: dead


title: L400T

tag: smoking


title: L401T

tag: age


title: T47D(PR-deficient)_E2+R5020_45 mins_INPUT_ChIP

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

description: INPUT

data_processing:
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using Bowtie2
The output from Bowtie2 (BAM files) was subjected to MACS14 to call ChIP-seq peaks. Corresponding inputs for each of the treatment conditions were used as the background.
If needed, the ChIP-seq peaks thus obtained were filtered based on false discovery rates and height of the peaks.
Vehicle treated ChIP-peaksets were subtracted from the hormone-treated ChIP-peaksets. For reChIP-seq, the reChIP peaks obtained after vehicle treatment as well as the reChIP peaks observed upon second pulldown with control IgG were used as controls. Hence, both of the reChIP controls were subtracted from the reChIP-signal obtained on joint estradiol plus R5020 treatment.
Genome_build: HG19
Supplementary_files_format_and_content: BED files

source_name: Breast cancer cells

growth_protocol: ChIP-seq and reChIP-seq: Cells were cultured for 48 hours in charcoal-stripped serum media to deprive them of steroids.

extract_protocol:
Hormone-treated were harvested and ChIP was performed as per the directions provided in materials and method (ChIP and ChIP-sequencing; reChIP and reChIP-sequencing)
ChIP-seq and reChIP-seq libraries were prepared using Kapa ChIP-seq kits.
Details of library preparation strategy are provided in the materials and methods section (ChIP and ChIP-seq; reChIP and reChIP-seq) of the paper.

treatment_protocol: Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 45 minutes.

tag: tissue type

value: ER+/PR-deficient cell models

tag: cell line

tag: er/pr status

value: ER+/PR-deficient

tag: drug treatment

value: 10nM Estradiol + 10 nM R5020

tag: hormone exposure time

value: 45 minutes


title: T47D(PR-deficient)_E2_45 mins_INPUT_ChIP

description: INPUT

value: 10 nM Estradiol


title: DPZcjESC2, passage 36


title: L440T

tag: ps who


title: T47D(PR-deficient)_Vehicle_45 mins_INPUT_ChIP

description: INPUT

value: Vehicle


title: T47D_Vehicle_45 mins_INPUT_reChIP

description: INPUT

value: ER+/PR+ cell models

value: ER+/PR+


title: L420T

tag: tumor (t) or normal (n)

value: female


title: T47D(PR-deficient)_R5020_45 mins_INPUT_ChIP

description: INPUT


title: T47D_E2+R5020_45 mins_INPUT_ChIP

description: INPUT


title: T47D_E2_45 mins_INPUT_ChIP

description: INPUT


title: T47D_E2+R5020_45 mins_INPUT_reChIP

description: INPUT


title: T47D_R5020_45 mins_INPUT_ChIP

description: INPUT


title: L404T

tag: stage tnm


title: T47D(PR-deficient)_R5020_45 mins_ER_ChIP

description:
anti-ER (SC biotech HC-20) ChIP
Processed data file: T47D(PR-deficient)_ER_R5020_YC3 (Vehicle subtracted).bed


title: T47D(PR-deficient)_E2+R5020_45 mins_ER_ChIP

description:
anti-ER (SC biotech HC-20) ChIP
Processed data file: T47D(PR-deficient)_ER_E2+R5020_YC4 (Vehicle subtracted).bed


title: ATAC-Seq DKO Act B cell 26276

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
Peaks were called in the doublecrosslinked E2A ChIP-seq sample with a P value of < 10-10 and in the corresponding singlecrosslinked E2A ChIP-seq sample with a P value of < 10-5 by using the MACS program version 1.3.6.1 with default parameters, a genome size of 2,654,911,517 bp (mm9) and a mature B cell input sample (14951). Second, the overlap of the called double- and single-crosslinked peaks was determined with the Multovl program21 by using a minimal overlap length of one and allowing for all possible overlaps, with the results being parsed and converted to tables with custom-made bash, perl and R scripts. The E2A peaks identified by this overlap analysis were then assigned to target genes as described22. For comparisons of E2A ChIP-seq data between different cell types, we down-sampled all reads before peak calling to the ChIP-seq experiment with the lowest number of aligned reads. Thus, samples 22337 and 22338 (FO B cells), 22331 and 22332 (activated B cells, anti-CD40 plus IL-4, 2 days) were down-sampled to 27.1 million reads, and all other samples such as 22327 and 22328 (activated B cells, LPS, 2 days), 22333 and 22334 (pre-plasmablasts, LPS, 4 days), 22335 and 22336 (plasmablasts, LPS, 4 days) were down-sampled to 15.5 million reads.
Concerning the ATAC-seq data, the DHS sites were identified by peak calling using the MACS 2.0.10 program. The peaks from wild-type and DKO cells were compiled. The peak regions were defined as peak summit ± 500 bp. Peaks were assigned to the genes as described for the ChIP-seq analysis. The read density was calculated as RPKM in each peak.
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (ref. 24) with the overlap resolution mode set to ‘union’. The datasets were grouped according to the performed stimulation experiments and analyzed using the R package DESeq2 version 1.4.1 (ref. 25). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. In detail, the following DESeq2 analyses were performed: FO B cell and all anti-CD40 and IL4 stimulation samples were analyzed together considering the genotype, time and genotype over time effects (model design formula: “~ genotype + time + genotype:time”). The genotype over time effect for each day was then tested based on log ratio tests (with a reduced formula of “~ genotype + time). FO B cell and 2 day LPS stimulation data were also grouped and analyzed in the same manner. Three day LPS-stimulated activated B cell (WT and DKO), pre-plasmablast (WT) and plasmablast (WT) samples were considered for sample normalization, dispersion estimation, rlog normalization of the gene counts and the comparison of 3 day LPS-stimulated DKO vs 3 day LPS-stimulated WT activated B cells (Wald test). The 500 most varying rlog normalized counts (option blind) of the 3 day LPS stimulation dataset were used for PCA in Fig. 7d. In general, genes with an adjusted Pvalue < 0.05 and a fold change > 3 as well as a mean RPKM (averaged within conditions) > 3 were called as significantly expressed. Immunoglobulin and T cell receptor genes were filtered from the list of significantly expressed genes and were also disregarded in the RPKM calculations. For the detailed expression analysis of the Igh and Igk loci (Fig. 4 and Supplementary Fig. 8), IghM, IghD, IghG, IghE and IghA were manually curated to provide detailed exon annotations and were split into constant, membrane, secreted, hinge and I exon regions. Ratios between secreted and membrane Igh transcripts were estimated by using the RPKM values of the secreted and membrane regions.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read coverage in reads per million; density bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs; text tab delim = RPKM values in ASCII text format tab delimited

source_name: Act B cell

extract_protocol: phenol-chloroform extraction

tag: strain

tag: genotype

value: Cd23-Cre Tcf3,4(fl/fl)

tag: cell preparation

value: 2-day anti-CD40 rIL-4 stimulation

tag: cell sorting strategy

value: whole population

tag: chip antibody


title: T47D(PR-deficient)_Vehicle_45 mins_ER_ChIP

description: anti-ER (SC biotech HC-20) ChIP


title: ATAC-Seq Act B cell 26275


title: T47D_E2+R5020_45 mins_ERIgG(Control)_reChIP

description:
anti-ER (SC biotech HC-20) ChIP plus anti-IgG Control
reChIP-seq
Processed data file: T47D(reChIP)_ERPRComplexes_E2+R5020_RC3 (subtracted Veh and IgG).bed


title: ATAC-Seq Pre-PB 26500

source_name: Pre-PB

value: 3-day LPS stimulation

value: FSC SSChi CD19+B220+CD22-CD138- FACS-sorted


title: ATAC-Seq DKO Act B cell 26501

value: FSC SSChi CD19+B220+CD22+CD138- FACS-sorted


title: T47D_E2+R5020_45 mins_ERPRComplex_reChIP

description:
anti-ER (SC biotech HC-20) ChIP plus anti-PR (inhouse KD68) ChIP
reChIP-seq
Processed data file: T47D(reChIP)_ERPRComplexes_E2+R5020_RC3 (subtracted Veh and IgG).bed


title: ATAC-Seq Act B cell 26499


title: T47D_Vehicle_45 mins_INPUT_ChIP

description: INPUT


title: H3K27Ac ChIP-Seq HCHO Act B cell 26022

value: 2-day anti-CD40 rIL-4 stimulation whole population

value: H3K27ac (abcam)


title: E2A ChIP-Seq HCHO Mature FO B cell 22338

source_name: FO B cell

value: Ex-vivo, MACS-sorted

value: CD43– and CD23+ MACS-sorted


title: T47D_Vehicle_45 mins_ERPRComplex_reChIP


title: T47D_R5020_45 mins_ER_ChIP

description:
anti-ER (SC biotech HC-20) ChIP
Processed data file: T47D_ER_R5020_WC6 (Vehicle subtracted).bed


title: T47D_E2+R5020_45 mins_ER_ChIP

description:
anti-ER (SC biotech HC-20) ChIP
Processed data file: T47D_ER_E2+R5020_WC8 (Vehicle subtracted).bed

value: 10nM Estradiol + 10 nM R5020


title: E2A ChIP-Seq DSG + HCHO Mature FO B cell 22337


title: E2A ChIP-Seq E2A ChIP-Seq HCHO CD138- 22334

value: 4-day LPS stimulation

value: CD138- MACS-sorted


title: T47D_Vehicle_45 mins_PR_ChIP

description: anti-PR (inhouse KD68) ChIP

value: Vehicle

value: 45 minutes


title: E2A ChIP-Seq DSG + HCHO Act B cell 22331


title: H3K27Ac ChIP-Seq HCHO DKO Act B cell 26023


title: T47D_R5020_45 mins_PR_ChIP

description:
anti-PR (inhouse KD68) ChIP
Processed data file: T47D_PR_R5020_WC5 (Vehicle subtracted).bed

value: ER+/PR+ cell models

value: ER+/PR+


title: T47D_E2+R5020_45 mins_PR_ChIP

description:
anti-PR (inhouse KD68) ChIP
Processed data file: T47D_PR_E2+R5020_WC7 (Vehicle subtracted).bed


title: Cells_MCF7_E2_12 Hours_RNAseq

description: Processed data file: MCF7.csv

data_processing:
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using TopHat.
Relative expression of transcripts were calculated by subjecting TopHat output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
Supplementary_files_format_and_content: CSV includes RPKM values for each each of the treatment conditions (E2, R5020 or E2+R5020) versus control treatment. Union of all estrogen and progestin-regulated genes for the respective samples is provided.

growth_protocol: Cell models RNA-seq: Cells were cultured for 48 hours in charcoal-stripped serum media to deprive them of steroids.

extract_protocol:
Hormone-treated cells were homogenized and total RNA was extracted using Qiagen RNAeasy kit
PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit.
Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper.

treatment_protocol: Steroid-deprived cell models were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 12 hours.

value: ER+/PR-deficient cell models

value: ER+/PR-deficient

value: 10 nM Estradiol

value: 12 hours


title: E2A ChIP-Seq HCHO PB 22336

source_name: PB

value: CD138+ MACS-sorted


title: E2A ChIP-Seq DSG + HCHO PB 22335


title: Cells_MCF7_Vehicle_12 Hours_RNAseq

description: Processed data file: MCF7.csv


title: T47D_E2_45 mins_ER_ChIP

description:
anti-ER (SC biotech HC-20) ChIP
Processed data file: T47D_ER_E2_WC4 (Vehicle subtracted).bed


title: Cells_T47D(PR-deficient)_R5020_12 Hours_RNAseq

description: Processed data file: PR-deficient T47D.csv


title: Cells_T47D(PR-deficient)_E2_12 Hours_RNAseq


title: E2A ChIP-Seq DSG + HCHO CD138- 22333


title: RNA-seq DKO Act B cell 26457

description: SuperScript® VILO™ cDNA Synthesis, strand-specific

extract_protocol: Rneasy Plus Mini Kit, Dynabeads mRNA purification kit

value: Cd23-Cre Tcf3,4(fl/fl)

value: 3-day LPS stimulation

value: FSC SSChi CD19+B220+CD22+CD138- FACS-sorted


title: T47D_Vehicle_45 mins_ER_ChIP

description: anti-ER (SC biotech HC-20) ChIP


title: T47D_Vehicle_45 mins_ERIgG(Control)_reChIP


title: T47D(PR-deficient)_E2_45 mins_ER_ChIP

description:
anti-ER (SC biotech HC-20) ChIP
Processed data file: T47D(PR-deficient)_ER_E2_YC2 (Vehicle subtracted).bed


title: E2A ChIP-Seq HCHO Act B cell 22332

value: 2-day anti-CD40 rIL-4 stimulation whole population

value: whole population


title: Cells_MCF7_E2+R5020_12 Hours_RNAseq

description: Processed data file: MCF7.csv

value: 10nM Estradiol + 10 nM R5020


title: Cells_MCF7_R5020_12 Hours_RNAseq

description: Processed data file: MCF7.csv


title: E2A ChIP-Seq HCHO Act B cell 22328

value: 2-day LPS stimulation whole population


title: RNA-seq PB 26453

value: FSC SSChi CD19+B220+CD22-CD138+ FACS-sorted


title: E2A ChIP-Seq DSG + HCHO Act B cell 22327


title: Cells_T47D_siFOXA1_R5020_12 Hours_RNAseq

description:
mRNA-seq (knockdown)
Processed data file: T47D_siFOXA1_annotated100kb.csv


title: RNA-seq DKO Act B cell 26458


title: T47D_E2_45 mins_PR_ChIP

description:
anti-PR (inhouse KD68) ChIP
Processed data file: T47D_PR_E2_WC3 (Vehicle subtracted).bed


title: Cells_T47D(PR-deficient)_E2+R5020_12 Hours_RNAseq


title: RNA-seq DKO Act B cell 22854

value: 4-day LPS stimulation


title: Cells_T47D_siNF1C_E2+R5020_12 Hours_RNAseq

description:
mRNA-seq (knockdown)
Processed data file: T47D_siNF1C.csv


title: Cells_T47D_siNF1C_R5020_12 Hours_RNAseq


title: Cells_T47D_siNF1C_Vehicle_12 Hours_RNAseq

value: Vehicle


title: RNA-seq PB 26456


title: RNA-seq Pre-PB 26455

value: FSC SSChi CD19+B220+CD22-CD138- FACS-sorted


title: Cells_T47D(PR-deficient)_Vehicle_12 Hours_RNAseq


title: Cells_T47D_siFOXA1_E2_12 Hours_RNAseq

value: ER+/PR+ cell models

value: ER+/PR+


title: RNA-seq Act B cell 26451


title: Cells_T47D_siControl_E2_12 Hours_RNAseq

description:
mRNA-seq (knockdown)
Processed data file: T47D_siControl.csv


title: Cells_T47D_siFOXA1_Vehicle_12 Hours_RNAseq


title: RNA-seq Act B cell 26454


title: RNA-seq DKO Act B cell 22855


title: Cells_T47D_siFOXA1_E2+R5020_12 Hours_RNAseq


title: RNA-seq PB 22851


title: Cells_T47D_siNF1C_E2_12 Hours_RNAseq


title: RNA-seq DKO Act B cell 21159

value: 2-day LPS stimulation

value: CD19+B220+FSC SSChiCD25+ GFP+ FACS-sorted


title: RNA-seq Act B cell 21157

value: CD19+B220+FSC SSChiCD25+ GFP- FACS-sorted


title: RNA-seq Act B cell 22849


title: Cells_ZR75_E2_12 Hours_RNAseq

description: Processed data file: ZR75.csv

value: 10 nM Estradiol

value: 12 hours


title: Cells_ZR75_Vehicle_12 Hours_RNAseq

description: Processed data file: ZR75.csv


title: Cells_ZR75_R5020_12 Hours_RNAseq

description: Processed data file: ZR75.csv


title: Cells_T47D_siControl_E2+R5020_12 Hours_RNAseq


title: RNA-seq PB 22848


title: RNA-seq Act B cell 22846


title: RNA-seq Pre-PB 22850


title: RNA-seq Pre-PB 26452

value: 3-day LPS stimulation


title: RNA-seq Pre-PB 22847


title: Cells_T47D_siControl_Vehicle_12 Hours_RNAseq


title: Cells_T47D_R5020_12 Hours_RNAseq

description: Processed data file: T47D.csv


title: RNA-seq Act B cell 16193

value: 3-day anti-CD40 rIL-4 stimulation

value: CD19+B220+FSC SSChiGFP- FACS-sorted


title: RNA-seq DKO Act B cell 21160

value: Cd23-Cre Tcf3,4(fl/fl)


title: Cells_ZR75_E2+R5020_12 Hours_RNAseq

description: Processed data file: ZR75.csv

value: 10nM Estradiol + 10 nM R5020


title: RNA-seq DKO Act B cell 16196

value: 2-day anti-CD40 rIL-4 stimulation

value: CD19+B220+FSC SSChiGFP+ FACS-sorted


title: RNA-seq Act B cell 21158


title: Cells_T47D_siControl_R5020_12 Hours_RNAseq


title: RNA-seq DKO Act B cell 16194


title: Cells_T47D_E2_12 Hours_RNAseq

description: Processed data file: T47D.csv


title: RNA-seq Act B cell 16192


title: Cells_T47D_E2+R5020_12 Hours_RNAseq

description: Processed data file: T47D.csv


title: Tumor_N4_R5020_24 Hours_RNAseq

description: Processed data file: Tumor N4.csv

growth_protocol: Tumor explants: Within one hour of surgery, sliced pieces of tumors were incubated on gelatin sponges for 36 hours in charcoal-stripped serum media. Representative pieces of tumors were in parallel fixed in 4% formalin and subsequently immunohistochemistry for ER and PR protein was performed to assess the status of tumors for these receptors.

extract_protocol:
Hormone-treated explant was homogenized and total RNA was extracted using Qiagen RNAeasy kit
PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit.
Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper.

treatment_protocol: Steroid-deprived tumor explants were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 24 or 48 hours. Finer details are provided in materials and methods section (Patient tumor explants)

value: ER+/PR- Human tumor explants

value: ER+/PR-

value: 24 Hours


title: Cells_T47D_Vehicle_12 Hours_RNAseq

description: Processed data file: T47D.csv

value: ER+/PR+ cell models

value: Vehicle


title: L456T

source_name: Human NSCLC tissue

tag: histology

tag: surgery date

tag: gender

value: male

tag: vital date


title: RNA-seq DKO Act B cell 16198


title: Tumor_N4_E2+R5020_24 Hours_RNAseq

description: Processed data file: Tumor N4.csv

tag: tissue type


title: RNA-seq DKO Act B cell 14714

value: 1-day anti-CD40 rIL-4 stimulation


title: RNA-seq Act B cell 14712


title: Tumor_N4_Vehicle_24 Hours_RNAseq

description: Processed data file: Tumor N4.csv


title: Tumor_N3_R5020_48 Hours_RNAseq

description: Processed data file: Tumor N3.csv

value: 48 Hours


title: Tumor_N3_E2_48 Hours_RNAseq

description: Processed data file: Tumor N3.csv

value: 10 nM Estradiol


title: RNA-seq DKO Act B cell 16195


title: RNA-seq Act B cell 16190


title: Tumor_N4_E2_24 Hours_RNAseq

description: Processed data file: Tumor N4.csv


title: RNA-seq Act B cell 16189


title: Tumor_N3_E2+R5020_48 Hours_RNAseq

description: Processed data file: Tumor N3.csv


title: Tumor_N3_Vehicle_48 Hours_RNAseq

description: Processed data file: Tumor N3.csv


title: Tumor_N2_E2+R5020_48 Hours_RNAseq

description: Processed data file: Tumor N2.csv


title: RNA-seq DKO Mature FO B cell 16188

value: Ex-vivo, FACS-sorted

value: CD19+B220+IgD+GFP+ FACS-sorted


title: RNA-seq DKO Act B cell 14715


title: RNA-seq DKO Mature FO B cell 16187


title: Tumor_N2_R5020_48 Hours_RNAseq

description: Processed data file: Tumor N2.csv


title: Tumor_N2_E2_48 Hours_RNAseq

description: Processed data file: Tumor N2.csv


title: RNA-seq Mature FO B cell 16186

value: CD19+B220+IgD+GFP- FACS-sorted


title: RNA-seq Mature FO B cell 16185


title: Tumor_N2_Vehicle_48Hours_RNAseq

description: Processed data file: Tumor N2.csv