title: sample Cov14, plate 4


title: sample Cov12, plate 4

status: Public on Sep 29 2021

type: SRA

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

country: USA

institute: University of Massachusetts Medical School

library_source: transcriptomic

data_processing:
Convert paired-end reads to single-ended, extracting the 12-base cell barcode and 8-base unique molecule identifier (UMI) from R1 read and appending them to the R2 read name as a colon-separated pair. Reads with Ns in either the cell barcode or UMI are discarded. (custom Python script)
Align reads to human hg38 genome, with GENCODE v28 gene annotations. (tophat2 v2.0.12)
Quantify transcript counts using GENCODE v28 gene annotations. (ESAT v1.0, https://github.com/garber-lab/ESAT)
Build t-SNE map of all cells (custom R script, using the dim_reduce() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Density-based clustering (custom R script, using the cluster_sc() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Cell type identification (custom R script based on density-based cluster boundaries and known marker genes to identify major cell types)
Viral transcript counting - NCBI magic-blast (https://ncbi.github.io/magicblast/) of all transcript sequence reads against all Influenza A and SARS-CoV2 genomes in the NCBI virus database as of 1 Agust 2020, followed by a custom Python script to quantify the number of unique viral transcripts in each cell, using UMIs to remove PCR duplicates.
Genome_build: hg38
Supplementary_files_format_and_content: raw transcript counts from ESAT.: 41442 genes x 29406 cell transcript counts matrix
Supplementary_files_format_and_content: per-cell phenotype information: 29406 cell x 13 column cell phenotype information. Columns: sampID (sample ID prefix), plateID (Seq-Well plate ID, 4 or 5 for each sample), status (disease status: COVID-19, fluA, healthy), donorID (unique ID for each donor), cDate (sample collection date), age (donor age), sex (donor sex - M or F), tSNE1, tSNE2 (t-SNE mapping coordinates), group (major cell type group), cellType (assigned cell type), SARS.CoV.2 (SARS-CoV2 virus transcript count), fluA (influenza A virus transcript count)

molecule: polyA RNA

organism: Homo sapiens

source_name: saline nasal wash

extract_protocol: Seq-Well S^3 Master Protocol (June 2019) (http://shaleklab.com/wp-content/uploads/2019/07/SeqWell-S3-Protocol.pdf)

tag: disease state


title: TH890

type: RNA

city: Homburg Saar

first: Masood

last: Abu-Halima

address: Kirrberger St 60

department: Human Genetics

country: Germany

institute: Univeristy of Saarland

description: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent.

molecule: total RNA

source_name: Blood/PAXgene

extract_protocol: Total RNA including miRNAs was isolated using the PAXgene™ Blood miRNA Kit on the QIAcube™ robot

tag: desease state

tag: age

tag: gender

value: Male


title: TH596

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations


title: TH583

label_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

value: Female


title: ChIP-Med1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

country: China

institute: Fudan University

library_source: genomic

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 with default parameters (Langmead and Salzberg, 2012).
All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The number of spike-in mm10 reads was counted with SAMtools v1.9 and normalization factor alpha = 1e6/mm10_count was calculated (Li et al., 2009).
Normalized bigwig was generated with deeptools v3.5.0 and reads mapped to the ENCODE blacklist regions were removed using bedtools v2.29.2 (Amemiya et al., 2019; Quinlan and Hall, 2010; Ramirez et al., 2016).
Peaks were called using macs2 v2.2.6 with a q-value threshold of 0.05 and peak annotation was performed with ChIPseeker R package v1.24.0 (Yu et al., 2015; Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: SPT5-dTAG DLD1

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
Lysates were clarified from sonicated cells and INTAC-DNA complexes were isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: One replicate was DMSO or dTAG treated for 3 hours.

tag: cell type

value: colorectal adenocarcinoma cell lines

tag: chip antibody

tag: treatment

value: treated with dTAG13 for 3 hours


title: TH533


title: sample Cov12, plate 3


title: sample Cov14, plate 3


title: ChIP-RPB1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1

value: untreated


title: TH553


title: sample Cov14, plate 1


title: ChIP-Med1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: Swr1_control_rep2

city: Daejeon

first: Hyelim

last: Jo

address: 335 Gwahangno, Yuseong-Gu

department: Biological science

country: South Korea

institute: KAIST

description:
Hi-C
all_Min_swr1_no_5000.cool

data_processing:
HiCPro pipeline (PMID26619908)
Convert .cool format using HiCExplorer (PMID29335486)
Genome_build: SaCcer3
Supplementary_files_format_and_content: 5kb resolution cool matrix

organism: Saccharomyces cerevisiae

growth_protocol: After 3hr of pre-incubation step, the yeast culture was diluted to 0.2 O.D. and treat auxin (+IAA) or ethanol and incubate for 3hr at 30℃.

extract_protocol:
Total 50 O.D.600 of final 3% formaldehyde fixed yeast cells was cultured and pre-incubated with β-ME buffer (20mM EDTA, 0.7M β-ME) for 10min at 30℃. The yeast cell pellet permeabilized with 2mg of zymolyase (USbiological, Z1004) with 2ml lyticase buffer (1M sorbitiol, 50mM Tris-Cl (pH 8.0), 5mM β-ME) for 20min at 30℃. The obtained spheroplast was re-suspended into 2ml of ice-cold PBS.
in situ Hi-C library preparation was performed as previously reported (PMID:25497547), with some modifications in yeast nucleus isolation steps. The generated libraries sequenced using 150bp paired-end reads on Novaseq6000 and/or HiSeqX.

treatment_protocol: Final conc. 0.5mM of auxin (+IAA) or same volume of 100% ethanol(Con.) was treated.

value: control

tag: strain


title: sample Cov12, plate 2


title: Swr1_control_rep1

description:
Hi-C
all_Min_swr1_no_5000.cool


title: sample Cov12, plate 1


title: ChIP-Input_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2

value: input


title: Swr1+IAA_rep2

description:
Hi-C
all_Min_swr1_IAA_5000.cool

value: 0.5mM IAA


title: ChIP-Med1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: TH510


title: sample Cov10N, plate 2


title: sample Cov10N, plate 4


title: TH513


title: Swr1+IAA_rep1

description:
Hi-C
all_Min_swr1_IAA_5000.cool


title: sample Cov10N, plate 3


title: TH497


title: ChIP-Input_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: TH491


title: ChIP-Input_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: TH505


title: TH490


title: ChIP-Input_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: Sth1_control_rep1

description:
Hi-C
all_Min_sth1_no_5000.cool


title: ChIP-H3K27ac_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: sample Cov06, plate 2


title: sample Cov06, plate 1


title: ChIP-H3K27ac_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: sample Cov06, plate 3


title: ChIP-H3K27ac_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: Isw2_control_rep2

description:
Hi-C
all_Min_isw2_no_5000.cool


title: ChIP-H3K27ac_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: Sth1+IAA_rep1

description:
Hi-C
all_Min_sth1_IAA_5000.cool


title: sample Cov05, plate 4


title: sample Cov06, plate 4


title: TH475


title: sample Cov10N, plate 1


title: sample Cov05, plate 3


title: sample Cov05, plate 2


title: TH467


title: TH479


title: Sth1+IAA_rep2

description:
Hi-C
all_Min_sth1_IAA_5000.cool


title: Isw2_control_rep1

description:
Hi-C
all_Min_isw2_no_5000.cool


title: Sth1_control_rep2

description:
Hi-C
all_Min_sth1_no_5000.cool


title: TH466


title: Isw2+IAA_rep2

description:
Hi-C
all_Min_isw2_IAA_5000.cool


title: ChIP-Flag-SPT5_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2

value: Flag


title: sample Cov05, plate 1


title: ChIP-Flag-SPT5_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: ChIP-Flag-SPT5_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: Isw1_control_rep2

description:
Hi-C
all_Min_isw1_no_5000.cool


title: Isw2+IAA_rep1

description:
Hi-C
all_Min_isw2_IAA_5000.cool


title: TH473


title: ChIP-Flag-SPT5_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: TH451


title: TH454


title: Isw1+IAA_rep2

description:
Hi-C
all_Min_isw1_IAA_5000.cool


title: TH476


title: Isw1+IAA_rep1

description:
Hi-C
all_Min_isw1_IAA_5000.cool


title: ChIP-BRG1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: Ino80_control_rep2

description:
Hi-C
all_Min_ino80_no_5000.cool


title: TH396


title: sample Cov04, plate 2


title: TH446


title: Ino80+IAA_rep2

description:
Hi-C
all_Min_ino80_IAA_5000.cool


title: sample Cov04, plate 1


title: Ino80_control_rep1

description:
Hi-C
all_Min_ino80_no_5000.cool


title: sample HC36, plate 5

value: healthy


title: Isw1_control_rep1

description:
Hi-C
all_Min_isw1_no_5000.cool


title: Ino80+IAA_rep1

description:
Hi-C
all_Min_ino80_IAA_5000.cool


title: shRING1B_E2_4Cseq_GREB1

city: Miami

first: Lluis

last: Morey

state: FL

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

data_processing:
Library strategy: 4C-seq
ATAC-seq: Paired-end ATAC-seq fastq files were processed using the ATAC-seq Pipeline from the Kundaje Lab (https://github.com/kundajelab/atac_dnase_pipelines). Reads were trimmed using cutadapt v1.9.1 using the following parameters: -m 5. Reads were aligned to the hg19 genome using Bowtie2 v2.2.6, and the SAMtools v1.7 was used to convert the output files into the BAM format using default parameters. Duplicate reads were removed using Picard tool v1.126 using default parameters. Peaks were called using MACS2 v2.1.0 using default parameters
ChIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
DRIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 using the "histone" setting, and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Besides using the "histone" setting, all other parameters used default values.
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq). Reads were trimmed using cutadapt v2.3 with the following parameters: -j 4 --netseq-trim=20 -m 18. Reads were aligned to the hg19 genome using STAR v2.6.1a along default parameters, and RSEM v1.3.0 was used to obtain the expected gene counts against the human refseq also along default parameters.
RNA-seq differential expression was determined using DESeq2 v1.18.1 and R (version 3.4.1) with q-value <0.05. Ruvseq v1.12.0 was used for factor analysis to remove count based on ERCC spike-in. GSEA analysis was performed using gsea-3.0.jar. These additional analysis steps were included in the Diderote LSF-RNAseq Pipeline.
4C-seq: The raw sequencing reads in fastq files are first trimmed to a fixed length (i.e., 36). The 4Cseqpipe [van de Werken et al, 2012] was used  to generate domainograms. The trimmed sequences was mapped to the human genome (build: hg19). The following parameters are used to generate final domainograms: "-nearcis -calc_from 11580000 -calc_to 11780000 -stat_type median -trend_resolution 5000.
Homer annotatePeaks v4.8.3 was used for peak  annotation and for assigning peaks to genes.
Bedtools v2.29.0 intersect was used to determine peak overlaps.
Genome_build: hg19
Supplementary_files_format_and_content: domainogram

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to 45 minutes of E2 treatment, at which point the cells were crosslinked for 4C-seq

extract_protocol:
4C-seq was performed following Brouwer et al. 2017 (16). Specifically, 8-10 x 10^6 cells from each experimental condition were resuspended in 10ml of culture media and 1ml of 16% methanol-free formaldehyde (Thermo Fisher Scientific 28908) was added to the cell suspension for a final concentration of 1.45% to crosslink the cells at room temperature for 10min. The crosslinking reaction was quenched with 575ml of 2.5M glycine (Sigma-Aldrich G8898). The cells were then centrifuged for 8min at 340 x g at 4°C before being lysed 10-15min on ice in 5ml of prechilled lysis buffer (10mM tris-HCl pH 8, 10mM NaCl, 0.2% NP-40) supplemented with protease inhibitors (Sigma-Aldrich S8830). Nuclei from the lysed cells were pelleted by centrifuging at 650 x g at 4°C for 5min, washed with 1x PBS, and aliquoted into 4-5 x 106 nuclei pellets before flash freezing and storing at -80°C. One aliquot of each experimental condition was resuspended in 0.5 ml of 1.2x buffer B (Thermo Fisher Scientific BB5) followed by incubation with 15ml of 10% SDS then with 50 ml of 20% Triton X-100, each for 1h at 37°C with gentle agitation at 900rpm. A 10ml aliquot was removed and stored at -20°C prior to chromatin digestion with 400U of CviQI (Thermo Fisher Scientific ER0211) overnight at 37°C and gentle agitation at 900rpm. A 10ml aliquot was removed prior to decrosslinking with 10ml of proteinase K (NEB P8107S) and 10mM tris-HCl pH 8 at 37°C for 1h in a final volume of 100ml. Digestion efficiency was determined by running 20ml of the pre- and post-digestion samples on a 0.6% agarose gel. If a smear was observed, CviQI was heat inactivated by incubating at 65°C for 20min.
To finish generating the 3C library, the samples were transferred to a 50ml tube for ligation overnight at 16°C with 6.125ml of 1.15x T4 ligation buffer (NEB B0202S) and 100U of T4 DNA ligase (NEB M0202L). Next, samples were decrosslinked with 30ml of proteinase K at 65°C for at least 4h and treated with 30ml of RNase A (10mg/ml, Thermo Fisher Scientific AM9780) for 30min at 37°C. After cooling the samples down to room temperature, 7ml of phenol/chloroform/isoamyl alcohol (Thermo Fisher Scientific 15-593-049) was added and samples were shaken vigorously then centrifuged at 3200 x g for 15min. The upper aqueous layer was transferred to a new 50ml tube to which 7ml of water, 1.5ml of 3M sodium acetate (pH 5.4), and 35ml of 100% ethanol were added. The samples were frozen at -80°C for 2h then centrifuged at 3200 x g at 4°C for 45min and washed with 10ml of 70% ethanol. After air drying the pellets, they were resuspended in 150ml of 10mM Tris-HCl, pH 8. Ligation efficiency was determined by running 5ml of 3C material on a 0.6% agarose gel, and a significant upward shift in the digested DNA should be observed. To generate the 4C library from the 3C material, the 3C library was digested with 50U of MboI (NEB R0147L) in a 500ml reaction overnight. A 10ml aliquot was removed from the reaction to determine digestion efficiency on a 1.5% agarose gel. If digestion was successful (the DNA appears as a smear of fragments smaller than 1000bp), the reaction was heat inactivated for 20min at 65°C. Next, samples were transferred to a 50ml tube to which 1.4ml of 10x T4 DNA ligase buffer, 200U of T4 DNA ligase, and water up to 14ml were added before ligation at 16°C overnight. The samples were then precipitated with 14ml of glycogen (Thermo Fisher Scientific R0561), 1.4ml of 3M sodium acetate (pH 5.4), and 35ml of 100% ethanol at -80°C for 2h. The samples were pelleted at 3200 x g for 45min and washed with 10ml of 70% ethanol before air drying and resuspending in 150ml of 10mM Tris-HCl, pH 7.5. The DNA samples were purified using the QIAquick PCR Purification Kit (Qiagen 28106) following the manufacturer’s protocol, and the concentration was measured via nanodrop. To amplify the DNA template and generate the 4C library, 3 equivalent PCR reactions with 200ng of input 4C material were ran simultaneously using the Expand Long Template PCR System (Sigma-Aldrich 11681842001) and 5ml from each reaction was ran on a 1.5% agarose gel to verify the success of the reaction. All successful reactions were combined and purified using the High Pure PCR Product Purification Kit (Sigma-Aldrich 11732676001) and analyzed on an Agilent Tapestation using the D5000 ScreenTape, reagents, and ladder (Agilent 5067-5588, 5067-5589, 5067-5590, respectively). The 4C libraries were sequenced (75bp, single-end) on an Illumina NovaSeq 6000 instrument for a total of 1 million reads per sample.

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-133

tag: modifications

value: pLKO-shRING1B stable


title: sample Cov04, plate 3


title: sample Cov04, plate 4


title: TH430


title: sample HC36, plate 2


title: TH427


title: TH395


title: ChIP-BRG1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: shRING1B_HD_4Cseq_GREB1


title: ChIP-BRG1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: TH383


title: ChIP-BRG1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: sample HC36, plate 4


title: Fun30_control_rep2

description:
Hi-C
all_Min_fun30_no_5000.cool


title: shCtrl_HD_4Cseq_GREB1

value: pLKO-shCtrl stable


title: TH370


title: Fun30_control_rep1

description:
Hi-C
all_Min_fun30_no_5000.cool


title: sample HC36, plate 1


title: Fun30+IAA_rep2

description:
Hi-C
all_Min_fun30_IAA_5000.cool


title: shCtrl_E2_4Cseq_GREB1


title: sample HC36, plate 3


title: Chd1_control_rep2

description:
Hi-C
all_Min_chd1_no_5000.cool


title: Chd1_control_rep1

description:
Hi-C
all_Min_chd1_no_5000.cool


title: sample HC33, plate 2


title: sample HC33, plate 3


title: Chd1+IAA_rep2

description:
Hi-C
all_Min_chd1_IAA_5000.cool


title: sample HC33, plate 1


title: sample HC27, plate 5


title: rep1_shCtrl_E2_rnaseq

data_processing:
ATAC-seq: Paired-end ATAC-seq fastq files were processed using the ATAC-seq Pipeline from the Kundaje Lab (https://github.com/kundajelab/atac_dnase_pipelines). Reads were trimmed using cutadapt v1.9.1 using the following parameters: -m 5. Reads were aligned to the hg19 genome using Bowtie2 v2.2.6, and the SAMtools v1.7 was used to convert the output files into the BAM format using default parameters. Duplicate reads were removed using Picard tool v1.126 using default parameters. Peaks were called using MACS2 v2.1.0 using default parameters
ChIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
DRIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 using the "histone" setting, and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Besides using the "histone" setting, all other parameters used default values.
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq). Reads were trimmed using cutadapt v2.3 with the following parameters: -j 4 --netseq-trim=20 -m 18. Reads were aligned to the hg19 genome using STAR v2.6.1a along default parameters, and RSEM v1.3.0 was used to obtain the expected gene counts against the human refseq also along default parameters.
RNA-seq differential expression was determined using DESeq2 v1.18.1 and R (version 3.4.1) with q-value <0.05. Ruvseq v1.12.0 was used for factor analysis to remove count based on ERCC spike-in. GSEA analysis was performed using gsea-3.0.jar. These additional analysis steps were included in the Diderote LSF-RNAseq Pipeline.
Homer annotatePeaks v4.8.3 was used for peak  annotation and for assigning peaks to genes.
Bedtools v2.29.0 intersect was used to determine peak overlaps.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shCtrl, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to 45 minutes of E2 treatment, at which point the cells were collected for RNA extraction

extract_protocol:
RNA was isolated from frozen cell pellets using the TRIzol reagent (Thermo Fisher Scientific cat# 15596018) according to manufacturer's instructions. RNA quantity was measured on a nanodrop, and RNA was diluted to 100 ng/ul or less. A total of 1.5 ug to 2 ug of RNA in 20 ul of nuclease-free water was treated using the TURBO DNA-free Kit (Thermo Fisher AM1907) along the Routine DNase treatment guideline.
Library preparation was performed on Dnase-treated RNA using the Illumina Truseq Stranded Total RNA Library Kit (Illumina 20020596). The Truseq RNA UD Indexes were used for the adapter ligation step (Illumina 20020591). Samples were normalized to a concentration of 250 ng for input, and 1 ul of ERCC spike-in Mix 1 (Thermo Fisher 4456740) diluted 1:200 was added to the samples. Minor protocol modifications were made: 1) during the "Elution 2 - Frag - Prime" step, samples were incubated for 6 minutes at 94°C instead of the listed 8 minutes, and 2) 10 cycles were used in the amplification step under the "Enrich RNA Fragments" section instead of the suggested 15 cycles.


title: rep2_shRING1B_HD_rnaseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to being collected for RNA extraction


title: sample HC33, plate 4


title: rep2_shCtrl_E2_rnaseq


title: rep2_shRING1B_E2_rnaseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to 45 minutes of E2 treatment, at which point the cells were collected for RNA extraction


title: rep1_shRING1B_E2_rnaseq


title: rep2_shCtrl_HD_rnaseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shCtrl, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to being collected for RNA extraction


title: HT9L: Tibetan placenta miRNA

city: xining

first: Tanna

last: Wuren

address: Kunlun Road No.16

institute: Qinghai University

description: miRNA  expression data from  Tibetan placenta

hyb_protocol: Before using 20X Eukaryotic Hybridization Controls for the first time, confirm whether  denatured at 65℃ for 5min has been performed. The hybridization solution was incubated in a constant temperature metal bath at 99°C for 5 min, and then 45°C for 5 min. The hybrid solution was removed from the thermostatic metal bath and centrifuged for 5 min at 13200rpm in a miniature centrifuge to remove insoluble substances in the hybrid mixture. Hybridized was preformed in a Agilent Hybridization Oven for 16hr at a rotation speed of 60 rpm at 48℃.

scan_protocol: Scanned on Affymetrix GeneChip Scanner 3000

data_processing: AGCC Software (Affymetrix® GeneChip® Command Console® Software) converts.DAT files from image signals to digital signals known as.CEL files. CEL files record probe level fluorescent signals

label: biotin

source_name: placenta

label_protocol: Starting from Total RNA, poly A tail was attached to the 3 'end of the small RNA under the guidance of poly A polymerase. Under the guidance of ligase, biotin labeled patented 3DNA Dendrimer was attached to the poly A tail of RNA.

extract_protocol: Total RNA from placentas was isolated using RNeasy Mini Kits according to the manufacturer’s instructions. RNA quantity was determined using an Agilent Bioanalyzer.Total RNA from placentas was purified using mirVanaTM miRNA Isolation Kits  and quantified.

tag: tissue

value: Placenta

tag: population

value: Tibetan


title: HT8L: Tibetan placenta miRNA


title: rep1_shRING1B_HD_rnaseq


title: HT7L: Tibetan placenta miRNA


title: HT10L: Tibetan placenta miRNA


title: Fun30+IAA_rep1

description:
Hi-C
all_Min_fun30_IAA_5000.cool


title: sample HC27, plate 4


title: rep1_shCtrl_HD_rnaseq


title: HT5L: Tibetan placenta miRNA


title: Chd1+IAA_rep1

description:
Hi-C
all_Min_chd1_IAA_5000.cool


title: sample HC27, plate 3


title: Piglet_18

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
The quality of raw sequences was checked with FastQC. The sequences were subjected to quality control using Trimmomatic.
The reads were then mapped to the pig reference genome Sscrofa11.1 using Hisat2 aligner.
The number of reads that mapped to the annotated genes (Ensembl annotation, Sus_scrofa.Sscrofa11.1.104.gtf) in each sample was determined from the sequence alignments by using the FeatureCounts tool.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Read count data in tab-limited text files. The 'counts_gene_wise' file contains number reads that map to each gene. The 'counts_exon_wise' file contains number reads that map to each exon. The 'counts_transcript_wise' file contains number reads that map to each trnascript.

organism: Sus scrofa

source_name: Fetal brain

growth_protocol: The gilts (Landrace x Large White) were obtained from the University of Missouri Swine Research Teaching and Research Farm, and bred to LR-M6 from Choice Genetics by artificial insemination (AI). Gestation day 1 (GD1) was considered the day of AI. Dams were euthanized on GD45, GD60 or GD90 via electrical stunning and exsanguination at the University of Missouri abattoir, an USDA inspected commercial unit (Establishment #5077A). The reproductive tract was removed from the pregnant dam at the abattoir, and transported to the lab for dissection. Individual fetuses of both sexes were removed from each uterine horn. No fetuses were taken from the tip of either horn or the body of the uterus. While collecting fetuses, the sex of the fetus taken for collection (analyzed in the current study) was recorded first followed by the sex of the fetus on the medial side (closer to the body of the uterus) and lastly the sex of the fetus on the lateral side (closer to the tip of the uterus horn). For example, the representation of sequence of fetal sexes as F.F.M means that we collected a female fetus where there was another female fetus on the medial side and a male fetus on the lateral side. Each fetus was weighed. The skin and skull were cut down the mid-sagittal plane with a scalpel and removed near the ears. The whole brain of each fetus was dissected. The weight of the dissected brain was recorded. Also, the longest distance of each brain was measured. In total, 18 fetal brain samples (3 gestation days x 2 sexes x 3 biological replicates) were collected.

extract_protocol:
Each fetal brain was homogenized with RLT buffer (Qiagen, Cat No./ID: 79216) and 200ul 2-mercaptoethanol. The RLT buffer amount was scaled up by 1ml per each mg of brain weight across all samples, and the brain tissue was homogenized using a benchtop VDI 25 tissue homogenizer (VWR). Total RNA from the brain samples was isolated from the brain samples using AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) as per manufacturer’s instruction.
After performing quality check of RNA, mRNA was enriched the total RNA using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA was removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.
Illumina paired end. Each library was sequenced to depth of 20 million paired end reads of 150 bases using NovaSeq 6000.

value: Fetal brain

tag: gestation day

tag: fetal sex

value: F

tag: brain weight (mg)

tag: brain length (cm)

tag: litter size

tag: sex of fetus on the medial side

value: M

tag: sex of the fetus on the lateral side


title: Piglet_17


title: sample HC27, plate 2

tag: disease state


title: sample HC17, plate 4


title: shRING1B_E2_NegCtrl_input_dripseq

data_processing:
Library strategy: DRIP-seq
ATAC-seq: Paired-end ATAC-seq fastq files were processed using the ATAC-seq Pipeline from the Kundaje Lab (https://github.com/kundajelab/atac_dnase_pipelines). Reads were trimmed using cutadapt v1.9.1 using the following parameters: -m 5. Reads were aligned to the hg19 genome using Bowtie2 v2.2.6, and the SAMtools v1.7 was used to convert the output files into the BAM format using default parameters. Duplicate reads were removed using Picard tool v1.126 using default parameters. Peaks were called using MACS2 v2.1.0 using default parameters
ChIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
DRIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 using the "histone" setting, and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Besides using the "histone" setting, all other parameters used default values.
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq). Reads were trimmed using cutadapt v2.3 with the following parameters: -j 4 --netseq-trim=20 -m 18. Reads were aligned to the hg19 genome using STAR v2.6.1a along default parameters, and RSEM v1.3.0 was used to obtain the expected gene counts against the human refseq also along default parameters.
RNA-seq differential expression was determined using DESeq2 v1.18.1 and R (version 3.4.1) with q-value <0.05. Ruvseq v1.12.0 was used for factor analysis to remove count based on ERCC spike-in. GSEA analysis was performed using gsea-3.0.jar. These additional analysis steps were included in the Diderote LSF-RNAseq Pipeline.
Homer annotatePeaks v4.8.3 was used for peak  annotation and for assigning peaks to genes.
Bedtools v2.29.0 intersect was used to determine peak overlaps.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to 45 minutes of E2 stimulation, at which point the cells were collected for DNA extraction

extract_protocol:
5 million cells were harvested, washed once with PBS, and resuspended in 1.55 mL of TE buffer to which 100 mL of 10% SDS and 5 mL of 20 mg/ml proteinase K (NEB P8107S) were added before incubation overnight at 37°C. Next day, DNA was extracted from the mixture with 1.6 ml of phenol/chloroform/isoamyl alcohol (Thermo Fisher Scientific 15-593-049) in a 15 mL high-density Maxtract phase-lock gel tube (Qiagen 129065). After spinning down at 1,500g for 10 minutes, the DNA was precipitated with 4 mL of 100% Ethanol and 160 mL of 3 M Sodium Acetate, pH 5.4. The DNA was washed with 80% ethanol three times before air drying and resuspending in 125 mL of TE buffer. Next, 100 mL of the DNA was digested overnight at 37°C using an enzyme cocktail consisting of 30 U each of EcoRI-HF (NEB R3101L), XbaI (NEB R0145L), BsrGI-HF (NEB R3575L), HindIII (NEB R0104L), and SspI (NEB R0132L) along with 1.5 mL of BSA (NEB B9000S), 15 mL of 10x Cutsmart Buffer (NEB B7204S), 1.5 mL of Spermidine (Sigma-Aldrich 05292-1ML-F), and water up to a total volume of 150 mL. Next day, upon examining the DNA mixture for drastic reduction in viscosity, the digested DNA as well as 100 mL of water and 250 mL of phenol/chloroform/isoamyl alcohol were added to 2-mL phase-lock gel, light tubes (VWR 10847-800). The DNA was extracted by spinning the tubes at 16,000 g for 10 minutes followed by incubation at -20°C with 1.5 mL of glycogen (Thermo Fisher Scientific R0561), 25 mL of 3 M sodium acetate, pH 5.4, and 625 mL of 100% ethanol. After one hour of freezing, DNA was precipitated by centrifuging at 16,000 g for 35 minutes at 4°C and washed with chilled 80% ethanol before air drying and resuspending in 50 mL of TE buffer. The DNA concentration was measured using a nanodrop, and 10 mg of the extracted digested DNA was digested with 4 mL of RNase H (NEB M0297L), 20 mL of RNase H buffer, and water up to 200 mL for 4 hours at 37°C to produce the RNase H treated negative control. 8 mg of DNA (both the untreated experiment and the treated control) of each sample was diluted in 500 mL of TE buffer, and 50 mL of the diluted DNA was removed and saved at -20°C as input DNA. R-loop was immunoprecipitated using 10 mL of S9.6 antibody (Millipore Sigma MABE1095) and 51 mL of 10x DRIP Binding Buffer (100 mM sodium phosphate, pH 7; 1.4 M NaCl; 0.5% Triton X-100) in a 500 mL reaction for 14 to 16h at 4°C. Next, the 50 mL of Dynabeads Protein G (Thermo Fisher Scientific 10004D) per sample were washed twice with 700 mL of 1x DRIP binding buffer, and the 500 mL of immunoprecipitation reaction was added to the beads for 2h at 4°C to pull down the DNA. The beads were separated from the solution on a magnetic rack and washed twice with 700 mL of 1x DRIP binding buffer. DNA was eluted from the beads with 300 mL of DRIP elution buffer (50 mM Tris-HCl, pH 8.0; 10 mM EDTA, pH 8.0; 0.5% SDS) and 7 mL of proteinase K at 55°C for 45 minutes. The same proteinase K digestion was performed for the input and the negative control samples. After incubation, the eluted DNA was extracted using a phase-lock gel tube with 300 mL of phenol/chloroform/isoamylalcohol while centrifuging at 16,000 g for 10 minutes. The aqueous layer was then moved to a new 1.5 mL centrifuge tube, and the DNA was precipitated with 1.8 mL of glycogen, 30 mL of 3 M sodium acetate, pH 5.4, and 750 mL of 100% Ethanol. The precipitated DNA was washed once with 80% ethanol, air dried, and resuspended in 50 mL of nuclease-free water. DRIP samples, negative controls, and inputs were diluted to a total volume of 100 mL in TE buffer and transferred into Diagenode Bioruptor NGS 0.65 mL Microtubes (Diagenode C30010011) for sonication on a Bioruptor Pico Sonication Device (Diagenode B01060010) for 19 total cycles of 30 seconds on, 30 seconds off with a 10-minute rest after the first 10 cycles to generate fragment sizes of around 250 bps. Sonication efficiency was verified on an Agilent Tapestation using High Sensitivity D1000 Screentapes and Reagents (Agilent Technologies 5067-5584 and -5585 respectively). DNA concentration was measured using the High Sensitivity D100 Screentape.
DRIP-seq libraries were prepared with at least 2 ng of DNA starting material using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7370L). Libraries were purified using the Agencourt AMPure XP beads (Beckman Coulter A63881), and library fragment sizes were measured again on an Agilent Tapestation using the High Sensitivity D1000 Screentapes and Reagents. The DRIP-seq libraries were sequenced on an Illumina Novaseq 6000 instrument.

value: Millipore Sigma MABE1095


title: sample HC27, plate 1


title: Piglet_15


title: shRING1B_HD_NegCtrl_input_dripseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to being collected for DNA extraction


title: shCtrl_E2_NegCtrl_input_dripseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shCtrl, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to 45 minutes of E2 stimulation, at which point the cells were collected for DNA extraction


title: HT6L: Tibetan placenta miRNA

tag: gender

value: Female


title: shCtrl_HD_NegCtrl_input_dripseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. After transduction with pLKO-shCtrl, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were then hormone deprived for 3 days prior to being collected for DNA extraction

tag: cell type

value: pLKO-sh+G89:G92Ctrl stable


title: sample HC17, plate 3


title: HT1L: Tibetan placenta miRNA


title: HT3L: Tibetan placenta miRNA


title: Piglet_16


title: HT4L: Tibetan placenta miRNA


title: P67: European placenta miRNA

description: miRNA  expression data from  European placenta

value: European


title: HT2L: Tibetan placenta miRNA


title: P58: European placenta miRNA


title: P69: European placenta miRNA


title: Piglet_11


title: Piglet_13


title: Piglet_12


title: Piglet_10


title: P57: European placenta miRNA


title: Piglet_14


title: shRING1B_HD_input_dripseq

tag: chip antibody


title: shCtrl_HD_input_dripseq


title: shRING1B_E2_input_dripseq


title: MV4;11_MS67_rep1

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

source_name: MV4;11 cells

growth_protocol: MV4;11 cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics; MIA PaCa-2 cells were grown in DMEM plus 10% FBS and 1% antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit.
NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used with 1 ug of total RNA for the construction of the multiplexed sequencing libraries.

treatment_protocol: For the WDR5 knockdown (KD) experiments, MV4;11 or MIA PaCa-2 cells bearing an inducible WDR5-targeted shRNA or empty vector mock (shEV) were subjected to treatment with 0.5 µg/mL of doxycycline (Dox) for four days. For compound treatment studies, MV4;11 cells were subjected to treatment with 0.1µM of either DMSO, OICR-9429, MS67 or MS67N for three days; MIA PaCa-2 cells were subjected to treatment with 1.0 µM of either DMSO, OICR-9429, MS67 or MS67N for six days.

tag: cell line

tag: agent


title: MV4;11_MS67_rep2


title: P56: European placenta miRNA


title: shCtrl_E2_input_dripseq

tag: cell source


title: sample HC17, plate 2


title: MV4;11_MS67N_rep2


title: sample HC17, plate 1


title: P55: European placenta miRNA


title: Piglet_8


title: Piglet_9


title: MV4;11_MS67N_rep1


title: P63: European placenta miRNA


title: Piglet_7


title: shRING1B_E2_NegCtrl_dripseq

tag: modifications


title: shRING1B_HD_NegCtrl_dripseq


title: shCtrl_E2_NegCtrl_dripseq


title: MV4;11_OICR-9429_rep2


title: P50: European placenta miRNA

tag: tissue


title: Piglet_5


title: Piglet_4


title: shRING1B_E2_dripseq


title: Piglet_6


title: MV4;11_DMSO_rep2

value: DMSO


title: P53: European placenta miRNA

tag: population


title: MV4;11_DMSO_rep1


title: MV4;11_OICR-9429_rep1


title: shCtrl_E2_dripseq


title: Piglet_2

tag: gestation day


title: Piglet_3

tag: fetal sex


title: MIAPACA2_MS67_H3K4me2-SPIKE-IN

data_processing:
All reads were mapped to both drosophila dm3 and human hg19 reference genomes using the STAR aligner. All mismatches are extended and low quality sequences are trimmed at this step . Non-primary alignment and PCR duplicates were then removed by samtools.  Scaling factors are calculated and normalization is done by the bamCompare function of deeptools  with bin size 10 and read length 250.
Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
Genome_build: hg19 is format -as dm3 is only for normalization
Supplementary_files_format_and_content: bigWig

source_name: MIAPACA2 cells/S2 cells

extract_protocol:
For ChIP-seq experiments, cells were grown in regular medium and collected, followed by cell fixation with 1% of formaldehyde and sonication. Across all samples, the cleared cell lysates from sonicated nuclei were added with the same fraction of the sonicated and cleared chromatin of Drosophila S2 cells, and then protein-DNA complexes were isolated with specific antibodies against H3K4me2 (Millipore cat# 07-030) and those against Drosophila-specific histone H2Av (Active Motif cat# 39715).
Following antibody enrichment, ChIP DNA was recovered for multiplexed library generation and parallel sequencing.

treatment_protocol: For ChIP-seq experiments, MV4;11 cells were treated with 0.1μM of either DMSO, OICR-9429, MS67N or MS67 for three days and collected; MIA PaCa-2 cells were treated with 2 μM of either DMSO, MS67N or MS67 for eight days and collected.

tag: spike-in control

value: Drosophila melanogaster

tag: antibody used

value: Anti-dimethyl Histone H3 (Lys4) Antibody(Millipore 07-030) and Histone H2Av antibody (Active Motif 39715 )

value: MS67_2 microM

tag: time point

value: 8 days


title: shCtrl_HD_NegCtrl_dripseq

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-133


title: shRING1B_HD_dripseq

value: pLKO-shRING1B stable


title: MIAPACA2_MS67N_H3K4me2-SPIKE-IN

value: MS67N_2 microM


title: Piglet_1

tag: brain weight (mg)

tag: brain length (cm)

tag: litter size

tag: sex of fetus on the medial side


title: shCtrl_HD_dripseq

tag: cell type

value: pLKO-shCtrl stable


title: MIAPACA2_DMSO_H3K4me2-SPIKE-IN


title: T47D_E2_NegCtrl_input_dripseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. Cells were hormone deprived for 3 days prior to 45 minutes of E2 treatment, at which point the cells were collected for DNA extraction

tag: chip antibody


title: HT9L: Tibetan placenta mRNA

description: Gene expression data from  Tibetan placenta

hyb_protocol: cRNA in hybridization solution was denatured at 99℃ for 5 min and 45℃ for 5 min prior to loading onto a microarray. Arrays were hybridized in a Agilent Hybridization Oven for 16hr at a rotation speed of 60 rpm at 45℃ and washed with Wash Buffer A and stained in the Affymetrix Fluidics Station 450.

data_processing: AGCC Software (Affymetrix® GeneChip® Command Console® Software) converts.DAT files from image signals to digital signals known as.CEL files. CEL files record probe level fluorescent signals.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA from placentas was isolated using RNeasy Mini Kits according to the manufacturer’s instructions. RNA quantity was determined using an Agilent Bioanalyzer.

tag: gender

value: Placenta

value: Tibetan


title: MIAPACA2_DMSO_INPUT

value: n/a (input)

tag: agent


title: HT10L: Tibetan placenta mRNA


title: T47D_HD_NegCtrl_input_dripseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. Cells were hormone deprived for 3 days prior to being collected for DNA extraction

tag: cell source


title: P54: European placenta miRNA


title: T47D_E2_NegCtrl_dripseq

tag: modifications

value: Millipore Sigma MABE1095


title: MV4;11_OICR-9429_H3K4me2-SPIKE-IN

source_name: MV4;11 cells/S2 cells

value: 3 days


title: HT7L: Tibetan placenta mRNA

value: Female

tag: tissue


title: HT8L: Tibetan placenta mRNA

tag: population


title: Arabidopsis thaliana

city: Montréal

first: Tarik

last: Moroy

address: 110 Pine Ave W, Montreal

country: Canada

institute: IRCM

description: Samples of Arabidopsis total RNA was generously provided by Dr. Richard Bélanger (Université Laval).

data_processing:
Adaptor were trimmed using Cutadapt V1.7.1
Quality Control was performed with fastqc V0.11.3
Identical sequences were collapsed into a single fasta sequence and were filtered to keep only those detected at least twice using a custom script
Genome_build: NA
Supplementary_files_format_and_content: Fasta files containing the aligned sequences that were detected at least twice in the dataset, separated in 2 groups based on the size (8-15nt and 16-30nt)

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana

growth_protocol: Please refer to the Samples section above

extract_protocol:
Total RNA samples were prepared using TRIzol® reagent or TRIzol LS® reagent for liquid samples (Invitrogen Life Technologies, Carlsbad, CA, USA) following the manufacturer’s recommendations. Contaminating DNA was degraded by DNase I (M0303S, New England Biolabs, MA, USA) treatment following manufacturer’s instructions. Total RNA was shipped on dry ice and analyzed by Arraystar Inc. RNA sequencing service (Rockville, MD).
The purity, quality, and concentration of total RNA samples were determined with NanoDrop ND-1000 (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent, Santa Clara, CA). Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: (1) 3′-adapter ligation, (2) 5′-adapter ligation, (3) cDNA synthesis, (4) PCR amplification, and (5) size selection of approximately 120 to 150 bp of PCR-amplified fragments (corresponding to approximately 8 to 30 nt of small RNA). The complete libraries were quantified by Agilent 2100 Bioanalyser. Samples were diluted to a final concentration of 8 pM, denatured as single-stranded DNA, and cluster generation was performed on the Illumina cBot using TruSeq Rapid SR cluster kit (GD-402-4001, Illumina, San Diego, USA). Afterward, the clusters were sequenced for 51 cycles on Illumina HiSeq 2000 using TruSeq Rapid SBS Kits (FC-402-4002, Illumina, San Diego, USA), as per the manufacturer's instructions.

tag: sample type

value: Arabidopsis thaliana


title: MV4;11_MS67_H3K4me2-SPIKE-IN


title: HT6L: Tibetan placenta mRNA


title: HT5L: Tibetan placenta mRNA


title: T47D_HD_NegCtrl_dripseq


title: HT4L: Tibetan placenta mRNA


title: MV4;11_MS67N_H3K4me2-SPIKE-IN


title: T47D_E2_input_dripseq


title: Drosophila melanogaster

description: Adult flies were purchased from the UCSD Drosophila Species Stock Center (San Diego) and snap-frozen in liquid nitrogen before storage at -80°C.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster

tag: age

value: Adult


title: Cryo-hESC-CEC2

city: Baltimore

first: S. Amer

last: Riazuddin

address: 600 N. Wolfe street

institute: Johns Hopkins University

description: mRNA library

data_processing:
The base calls were assigned through the Illumina real-time analysis (RTA) software (Ver. 1.17.20) and base call files were converted from a binary format (BCL) to flat-file format (qseq.txt) using Illumina BCL converter software (Ver. 1.9.4).
The raw RNA-Seq reads (FASTQ) were processed and analyzed using Lasergene Genomics Suite (DNASTAR, Madison, WI, USA).
The paired-end reads were assembled with SeqMan NGen (Ver. 12), using default parameters and aligned to the human reference genome (GRCh38.p11). The ArrayStar (Ver. 12; DNASTAR) was used for normalization, differential gene expression, and statistical analysis of mapped paired-end reads using the default parameters. FPKM was used for the normalization and quantification of gene expression
Differential expression of non-cryopreserved hESC-derived CECs and cryopreserved hESC-derived CECs was estimated using Spotfire DecisionSite with Functional Genomics (TIBCO Spotfire, Boston, MA). We chose >2 standard deviations from the mean of 0 that represents no change, as the cutoff value.
Genome_build: Human reference genome (GRCh38.p11)
Supplementary_files_format_and_content: Gene expression values (FPKM) in txt format

source_name: human embryonic stem cell (hESC)

growth_protocol: H9 hESCs were used to generate CECs under xeno-free conditions by modifying our published procedure (Ali et al., 2018b). Briefly, hESCs were seeded on 35 mm Vitronectin coated plates in 1:7 dilutions (85% confluent plate was split into 7 plates) on day 0 using 0.5 mM EDTA. The hESCs were grown for four days in E8 media. On day 4, E8 media was replaced with dual Smad inhibitors media containing 500 ng/ml recombinant human Noggin and 10 μM SB431542 in a basal media of 80% DMEM-F12, 20% knockout serum replacement, 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, and 8 ng/ml basic fibroblast growth factor. On day 6, dual Smad inhibitors media was replaced by cornea medium containing 0.1× B27 supplement, 10 ng/ml recombinant human platelet-derived growth factor-BB, and 10 ng/ml recombinant human Dickkopf related protein-2 in a basal media of 80% DMEM-F12, 20% KSR, 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, and 8 ng/ml bFGF. On day 7, the differentiating CECs were transferred to new Vitronectin coated plates (35 mm) and were grown in cornea medium for 13 additional days.

extract_protocol:
Total RNA was isolated from each sample using TRIzol reagent. The extracted RNA was examined using a NanoDrop Lite spectrophotometer and RNA 6000 Pico kit on an Agilent 2100 Bioanalyzer for RNA-Seq library prepration.
Total RNA was subjected to RNA-Seq library preparation using NEBNext Ultra II RNA Library Prep Kit for Illumina. Approximately, 1.0 μg of high-quality total RNA (≥8.0 RIN Score) was used for polyadenylated RNA selection using oligo dT beads, followed by the fragmentation of selected polyadenylated RNA. The fragmented RNA was used as a template for cDNA synthesis by reverse transcriptase with random primers. The cDNA was further converted into double-stranded DNA that was end-repaired to incorporate the specific index adapters for multiplexing, followed by a purification step and amplification for 15 cycles. The amplified libraries were examined on an Agilent 2100 Bioanalyzer and quantitative PCR (qPCR) according to the manufacturer's instructions. RNA-Seq libraries with unique index sequences were pooled in an equimolar ratio, and a final size selection of 400–500 bp was performed. After the quality control confirmation, RNA-Seq bar-coded pooled libraries were sequenced using HiSeq 2500 (rapid run mode) genome analyzer.

treatment_protocol: Human embryonic stem cell (hESC)-derived CECs at day 20 were cryopreserved in liquid nitrogen for 40 days.

value: hESC-derived corneal endothelial cells (CECs)


title: HT2L: Tibetan placenta mRNA


title: HT1L: Tibetan placenta mRNA


title: T47D_HD_input_dripseq


title: MV4;11_DMSO_H3K4me2-SPIKE-IN

tag: spike-in control

value: Drosophila melanogaster

value: Anti-dimethyl Histone H3 (Lys4) Antibody(Millipore 07-030) and Histone H2Av antibody (Active Motif 39715 )

value: DMSO


title: HT3L: Tibetan placenta mRNA


title: T47D_E2_dripseq

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site


title: T47D_HD_dripseq

value: ATCC #HTB-133


title: Cryo-hESC-CEC3

description: mRNA library


title: P67: European placenta mRNA

description: Gene expression data from  European placenta

value: European


title: Non-Cryo-hESC-CEC3

description: mRNA library


title: MV4;11_DMSO_INPUT

tag: antibody used


title: rep2_rChIP_ER_chipseq

description: 17_rChIP_ER_pooled.chip.fc.signal.bigwig

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. Cells were hormone deprived for 3 days prior to 9 hours of DMSO treatment followed by 45 minutes of E2 stimulation, at which point the cells were crosslinked and collected for sonication and ChIP-seq.

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and washed once with PBS and fixed with 1% formaldehyde (Thermo Fisher #28908) in 10 ml PBS for 10 min. To quench the cross-linking reaction, 1/20 volume of 2.5 M glycine was added to the plate for a final concentration of 0.125M for 5 min. The supernatant was aspirated, and the cells were washed twice with 5 ml PBS and harvested on ice using cell scrapers into 15ml sonication tubes (Diagenode cat# C01020031). Cells were pelleted at 1000g for 5 min at 4°C, washed 1x with 5 ml cold PBS, and pelleted once more. Cell pellet collected from 6 plates of cells was resuspended in 3 ml of Lysis Buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), allowed to rotate for 10 min at 4°C, and pelleted at 1000 x g for 5 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 2 (10 mM Tris-HCL pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), allowed to rotate for 10 min at room temperature, and pelleted at 1000 x g for 5 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and then sonicated on a Bioruptor Pico at 4°C for 20min of 30’’ ON-OFF cycles with 1.2 g of sonication beads. After sonication, samples were transferred to 2 separate 1.5 ml microtube and centrifuged at 20,000 x g for 15 minutes at 4°C. The supernatant was transferred to new 15 ml tubes. To check sonication efficiency, 20µl of sonicated samples was transferred to a new microtube with 80µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl EB buffer. 1 ug of decrosslinked chromatin from each sample were run in a 1% agarose gel at 100V for 45min and imaged on a Bio-rad ChemiDoc XRS+. DNA concentration in the sonicated decrosslinked samples were measured via qubit, and this concentration was then used to estimate the concentration of chromatin in the un-decrosslinked samples. 30 ug of total chromatin were transferred to a 1.5ml LoBind tube (Eppendorf cat# 0030108051) and brought up to 500µl final volume with Lysis Buffer 3. 5µl was removed as input material (1%) and placed in a separate microtube at 4°C. 5ug antibody was used for transcription factor ChIP (see Key Resources table for list of antibodies). Antibodies were pre-bound to 50 ul of Dynabeads Protein G (Thermo Fisher 10004D), which was washed in 1 ml of 0.5% BSA in 1x PBS three times before and after overnight pre-binding at 4°C. The chromatin samples were added to the pre-bound Dynabeads and rotated end-to-end overnight at 4°C with 2 ug of RNase A (Thermo Fisher Scientific AM9780). Beads were washed 5x with 1 ml Wash Buffer (50 mM Hepes-KOH, pH 7.6; 500 mM LiCl, 1 mM EDTA, 1% NP-40; 0.5% Na-Deoxycholate) and once with 1 ml TE containing 50 mM NaCl. Beads were dried after the last wash by removing as much TE as possible. 210 ul of Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) was added to each sample and 45 ul Lysis Buffer 3 plus 150 ul elution buffer were added to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 15 minutes on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 2000rpm at RT and 200µl of supernatant was transferred to a new tube and reverse crosslinked overnight at 65°C. Next day, 200 ul of TE was added to each decrosslinked sample, and the samples were treated sequentially with 0.2 mg/ml RNAse A (Sigma R5503) at 37°C and 0.2 ug/ml Proteinase K (NEB P8107S) at 55°C for two hours each. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl EB buffer and quantified by Qubit.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: Abcam 3575


title: rep2_rChIP_RING1B_chipseq

description: 18_rChIP_RING1B_pooled.chip.fc.signal.bigwig

value: Active Motif 39663


title: Non-Cryo-hESC-CEC2

description: mRNA library


title: rep1_rChIP_RING1B_chipseq


title: Non-Cryo-hESC-CEC1

description: mRNA library


title: Cryo-hESC-CEC1

description: mRNA library


title: T_081

city: Washington

first: Rency

middle: S

last: Varghese

state: District of Columbia

address: 4000 Reservoir Rd NW, Building D

department: Oncology

institute: Georgetown University

data_processing:
The fastq files were imported into Partek Flow for quality assessment, alignment, and estimating transcript abundance.
Alignment was performed using the spliced transcripts alignment (STAR) algorithm. The aligned reads were quantified to the transcriptome through Expectation Maximization (E/M) method implemented in Partek Flow and normalized using the TMM method.
Supplementary_files_format_and_content: gene counts

source_name: Liver

extract_protocol:
RNA samples from the 32 fresh-frozen samples (16 HCC and 16 adjacent normal) were isolated using the RNeasy Plus Universal Mini Kit (Qiagen) with on-column RNase-free DNase treatment. The RNA quality and quantity were estimated based on ultraviolet-visible (UV-VIS) spectrophotometry using the NanoDrop ND-1000 spectrophotometer. The RNA integrity was assessed using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer.
Aliquots of the RNA samples described above were indexed using the TruSeq RNA Access Library Prep Kit prior to sequencing by Illumina HiSeq 4000 using 150 bp pair end (PE150). The mRNA-seq data contained an average of 33M reads per sample

tag: disease status

value: Adjacent Normal

tag: race

value: AA


title: T_080

value: HCC


title: rep1_rChIP_ER_chipseq


title: rep2_Trip_E2_input

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. Cells were hormone deprived for 3 days prior to 9 hours of triptolide treatment at 10 uM followed by 45 minutes of E2 stimulation, at which point the cells were crosslinked and collected for sonication and ChIP-seq.

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and washed once with PBS and fixed with 1% formaldehyde (Thermo Fisher #28908) in 10 ml PBS for 10 min. To quench the cross-linking reaction, 1/20 volume of 2.5 M glycine was added to the plate for a final concentration of 0.125M for 5 min. The supernatant was aspirated, and the cells were washed twice with 5 ml PBS and harvested on ice using cell scrapers into 15ml sonication tubes (Diagenode cat# C01020031). Cells were pelleted at 1000g for 5 min at 4°C, washed 1x with 5 ml cold PBS, and pelleted once more. Cell pellet collected from 6 plates of cells was resuspended in 3 ml of Lysis Buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), allowed to rotate for 10 min at 4°C, and pelleted at 1000 x g for 5 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 2 (10 mM Tris-HCL pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), allowed to rotate for 10 min at room temperature, and pelleted at 1000 x g for 5 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and then sonicated on a Bioruptor Pico at 4°C for 20min of 30’’ ON-OFF cycles with 1.2 g of sonication beads. After sonication, samples were transferred to 2 separate 1.5 ml microtube and centrifuged at 20,000 x g for 15 minutes at 4°C. The supernatant was transferred to new 15 ml tubes. To check sonication efficiency, 20µl of sonicated samples was transferred to a new microtube with 80µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl EB buffer. 1 ug of decrosslinked chromatin from each sample were run in a 1% agarose gel at 100V for 45min and imaged on a Bio-rad ChemiDoc XRS+. DNA concentration in the sonicated decrosslinked samples were measured via qubit, and this concentration was then used to estimate the concentration of chromatin in the un-decrosslinked samples. 30 ug of total chromatin were transferred to a 1.5ml LoBind tube (Eppendorf cat# 0030108051) and brought up to 500µl final volume with Lysis Buffer 3. 5µl was removed as input material (1%) and placed in a separate microtube at 4°C. 5ug antibody was used for transcription factor ChIP (see Key Resources table for list of antibodies). Antibodies were pre-bound to 50 ul of Dynabeads Protein G (Thermo Fisher 10004D), which was washed in 1 ml of 0.5% BSA in 1x PBS three times before and after overnight pre-binding at 4°C. The chromatin samples were added to the pre-bound Dynabeads and rotated end-to-end overnight at 4°C. Beads were washed 5x with 1 ml Wash Buffer (50 mM Hepes-KOH, pH 7.6; 500 mM LiCl, 1 mM EDTA, 1% NP-40; 0.5% Na-Deoxycholate) and once with 1 ml TE containing 50 mM NaCl. Beads were dried after the last wash by removing as much TE as possible. 210 ul of Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) was added to each sample and 45 ul Lysis Buffer 3 plus 150 ul elution buffer were added to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 15 minutes on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 2000rpm at RT and 200µl of supernatant was transferred to a new tube and reverse crosslinked overnight at 65°C. Next day, 200 ul of TE was added to each decrosslinked sample, and the samples were treated sequentially with 0.2 mg/ml RNAse A (Sigma R5503) at 37°C and 0.2 ug/ml Proteinase K (NEB P8107S) at 55°C for two hours each. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl EB buffer and quantified by Qubit.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.


title: SKG-1_Control vs. HOXD9 knock out

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

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

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

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

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

extract_protocol: Total RNA was extracted from CC cell lines and tissues using the RNeasy Mini Kit (Qiagen).

tag: cell line

value: cervical cancer cells

tag: genotype/variation

value: control


title: P69: European placenta mRNA

value: Female

value: Placenta


title: P63: European placenta mRNA


title: rep2_Trip_E2_ER

description: 14_Trip_E2_ER_pooled.chip.fc.signal.bigwig


title: P57: European placenta mRNA


title: ACSA-2 negative/GLAST positive cells_Biological replicate 3

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

description: gene expression analysis of T7-amplified polyA RNA

hyb_protocol: 600 ng Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Mouse Human Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

organism: Mus musculus

source_name: Neonatal (P1-P3) cerebellar tissue (wild-type (Mouse strain: CD1))

label_protocol: Total RNA (up to 50 ng) was amplified and Cy3-labeled according to the manufacturer’s protocol (Agilent Low Input Quick Amp Labeling Kit). Dye-incorporation and yield of cRNA were measured on the NanoDrop.

extract_protocol: Biological triplicates of A-/G+ and A+/G+ were isolated by magnetic cell separation (50.000 cells/sample) and shock frozen. RNA was isolated with the RNeasy Mini Kit (Quiagen) and a quality check was performed on the Agilent 2100 Bioanalyzer platform.

tag: strain

tag: developmental stage

value: Neonatal (P1-P3)

value: Cerebellum (Brain)


title: T_074


title: ACSA-2 negative/GLAST positive cells_Biological replicate 2


title: P56: European placenta mRNA


title: rep2_Trip_E2_RING1B

description: 13_Trip_E2_RING1B_pooled.chip.fc.signal.bigwig

tag: cell type

tag: chip antibody


title: ACSA-2 negative/GLAST positive cells_Biological replicate 1


title: Reprogramming MEFs_10 dpi_+4OHT_rep3 [iPS6]

city: Sagamihara

first: Yoichi

last: Sekita

address: 1-15-1 Kitasato, Minami-ku

department: Biosciences

institute: Kitasato University School of Science

description:
AKT-MER was activated
iPS6_L001

data_processing:
Mapped to mouse transcriptome by Salmon
TPM were calculated using tximport
Supplementary_files_format_and_content: Comma separated value files include TPM values for each Samples

source_name: Reprogramming MEFs_10 dpi_+4OHT

extract_protocol:
Total RNA was isolated from cells using the AllPrep DNA/RNA Mini Kit (QIAGEN) according to the manufacturer’s instructions.
Standard polyA libraries were prepared using the KAPA Stranded mRNA-Seq Kit for Illumina (Kapa Biosystems).

tag: strain background

value: mixed; C57BL/6, DBA/2, and ICR

value: Oct4-EGFP transgenic mouse

tag: Sex

value: male

value: E13.5 embryos

value: mouse embryonic fibroblasts (MEFs)

tag: treatment

value: 4OHT administration


title: T_066


title: T_075


title: T_064

value: EA


title: P55: European placenta mRNA

tag: gender

tag: tissue

value: European


title: ACSA-2 positive/GLAST positive cells_Biological replicate 2


title: ACSA-2 positive/GLAST positive cells_Biological replicate 3


title: P53: European placenta mRNA

tag: population


title: P54: European placenta mRNA


title: P50: European placenta mRNA


title: sample HC33, plate 5

data_processing:
Convert paired-end reads to single-ended, extracting the 12-base cell barcode and 8-base unique molecule identifier (UMI) from R1 read and appending them to the R2 read name as a colon-separated pair. Reads with Ns in either the cell barcode or UMI are discarded. (custom Python script)
Align reads to human hg38 genome, with GENCODE v28 gene annotations. (tophat2 v2.0.12)
Quantify transcript counts using GENCODE v28 gene annotations. (ESAT v1.0, https://github.com/garber-lab/ESAT)
Build t-SNE map of all cells (custom R script, using the dim_reduce() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Density-based clustering (custom R script, using the cluster_sc() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Cell type identification (custom R script based on density-based cluster boundaries and known marker genes to identify major cell types)
Viral transcript counting - NCBI magic-blast (https://ncbi.github.io/magicblast/) of all transcript sequence reads against all Influenza A and SARS-CoV2 genomes in the NCBI virus database as of 1 Agust 2020, followed by a custom Python script to quantify the number of unique viral transcripts in each cell, using UMIs to remove PCR duplicates.
Genome_build: hg38
Supplementary_files_format_and_content: raw transcript counts from ESAT.: 41442 genes x 29406 cell transcript counts matrix
Supplementary_files_format_and_content: per-cell phenotype information: 29406 cell x 13 column cell phenotype information. Columns: sampID (sample ID prefix), plateID (Seq-Well plate ID, 4 or 5 for each sample), status (disease status: COVID-19, fluA, healthy), donorID (unique ID for each donor), cDate (sample collection date), age (donor age), sex (donor sex - M or F), tSNE1, tSNE2 (t-SNE mapping coordinates), group (major cell type group), cellType (assigned cell type), SARS.CoV.2 (SARS-CoV2 virus transcript count), fluA (influenza A virus transcript count)

extract_protocol: Seq-Well S^3 Master Protocol (June 2019) (http://shaleklab.com/wp-content/uploads/2019/07/SeqWell-S3-Protocol.pdf)

tag: disease state

value: healthy


title: P58: European placenta mRNA


title: ACSA-2 positive/GLAST positive cells_Biological replicate 1


title: IMS32_15mMGlc_Pyr-

city: Hachioji

first: Hideji

last: Yako

state: Tokyo

address: 1432-1, Horinouchi

institute: Tokyo University of Farmacy and Life Science

description: Gene expression after 1 h in IMS32 cells under exposure to DMEM/5% FBS containing 15 mM glucose (pyruvate free)

hyb_protocol: The labelled samples were hybridized to Agilent Whole Mouse Genome version 2.0 Microarray (G4846A) for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5 µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters and analyzed with GeneSpring GX software

source_name: IMS32 cells

label_protocol: Cy3-labelled cRNA was prepared using a Low Input Quick Amp Labeling Kit,  according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from IMS32 cells using TRIzol solution and the quality of the RNA was assessed by electrophoresis and a bioanalyzer

treatment_protocol: IMS32 cells were incubated for 1 h in DMEM/5%FBS containing 5 or 15 mM glucose in the presence or absence of 1 mM pyruvate.

value: Immortalized mouse Schwann cells (IMS32 cells)

value: 1 h, 15 mM glucose and no pyruvate


title: IMS32_15mMGlc_Pyr+

description: Gene expression after 1 h in IMS32 cells under exposure to DMEM/5% FBS containing 15 mM glucose and 1 mM pyruvate

value: 1 h, 15 mM glucose and 1 mM pyruvate


title: Reprogramming MEFs_10 dpi_+4OHT_rep1 [iPS4]

description:
AKT-MER was activated
iPS4_L001


title: rep2_DMSO_E2_input

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-133

tag: modifications


title: T_067

tag: disease status

value: Adjacent Normal

value: AA


title: rep2_Trip_HD_input_chipseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. Cells were hormone deprived for 3 days prior to 9 hours of Triptolide treatment at 9 uM, at which point the cells were crosslinked and collected for sonication and ChIP-seq.


title: Reprogramming MEFs_10 dpi_-4OHT_rep3 [iPS3]

description:
AKT-MER was not activated
iPS3_L001

source_name: Reprogramming MEFs_10 dpi_-4OHT

value: Mock administration


title: Reprogramming MEFs_10 dpi_+4OHT_rep2 [iPS5]

description:
AKT-MER was activated
iPS5_L001

value: mixed; C57BL/6, DBA/2, and ICR


title: rep2_DMSO_E2_ER_chipseq

description: 10_DMSO_E2_ER_pooled.chip.fc.signal.bigwig

value: Abcam 3575


title: IMS32_5mMGlc_Pyr+

description: Gene expression after 1 h in IMS32 cells under exposure to DMEM/5% FBS containing 5 mM glucose and 1 mM pyruvate

value: 1 h, 5 mM glucose and 1 mM pyruvate


title: IMS32_5mMGlc_Pyr-

description: Gene expression after 1 h in IMS32 cells under exposure to DMEM/5% FBS containing 5 mM glucose (pyruvate free)

value: 1 h, 5 mM glucose and no pyruvate


title: rep2_DMSO_E2_RING1B_chipseq

description: 09_DMSO_E2_RING1B_pooled.chip.fc.signal.bigwig

value: Active Motif 39663


title: TnfrKO-72 hr O3 Replicate 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Comparisons: Genotype effect & exposure effect on lung gene expression

hyb_protocol: The biotinylated RNA was fragmented and hybridized to the Affymetrix array (MOE430A) for 16 hr at 45 degree C in a hybridization oven rotating at 60 rpm. The array was washed and stained with streptavidin–phycoerythrin using an Affymetrix Fluidics Station 450.

scan_protocol: The array was scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console and Expression Console Software (AGCC; Version 3.2 and Expression Console; Version 1.2) using the MAS5 algorithm to generate .CHP files.

source_name: TnfrKO-72 hr O3_homogenized mouse lung tissue

label_protocol: cDNA was synthesized from RNA using a one-cycle cDNAsynthesis kit. Biotinylated RNA was then synthesized from cDNA using an IVT labeling kit after incubating at 37◦C for 16 hr.

extract_protocol: Total RNA was extracted from left lung homogenates of each mouse (n= 3 per group) using Trizol (Invitrogen, Waltham, MA) and RNA quality was evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Tnfr1/2-deficient (Tnfr-/-) and wild-type (Tnfr+/+, C57BL/6J) mice were exposed to air or 0.3-ppm O3 continuously for 24, 48, or 72 hr in individual stainless-steel wire cages within a Hazelton 1000 chamber  (Lab Products, Maywood, NJ) equipped with a charcoal and high-efficiency particulate air-filtered air supply. Mice had free access to water and diet. O3 was generated from ultra-high purity air (<1 ppm total hydrocarbons; National Welders, Inc., Raleigh, NC) using a silent arc discharge O3 generator (Model L-11, Pacific Ozone Technology, Benicia, CA). Constant chamber air temperature (72 ± 3° F) and relative humidity (50 ± 15%) were maintained. O3 concentration was continually monitored (Dasibi model 1008-PC, Dasibi Environmental Corp.). Parallel exposure to filtered air was done in a separate chamber. Immediately following the end of exposure, mice were euthanized by sodium pentobarbital overdose (104 mg/Kg).

tag: genotype

value: Tnfr-/- (KO)

tag: exposure

value: Homogenized mouse lung tissues


title: T_063

value: HCC

tag: race

value: EA


title: Reprogramming MEFs_10 dpi_-4OHT_rep2 [iPS2]

description:
AKT-MER was not activated
iPS2_L001

tag: genotype/variation

value: Oct4-EGFP transgenic mouse

value: male

value: E13.5 embryos

value: mouse embryonic fibroblasts (MEFs)


title: T_062


title: TnfrKO-72 hr O3 Replicate 2


title: rep2_DMSO_HD_input_chipseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. Cells were hormone deprived for 3 days prior to 9 hours of DMSO treatment, at which point the cells were crosslinked and collected for sonication and ChIP-seq.

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-133


title: T_057

value: Adjacent Normal

value: AA


title: T_061


title: Reprogramming MEFs_10 dpi_-4OHT_rep1 [iPS1]

description:
AKT-MER was not activated
iPS1_L001

value: mixed; C57BL/6, DBA/2, and ICR

tag: developmental stage

value: Mock administration


title: rep2_Trip_HD_ER_chipseq

description: 06_Trip_HD_ER_pooled.chip.fc.signal.bigwig

tag: cell type

value: Abcam 3575


title: rep2_DMSO_HD_ER_chipseq

description: 02_DMSO_HD_ER_pooled.chip.fc.signal.bigwig

tag: chip antibody


title: T_053


title: rep2_Trip_HD_RING1B_chipseq

description: 05_Trip_HD_RING1B_pooled.chip.fc.signal.bigwig


title: T_054


title: rep2_DMSO_HD_RING1B_chipseq

description: 01_DMSO_HD_RING1B_pooled.chip.fc.signal.bigwig


title: WT at reprogramming day 2

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

data_processing:
ChIP-seq reads were mapped to the mouse genome (mm10 assembly) using BWA-MEM version 0.7.17 (Li and Durbin, 2010) .
To identify regions of ChIP-seq of TF enrichment over background, peak callings were performed by MACS2 version 2.2.7 (Zhang et al., 2008). Peak regions were filtered for false discovery rate values < 0.05.
To visualize ChIP-seq tag counts in the IGV (Robinson et al., 2011) , mapped reads were extended and converted into the bigWig format using bedGraphToBigWig.
To link site accessibility to regulation of gene expression, we associated each peak to its nearest gene in the mm10 genome using ChIPpeakAnno version 3.22.2 (Zhu et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: Reprogramming cells

growth_protocol: NANOG-GFP reporter MEFs were seeded one-day before SeVdp infection and cultured in the conditioned knockout serum replacement (KSR) mESC medium supplemented with Shield1 (25 mcM) each medium change and Blasticidin S (5 µg/ml) added from day 3 to day 5; medium change performed once in two days.

extract_protocol:
All ChIP experiments were performed with ChIP-IT Express Chromatin Immunoprecipitation kit (Active Motif), following the kit protocol with minor modifications. Briefly, day 10 reprogramming cells (6.0X105 seeding density) in a 60-mm dish were crosslinked with 0.09 mL of 37% formaldehyde to 3.3 mL of growth medium. 1.5 mL of glycine (20X) was added to quench the unreacted formaldehyde. Cells in each 60-mm plate were collected and resuspended in 0.2 ml of lysis buffer. Genomic DNA was sheared to a targeted length of 150-200 bp on Covaris S220 Focused-ultrasonicator with optimized conditions. Sheared chromatin was subjected to cross-link reversal, treated with Proteinase K and RNase A, then phenol/chloroform extracted and analysed for the shearing efficiency on 1% agarose gel electrophoresis. For KLF4 ChIP ~3.2X106 reprogramming cells and 5 mg of antibody were used for each experiment. Finally, DNA fragments were purified using Chromatin IP DNA Purification kit (Active Motif) following the manufacturer’s protocol and used for real time qPCR and ChIP-seq library preparation. The primary antibodies used as follows: Anti-Human KLF4 (R&D, AF3640).
ChIP-seq library was generated using KAPA Hyper Plus kit (Roche) by Lab Droid “Maholo” (Robotic Biology Institute) automatically.

value: Nanog-GFP MEF-derived cells

tag: strain

tag: antibody

value: Anti-human KLF4 (R&D systems)

tag: time point

value: reprogramming day 2


title: Mutant at reprogramming day 2


title: T_056


title: Schizosaccharomyces pombe

description: Total RNA sample from this yeast strain was generously provided by Dr. Karl Ekwall (Karolinska Institutet).

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

tag: sample type

value: Schizosaccharomyces pombe


title: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

value: Saccharomyces cerevisiae


title: TnfrKO-72 hr O3 Replicate 1

value: Tnfr-/- (KO)

tag: tissue

value: Homogenized mouse lung tissues


title: T_052


title: TnfrKO-48 hr O3 Replicate 3

source_name: TnfrKO-48 hr O3_homogenized mouse lung tissue


title: T_051

value: HCC


title: TnfrKO-48 hr O3 Replicate 1


title: 30 DPI

city: Chongqing

first: Haiyang

last: He

address: Gaotanyan street

institute: Arm medical university

data_processing:
the sequencing was performed with paired-end sequencing of 150nt each end on one lane of NovaSeq 6000 per sample
The reads were mapped onto the ENSEMBL Mouse Genome (GRCm38.p6)
Data was demultiplexed by using Cell Ranger 3.0.1
Data was further analyzed using Seurat 3.0.
A global-scaling normalization method “LogNormalize” was used to normalize the gene expression
Genome_build: mm9
Supplementary_files_format_and_content: barcodes.tsv file
Supplementary_files_format_and_content: genes.tsv file
Supplementary_files_format_and_content: matrix.mtx file

source_name: CD8+ T cells

extract_protocol:
Cellular suspensions (6000 effector or memory cells) were loaded on the Chromiu Controller (10x Genomics, Pleasanton) to generate Gel Bead-In-Emulsions (GEMs).
Barcoded sequencing libraries were conducted following the instruction manual of the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics).

treatment_protocol: 1X104 naïve P14 CD8+ T cells (CD45.1) were intravenously injected into recipient C57BL/6 mice (CD45.2), which were then infected with 2X105 PFU of LCMV Armstrong viruses intraperitoneally the next day. The P14 CD8+Teffs and P14 memory CD8+ T cells were sorted by flow cytometry at 8 and 30 days after infection respectively.

value: spleen

tag: days post infection

tag: agent

value: LCMV Armstrong virus


title: 8 DPI


title: TnfrKO-48 hr O3 Replicate 2


title: T_048

value: EA


title: RnA-seq of Stroma IL6KO 4

city: Cambridge

first: Daniel

middle: Robert

last: Goulet

state: MA

address: 500 Main St

department: Koch Institute

institute: Massachusetts Institute of Technology

description:
RNA-seq of host stroma isolated from the bone marrow of IL6KO C57BL/6J mouse
processed data file:
Stroma_Normalized_Counts.txt
Stroma_DESeq_Results.txt

data_processing:
Fastq files were aligned to mm10 genome using salmon (version 1.3.0). The salmon quant command was executed with the following flags: --validateMappings --gcBias --seqBias
Salmon quant files were normalized and differentially expressed genes were identified using the DESeq2 R package (version 1.28.1). The DESeq command was executed with default options.
Table of read counts normalized by DESeq2 was output to a tab-delimited txt file.
Results of DESeq analysis of WT ~ IL6KO was output to a tab-delimited txt file.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized read counts and DESeq2 analysis output to tab delimited txt

source_name: RNA-seq of Stroma IL6KO

growth_protocol: 500,000 BCR-ABL+ B-ALL cells were injected into the tail vein of wild-type or IL6KO C57BL/6J mice.

extract_protocol:
Extracted RNA as directed using Qiagen RNeasy Kit (Qiagen cat. # 74134)
Prepared library as directed using NEB Ultra II Directional RNA with rRNA Depletion Kit (NEB cat. # E7400)

tag: strain background

value: IL6 KO

value: Bone marrow

value: Bone-marrow derived mCh- host stromal cells


title: rep1_Trip_E2_input_chipseq

data_processing:
ATAC-seq: Paired-end ATAC-seq fastq files were processed using the ATAC-seq Pipeline from the Kundaje Lab (https://github.com/kundajelab/atac_dnase_pipelines). Reads were trimmed using cutadapt v1.9.1 using the following parameters: -m 5. Reads were aligned to the hg19 genome using Bowtie2 v2.2.6, and the SAMtools v1.7 was used to convert the output files into the BAM format using default parameters. Duplicate reads were removed using Picard tool v1.126 using default parameters. Peaks were called using MACS2 v2.1.0 using default parameters
ChIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
DRIP-seq: Single-end ChIP-seq fastq files were processed using the Encode ChIP-seq-pipeline2 from the Kundaje Lab (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4 using the "histone" setting, and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Besides using the "histone" setting, all other parameters used default values.
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq). Reads were trimmed using cutadapt v2.3 with the following parameters: -j 4 --netseq-trim=20 -m 18. Reads were aligned to the hg19 genome using STAR v2.6.1a along default parameters, and RSEM v1.3.0 was used to obtain the expected gene counts against the human refseq also along default parameters.
RNA-seq differential expression was determined using DESeq2 v1.18.1 and R (version 3.4.1) with q-value <0.05. Ruvseq v1.12.0 was used for factor analysis to remove count based on ERCC spike-in. GSEA analysis was performed using gsea-3.0.jar. These additional analysis steps were included in the Diderote LSF-RNAseq Pipeline.
Homer annotatePeaks v4.8.3 was used for peak  annotation and for assigning peaks to genes.
Bedtools v2.29.0 intersect was used to determine peak overlaps.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. Cells were hormone deprived for 3 days prior to 9 hours of triptolide treatment at 9 uM followed by 45 minutes of E2 stimulation, at which point the cells were crosslinked and collected for sonication and ChIP-seq.

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-133

tag: modifications


title: TnfrKO-24 hr O3 Replicate 2

source_name: TnfrKO-24 hr O3_homogenized mouse lung tissue

tag: genotype


title: rep1_Trip_E2_ER_chipseq

value: Abcam 3575


title: TnfrKO-24 hr O3 Replicate 3

tag: exposure


title: TnfrKO-24 hr O3 Replicate 1


title: DMSO_E2_RNAP_chipseq

value: Cell Signaling 14958S


title: TnfrKO-Air Replicate 2

source_name: TnfrKO-Air_homogenized mouse lung tissue

value: Air


title: T_045

tag: disease status

tag: race

value: AA


title: T_049

value: Adjacent Normal


title: RNA-seq of Stroma IL6KO 2


title: T_043


title: Trip_E2_RNAP_chipseq


title: TnfrKO-Air Replicate 3


title: rep1_DMSO_E2_RING1B_chipseq

value: Active Motif 39663


title: rep1_DMSO_E2_ER_chipseq


title: RNA-seq of Stroma IL6KO 1


title: RNA-seq of Tumor IL6KO 4

description:
RNA-seq of mCh+ tumor cells isolated from the bone marrow of IL6KO C57BL/6J mouse
processed data file:
Tumor_Normalized_Counts.txt
Tumor_DESeq_Results.txt

source_name: RNA-seq of Tumor IL6KO

value: BCR-ABL+, Arf-/-

value: Bone-marrow derived mCh+ transplanted ALL


title: RNA-seq of Tumor IL6KO 3


title: RnA-seq of Stroma IL6KO 3


title: rep1_DMSO_E2_input


title: RNA-seq of Tumor IL6KO 2


title: rep1_Trip_HD_input_chipseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax. Cells were hormone deprived for 3 days prior to 9 hours of Triptolide treatment at 10 uM, at which point the cells were crosslinked and collected for sonication and ChIP-seq.


title: rep1_Trip_E2_RING1B_chipseq


title: WT-72 hr O3 Replicate 3

source_name: WT-72 hr O3_homogenized mouse lung tissue

value: Tnfr+/+ (WT, B6)

value: Homogenized mouse lung tissues


title: T_042

value: HCC


title: T_038

value: EA


title: T_046


title: WT-72 hr O3 Replicate 2


title: T_039


title: T_032


title: Trip_HD_RNAP_chipseq


title: WT-72 hr O3 Replicate 1


title: RNA-seq of Tumor IL6KO 1


title: T_031


title: rep1_Trip_HD_ER_chipseq


title: RNA-seq of WT Stroma 3

description:
RNA-seq of stroma isolated from the bone marrow of wild-type C57BL/6J mouse
processed data file:
Stroma_Normalized_Counts.txt
Stroma_DESeq_Results.txt

source_name: RNA-seq of WT Stroma

value: WT


title: RNA-seq of WT Stroma 4

value: Bone marrow


title: rep1_DMSO_HD_input_chipseq


title: rep1_Trip_HD_RING1B_chipseq


title: T_018

source_name: Liver


title: TnfrKO-Air Replicate 1

value: Tnfr-/- (KO)


title: T_019


title: RNA-seq of WT Stroma 2

value: Bone-marrow derived mCh- host stromal cells


title: RNA-seq of WT Stroma 1


title: DMSO_HD_RNAP_chipseq

description: 03_DMSO_HD_RNAP_rep.chip.fc.signal.bigwig

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-133


title: WT-48 hr O3 Replicate 2

source_name: WT-48 hr O3_homogenized mouse lung tissue


title: T_010


title: T_011


title: RNA-seq of Tumor WT 4

description:
RNA-seq of mCh+ tumor cells isolated from the bone marrow of wild-type C57BL/6J mouse
processed data file:
Tumor_Normalized_Counts.txt
Tumor_DESeq_Results.txt

source_name: RNA-seq of Tumor WT


title: rep1_DMSO_HD_ER_chipseq

value: Abcam 3575


title: WT-48 hr O3 Replicate 1


title: RNA-seq of Tumor WT 3


title: rep1_DMSO_HD_RING1B_chipseq