title: T47D_shRING1B_24hr_FOXA1_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. After transduction with pLKO-tet-on-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were treated with 100 ng/ml doxycycline for 5 days. After two days of doxycycline treatment, cells were washed and cultured in hormone-deprived media containing 100 ng/ml doxycycline for 3 days. After hormone deprivation, cells were treated with 10 nM estradiol for 24 hours before cross-linking with formaldehyde and collection for 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 and 50 ng of Spike-in chromatin (Active Motif 53083) weres 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. 2µg antibody was used for each histone ChIP, and 5ug was used for transcription factor ChIP (see Key Resources table for list of antibodies) along with 1ug of Spike-in antibodies (Active Motif 61686). 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.

value: pLKO-tet-on-shRING1B dox-inducible


title: T47D_shRING1B_24hr_RING1B_chipseq

status: Public on Jun 08 2020

type: SRA

city: Miami

first: Lluis

last: Morey

state: FL

department: Sylvester Comprehensive Cancer Center

country: USA

institute: University of Miami Miller School of Medicine

library_source: genomic

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. Shuf was used to subsample reads to 50 million. Peaks were called using MACS2 v2.1.0 using default parameters
ChIP-seq: Single-end ChIP-seq fastq files were processed using the AQUAS ChIP-seq Pipeline from the Kundaje Lab (https://github.com/kundajelab/chipseq_pipeline). Reads were trimmed using cutadapt v1.9.1. Reads were aligned to the hg19 genome using Bowtie2 v2.2.6, and the SAMtools v1.7 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v1.126. Peaks were called/signal tracks were generated using MACS2 v2.1.0, and peaks with fold change > 4 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
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 v2.7.1a 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 v2.26.0 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.

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

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

tag: cell source

value: ATCC #HTB-133

tag: modifications

tag: chip antibody

value: Active Motif C39663


title: GDNF12, primary cell tubuloids

city: Saint Louis

first: Eryn

middle: E

last: Dixon

state: MO

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

library_source: transcriptomic

data_processing:
For Expression Counts using BasePair, trim smallRNA adapters, align reads using STAR, count using FeatureCounts
For Differential Expression via DESeq2 algorithm, generate up/down lists, gct/cls files, volcano plot, heatmap
Genome_build: STAR alignment using NCBI reference (mouse genome mm10 or GRCm38)
Supplementary_files_format_and_content: Expression count

molecule: total RNA

organism: Mus musculus

source_name: primary cell tubuloids

growth_protocol: Primary cell fragments were plated in Matrigel, differentiated with growth factors, and cultured for seven days before extraction.

extract_protocol:
Tubuloids were removed from Matrigel using Corning recovery solution and RNA was isolated with Rneasy Plus Mini Kit.
Libraries were made with Clontech SMART-Seq v4 Ultra Low Input RNA kit (minimum concentration 2 ng/uL; with poly-A selection).

treatment_protocol: Tubuloids were plated and then received either growth factor enriched media with or without GDNF for a 24 hour pulse. After this timepoint, GDNF was removed from pulsed cultures and then all tubuloids continued to receive growth factor enriched media until extraction.

tag: tissue

value: postnatal day 7-10 kidney

tag: genotype

value: Pkd2fl/fl Pax8rtTA TetOCre mTmG

tag: treatment

value: GDNF


title: GDNF17, primary cell tubuloids


title: T47D_shRING1B_24hr_K27Ac_chipseq

value: Diagenode C15410196


title: T47D_RING1B_R98A_0hr_RNAseq_rep2

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 lentivirus made using the pLVK-RNF2-R98A plasmid, Fluorescence-Activated Cell Sorting (FACS) was used to select cells whose mCherry expression levels were in the top 25% of all cells. Cells were expanded, and FACS was performed once more to remove any cells without mCherry expression. The re-sorted cells were expanded, and the mutant RING1B expression level was compared with the endogenous RING1B expression level using immunoblot to make sure that the two levels are similar. Cells were then transduced with pLKO-shRING1B, and transduced cells were selected using a puromycin concentration of 2ug/ml. After 7 days of selection, 5 x 10^5 cells were plated into each well on a six-well plate in charcoal-stripped media containin 2ug/ml puromycin. Cells were hormone-deprived for 3 days before collection and RNA extraction for library preparation.

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: GDNF22, primary cell tubuloids


title: T47D_shRING1B_24hr_input_chipseq

value: none (input)


title: T47D_shCtrl_24hr_ER_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. After transduction with LT3GEPIR-shRenilla Luciferase, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were treated with 100 ng/ml doxycycline for 5 days. After two days of doxycycline treatment, cells were washed and cultured in hormone-deprived media containing 100 ng/ml doxycycline for 3 days. After hormone deprivation, cells were treated with 10 nM estradiol for 24 hours before cross-linking with formaldehyde and collection for ChIP-seq.

value: LT3GEPIR-shRenilla Luciferase dox inducible

value: Diagenode C15100061


title: naïve_FM-_rep2

city: Durham

first: Mari

middle: L

last: Shinohara

state: NC

department: Immunology

institute: Duke University School of Medicine

description:
repeat 2 pooled from 3 mice
SX-S8_S38

data_processing:
TrimGalore v0.4.0 for initial processing of fastq files
STAR v2.4.1d was used to align the reads ('--outFilterMultimapNmax 1' and '--alignSJoverhangMin 500' were the non-default parameters used)
HTSeq v0.6.1p1 to quantify gene expression ('-s reverse' was the non-default parameter used)
Genes were removed prior to normalization if they didn't have at least 10 reads in any one sample
EdgeR v3.8.5 was used for normalization and differential expression
Genome_build: ENSEMBL release GRCm38v73 of the mouse genome and transcriptome
Supplementary_files_format_and_content: Tab separated text files (.tsv) that contain the raw HTSeq counts as well as the EdgeR normalized expression values

source_name: alveolar macrophages

extract_protocol:
Lungs were removed, single suspension cells were achieved by enzymatic digestion of tissue, and alveolar macrophage subsets were harvested by FACS. RNA was harvested using Qiagen RNA micro plus kit.
Clontech Ultra Low Input RNA SMARTer mRNA amplification kit was used for the initial RNA amplification. The obtained dscDNA is then converted into a sequencing library using Kapa Hyper Prep Kit.
Sequenced on Illumina HiSeq 4000 with 50bp paired end reads

treatment_protocol: The animals were infected with Cryptococcus neoformans (intratracheally) for 9 hours

tag: strain

value: lung

tag: age

value: 6 weeks old


title: naïve_FM-_rep1

description:
repeat 1 pooled from 3 mice
SX-S6_S36


title: T47D_shCtrl_24hr_FOXA1_chipseq

value: Abcam ab23738


title: naïve_FM+_rep2

description:
repeat 2 pooled from 3 mice
SX-S7_S37


title: naïve_FM+_rep1

description:
repeat 1 pooled from 3 mice
SX-S5_S35


title: T47D_shCtrl_24hr_K27Ac_chipseq


title: T47D_RING1B_R98A_24hr_RNAseq_rep1

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 lentivirus made using the pLVK-RNF2-R98A plasmid, Fluorescence-Activated Cell Sorting (FACS) was used to select cells whose mCherry expression levels were in the top 25% of all cells. Cells were expanded, and FACS was performed once more to remove any cells without mCherry expression. The re-sorted cells were expanded, and the mutant RING1B expression level was compared with the endogenous RING1B expression level using immunoblot to make sure that the two levels are similar. Cells were then transduced with pLKO-shRING1B, and transduced cells were selected using a puromycin concentration of 2ug/ml. After 7 days of selection, 5 x 10^5 cells were plated into each well on a six-well plate in charcoal-stripped media containin 2ug/ml puromycin. Cells were hormone-deprived for 3 days before 24 hours of 10 nM E2 treatment. Cells were then collected, and RNA was extracted for library preparation.


title: T47D_shCtrl_24hr_input_chipseq


title: T47D_shCtrl_24hr_RING1B_chipseq


title: infected_FM-_CXCL2-_rep1

description:
repeat 1 pooled from 3 mice
SX-S4_S24


title: T47D_shRING1B_24hr_ER_chipseq


title: infected_FM-_CXCL2-_rep2

description:
repeat 2 pooled from 3 mice
SX-S4_S34


title: GDNF6, primary cell tubuloids


title: infected_FM-_CXCL2+_rep2

description:
repeat 2 pooled from 3 mice
SX-S3_S33


title: T47D_shRING1B_8hr_FOXA1_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. After transduction with pLKO-tet-on-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were treated with 100 ng/ml doxycycline for 5 days. After two days of doxycycline treatment, cells were washed and cultured in hormone-deprived media containing 100 ng/ml doxycycline for 3 days. After hormone deprivation, cells were treated with 10 nM estradiol for 8 hours before cross-linking with formaldehyde and collection for ChIP-seq.


title: infected_FM+_CXCL2-_rep2

description:
repeat 2 pooled from 3 mice
SX-S2_S32


title: infected_FM+_CXCL2-_rep1

description:
repeat 1 pooled from 3 mice
SX-S2_S22


title: infected_FM-_CXCL2+_rep1

description:
repeat 1 pooled from 3 mice
SX-S3_S23


title: infected_FM+_CXCL2+_rep2

description:
repeat 2 pooled from 3 mice
SX-S1_S31


title: T47D_shRING1B_8hr_ER_chipseq


title: infected_FM+_CXCL2+_rep1

description:
repeat 1 pooled from 3 mice
SX-S1_S21


title: T47D_shRING1B_8hr_input_chipseq


title: T47D_shCtrl_8hr_RING1B_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. After transduction with LT3GEPIR-shRenilla Luciferase, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were treated with 100 ng/ml doxycycline for 5 days. After two days of doxycycline treatment, cells were washed and cultured in hormone-deprived media containing 100 ng/ml doxycycline for 3 days. After hormone deprivation, cells were treated with 10 nM estradiol for 8 hours before cross-linking with formaldehyde and collection for ChIP-seq.


title: T47D_shCtrl_8hr_FOXA1_chipseq


title: T47D_shCtrl_8hr_K27Ac_chipseq


title: T47D_shRING1B_45min_ER_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. After transduction with pLKO-tet-on-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were treated with 100 ng/ml doxycycline for 5 days. After two days of doxycycline treatment, cells were washed and cultured in hormone-deprived media containing 100 ng/ml doxycycline for 3 days. After hormone deprivation, cells were treated with 10 nM estradiol for 45 minutes before cross-linking with formaldehyde and collection for ChIP-seq.


title: T47D_shCtrl_8hr_input_chipseq


title: T47D_shRING1B_45min_FOXA1_chipseq


title: T47D_shRING1B_45min_RING1B_chipseq


title: T47D_shRING1B_45min_K27Ac_chipseq


title: T47D_shRING1B_45min_input_chipseq


title: T47D_shRING1B_8hr_K27Ac_chipseq


title: T47D_shCtrl_45min_ER_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. After transduction with LT3GEPIR-shRenilla Luciferase, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were treated with 100 ng/ml doxycycline for 5 days. After two days of doxycycline treatment, cells were washed and cultured in hormone-deprived media containing 100 ng/ml doxycycline for 3 days. After hormone deprivation, cells were treated with 10 nM estradiol for 45 minutes before cross-linking with formaldehyde and collection for ChIP-seq.


title: T47D_shCtrl_8hr_ER_chipseq


title: T47D_shCtrl_45min_RING1B_chipseq


title: T47D_shCtrl_45min_FOXA1_chipseq


title: T47D_shCtrl_45min_K27Ac_chipseq


title: T47D_shRING1B_0_ER_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. After transduction with pLKO-tet-on-shRING1B, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were treated with 100 ng/ml doxycycline for 5 days. After two days of doxycycline treatment, cells were washed and cultured in hormone-deprived media containing 100 ng/ml doxycycline for 3 days. Cells were then cross-linked and collected for ChIP-seq.


title: T47D_shRING1B_0_FOXA1_chipseq


title: T47D_shCtrl_45min_input_chipseq


title: T47D_shRING1B_0_RING1B_chipseq


title: T47D_shRING1B_0_K27Ac_chipseq


title: Crohn's_Disease__patient34

type: RNA

city: Barcelona

first: Adrià

last: Aterido

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

description: RNA extracted from an instestinal biopsy of a CD patient

hyb_protocol: Biotin labeled cRNA (10ug) was hybridized on CodeLink™ Human Whole Genome Bioarray overnight at 37°C (Applied Microarrays, AZ, USA). Labeling with Cy5-streptavidin was performed.

scan_protocol: Scanning was performed on InnoScan® 700 microarray scanner and Mapix Software (ArrayIt Corporation, CA, USA)

data_processing: Raw data include raw intensity values from all gene expression microarray probes (n=56,448 probes, Platform GPL2895). Non-normalized data include intensity values on the log2 scale for a total of 20,902 probes that passed the quality control analysis (Probes with RefSeq annotation -April 2015- and mapping to a single gene).  Log2 transformation of GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray raw data, RefSeq probe annotation update (16th April, 2015), quantile normalization and batch effect adjustment using the preprocessCore and Combat R packages, respectively.

label: Biotin

source_name: intestinal mucosa

label_protocol: Total RNA (1μg) was primed for reverse transcription with oligo-dT primer containing the T7 RNA polymerase promoter site. After second-strand cDNA synthesis, the dscDNA served as the template for an in vitro transcription (IVT) reaction to produce the target cRNA. IVT was performed by the linear amplification method in the presence of biotin-modified UTP to label the target cRNA. MessageAmp TM II-Biotin Enhanced kit was used (Ambion, Ma, USA).

extract_protocol: Total RNA, including small RNA, from ileocolectomy samples was insolated using RNAeasy® Mini Kit extraction (QIAGEN Inc., CA, USA) following manufacturer's instructions. The samples were previously stabilizaded with RNAlater reagent during 24h. RNA quality and integrity were analyzed by Experion bioanalyzer (Bio-Rad, CA, USA).

value: intestinal mucosa

tag: inflammation

value: Non-inflamed margin


title: Crohn's_Disease__patient35


title: Crohn's_Disease__patient37


title: Crohn's_Disease__patient39


title: Crohn's_Disease__patient36


title: Crohn's_Disease__patient33


title: Crohn's_Disease__patient32


title: Crohn's_Disease__patient28


title: Crohn's_Disease__patient30


title: T47D_shRING1B_0_input_chipseq


title: Crohn's_Disease__patient29


title: Crohn's_Disease__patient31


title: Crohn's_Disease__patient38


title: Crohn's_Disease__patient24


title: T47D_shCtrl_0hr_ER_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. After transduction with LT3GEPIR-shRenilla Luciferase, cells were selected and maintained in media containing 2 ug/ml puromycin. Cells were treated with 100 ng/ml doxycycline for 5 days. After two days of doxycycline treatment, cells were washed and cultured in hormone-deprived media containing 100 ng/ml doxycycline for 3 days. Cells were then cross-linked and collected for ChIP-seq.


title: Crohn's_Disease__patient23


title: T47D_shCtrl_0hr_FOXA1_chipseq


title: Crohn's_Disease__patient26


title: Crohn's_Disease__patient25


title: T47D_shCtrl_0hr_input_chipseq


title: T47D_shCtrl_0hr_K27Ac_chipseq


title: Crohn's_Disease__patient27


title: Healthy_control_subject14

description: RNA extracted from an instestinal biopsy of a healthy control subject

value: Control


title: T47D_rep2_shRING1B_24hr_atacseq

description: rep2 combined with rep 1 (see sample 10)

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 24 hrs of E2 treatment followed by cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.

extract_protocol:
ATAC-seq experiments were performed as previously described (Buenrostro et al., 2013). Cells were previously cryopreserved and thawed immediately preceding the experiment. 50,000 alive cells were used for the experiment. Samples were purified with a MinElute Reaction Cleanup kit (Qiagen cat# 28206) and DNA eluted in 10μl of EB Buffer.
The ATAC-seq library construction was performed as previously described (Buenrostro et al, 2013) with the additional following step: size selection was performed by using the AMPure XP beads (Beckman Coulter #A63881) at 1.8x the PCR volume to remove fragments smaller than 100 bp. To determine the average fragment size of each library, samples were run through a High-sensitivity DNA screentape (Agilent Technologies cat# 5067-5584) following the manufacturer’s instructions on an Agilent Technologies 2200 TapeStation machine. To determine the concentration of each library, Qubit dsDNA high sensitivity reagents (Thermo Fisher Scientific cat# Q32851) were used following the manufacturer’s instructions on a Qubit 3 fluorometer.

value: pLKO-shRING1B stable


title: Crohn's_Disease__patient20


title: Crohn's_Disease__patient21


title: T47D_rep2_shRING1B_12hr_atacseq

description: rep2 combined with rep 1 (see sample 9)

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 12 hrs of E2 treatment followed by cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.

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


title: T47D_rep2_shRING1B_4hr_atacseq

description: rep2 combined with rep 1 (see sample 7)

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 4 hrs of E2 treatment followed by cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.

value: ATCC #HTB-133


title: T47D_rep2_shRING1B_0hr_atacseq

description: rep2 combined with rep 1 (see sample 6)

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 cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.


title: T47D_rep2_shRING1B_8hr_atacseq

description: rep2 combined with rep 1 (see sample 8)

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 8 hrs of E2 treatment followed by cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.


title: T47D_shCtrl_0hr_RING1B_chipseq

value: Active Motif C39663


title: T47D_rep2_shCtrl_24hr_atacseq

description: rep2 combined with rep 1 (see sample 5)

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 24 hrs of E2 treatment followed by cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.

value: pLKO-shCtrl stable


title: T47D_rep2_shCtrl_12hr_atacseq

description: rep2 combined with rep 1 (see sample 4)

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 12 hrs of E2 treatment followed by cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.


title: Crohn's_Disease__patient22


title: Healthy_control_subject13


title: T47D_rep2_shCtrl_4hr_atacseq

description: rep2 combined with rep 1 (see sample 2)

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 4 hrs of E2 treatment followed by cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.


title: T47D_rep2_shCtrl_0hr_atacseq

description: rep2 combined with rep 1 (see sample 1)

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 cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.


title: T47D_rep1_shRING1B_24hr_atacseq


title: Healthy_control_subject12


title: T47D_rep1_shRING1B_12hr_atacseq


title: Crohn's_Disease__patient17

value: Inflamed margin


title: Crohn's_Disease__patient18


title: T47D_rep1_shRING1B_8hr_atacseq


title: Healthy_control_subject11


title: Healthy_control_subject9


title: Healthy_control_subject10


title: Crohn's_Disease__patient16


title: Crohn's_Disease__patient19


title: Crohn's_Disease__patient15


title: Healthy_control_subject8


title: T47D_rep2_shCtrl_8hr_atacseq

description: rep2 combined with rep 1 (see sample 3)

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 8 hrs of E2 treatment followed by cryopreservation. At a later day, these same cells were thawed and immediately used for the transposase reaction.


title: Crohn's_Disease__patient14


title: T47D_rep1_shCtrl_12hr_atacseq


title: T47D_rep1_shCtrl_24hr_atacseq


title: Crohn's_Disease__patient13


title: T47D_rep1_shCtrl_8hr_atacseq


title: T47D_rep1_shCtrl_4hr_atacseq


title: Crohn's_Disease__patient10


title: Healthy_control_subject7


title: Crohn's_Disease__patient9


title: Crohn's_Disease__patient8


title: Healthy_control_subject6


title: T47D_rep1_shRING1B_4hr_atacseq


title: ChIP-Seq: ARID1A-KO1 H3K27me3 rep3

city: Baltimore

first: Yohan

last: Suryo Rahmanto

state: MD

address: CRB-2, Rm 376, 1550 Orleans St

department: Department of Pathology

institute: Johns Hopkins School of Medicine

data_processing:
Alignment - For each sample, single-end ChIP-seq reads were aligned to hg19 by Bowtie v0.12.7 (PMID: 19261174), and uniquely mapped reads were selected for analysis, using the parameter option ‘-m 1’. Aligned reads were stored in BAM format using SAMtools v0.1.19 (PMID: 19505943).    Peak calling - ChIP-seq peaks were called by MACS2 v2.1.0 (PMID: 18798982) using matched sample and input BAM files. For each transcription factor (ARID1A, BRG1, and RNA Pol II), narrow peaks were called by setting the q-value at 0.01. For histone markers (H3K9me3, H3K27me3, H3K9Ac, and H3K27Ac), broad peaks were called using the broad peak detection mode of MACS2 with a q-value cutoff of 0.05.    Peak comparison, annotation, and quantification - ChIP-seq peaks were further compared and annotated using HOMER v4.7.2 (PMID: 20513432). ARID1A consensus peaks and ARID1A/BRG1 consensus peaks were identified by the tool ‘mergePeaks’ considering peaks separated by less than 100 bp as common peaks. We annotated each peak using the ‘annotatePeaks.pl’ function of HOMER. A histogram of read intensities in a 6 kb window around the peak center (option ‘-size 3000 -bin 50’) was generated. For each pair of ARID1AWT and ARID1AKO ChIP-seq experiments, we drew their read intensity histograms based on both ARID1A consensus peaks and ARID1A/BRG1 consensus peaks.    PCA analysis - ChIP-seq read coverage was quantified in bedGraph format by MACS2 with ‘-B’ option and further converted to bigwig files by deepTools v2.4.3 (PMID: 24799436). PCA analysis was performed using the plotPCA function. The first 3 principle components were extracted to plot the figure in three dimensions.    ChIP-seq intensities in gene regions - The gene region information for hg19 was extracted from the RefSeq annotation file, which was downloaded from the UCSC genome browser (PMID: 25428374), and included 28,830 genes. The ChIP-seq read intensity plots at gene regions were generated by deepTools. In detail, first, ChIP-seq read coverage was quantified using ‘bamCoverage’ with options ‘--normalizeTo1x 2451960000 --ignoreDuplicates --extendReads 200’. Read intensities at gene regions from 3 kb before the transcription start site (TSS) until 3 kb after the transcription end site (TES) were extracted from the read coverage using the ‘scale-region’ command of ‘computeMatrix’. Here, we scaled the length of gene regions to 5 kb. Finally, read intensity curves were plotted by ‘plotProfile’.    ChIP-seq intensities in active enhancer regions - First, we identified enhancer marker H3K27Ac peaks in ARID1AWT cells using MACS2 with a q-value cutoff 0.05. As candidate enhancer regions, we selected distal H3K27Ac peaks which were at least 3 kb from the nearest downstream TSS. We limited the distance to 200 kb and identified 13,098 candidate enhancer regions. For each paired ARID1AWT and ARID1AKO ChIP-seq data point, read tag intensity was calculated in a 6 kb window around the center of each enhancer region using the function ‘annotatePeaks.pl’ of HOMER, and further transformed into log2 format for plotting. In the same figure, we plotted three reference lines of fold-change 0.5, 1, and 2.
Genome_build: hg19

source_name: endometrial epithelial cells

growth_protocol: The cell lines used in this study were maintained at 37°C and 5% CO2, and included immortalized isogenic human endometrial epithelial ARID1AWT and ARID1AKO cells. ARID1AWT and ARID1AKO cells were cultured in RPMI 1640 medium supplemented with 15% FBS, 1% MEM non-essential amino acids, and 1% penicillin/streptomycin.

extract_protocol:
The chromatin immunoprecipitation (ChIP) assay was performed as previously described on the two independent clones of human endometrial epithelial ARID1AWT and ARID1AKO cells (PMID: 26953344) with the following modifications. Cells were grown in 15 cm dishes, and approximately 1.2×107 cells were cross-linked using Diagenode ChIP cross-link Gold and 1% formaldehyde according to the manufacturer’s instruction. Nuclear contents were extracted using the truChIP Chromatin Shearing kit (Covaris) according to the manufacturer's instructions. Chromatin was sheared for 12 mins in shearing buffer by using a Covaris E220 focused ultrasonicator. The fragment size was ensured to be between 200-600 bp. The sonicated lysates were diluted 5-fold with ChIP dilution buffer (0.1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 7.5, 150 mM NaCl, and 1× protease inhibitor), and immunoprecipitated with rotation overnight at 4°C with 0.5-3 µg of antibodies. The antibody/chromatin complex was then precipitated for 3 h by Protein A/G DYNAL magnetic beads (40 µl of 1:1 mixture). Antibody-protein complexes bound to beads were washed once with low salt buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% SDS, 1% Triton-X100, and 2 mM EDTA), once with high salt buffer (20 mM Tris-HCl pH 7.5, 500 mM NaCl, 0.1% SDS, 1% Triton-X100, and 2 mM EDTA), once with LiCl buffer (250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8.0), and twice with TE, pH 8.0. For sequential ChIP, immunocomplex from the first ChIP was eluted with 10 mmol/L dithiothreitol in Tris-EDTA buffer at 37°C and subjected to second round of ChIP. DNA and protein complexes were digested in TE buffer containing 1% SDS, 200 mM NaCl and 1U Proteinase K (Thermo Scientific) at 56°C for 2h, and cross-linking was reversed by heating at 65°C for 4h. DNA fragments were purified using a QIAquick PCR Purification Kit in 55 µl of EB elution buffer.
Tru-seq ChIP-seq library preparation and sequencing using a NextSeq500 platform with single-end reads of 75 bases were performed by JHMI Deep Sequencing and Microarray Core

treatment_protocol: Two biological pairs of wild-type (ARID1AWT) and knockout (ARID1AKO) cells were used (PMID: 26953344). These pairs of isogenic ARID1A wildtype and knockout cell lines were established from human endometrial using a CRISPR/Cas9 genome editing method.

value: endometrial epithelial cells

value: ARID1A KO

tag: biological replicate

tag: technical replicate

value: trimethyl-Histone H3 Lys27  (Millipore, #07-449)


title: T47D_rep1_shCtrl_0hr_atacseq


title: ChIP-Seq: ARID1A-KO1 H3K27me3 rep2


title: ChIP-Seq: ARID1A-KO1 H3K27me3 rep1


title: Crohn's_Disease__patient6


title: T47D_rep1_shRING1B_0hr_atacseq


title: Crohn's_Disease__patient7


title: Crohn's_Disease__patient12


title: ChIP-Seq: ARID1A-WT1 H3K27me3 rep3

value: ARID1A WT


title: ChIP-Seq: ARID1A-WT1 H3K27me3 rep2


title: ChIP-Seq: ARID1A-WT1 H3K27me3 rep1


title: ChIP-Seq: ARID1A-KO2 H3K27Ac rep3

value: Acetyl-Histone H3 (Lys27) (CST, #8173)


title: Healthy_control_subject5


title: ChIP-Seq: ARID1A-KO2 H3K27Ac rep2


title: ChIP-Seq: ARID1A-KO2 H3K27Ac rep1


title: Crohn's_Disease__patient4


title: Crohn's_Disease__patient11


title: Crohn's_Disease__patient5


title: ChIP-Seq: ARID1A-WT2 H3K27Ac rep2


title: Healthy_control_subject4


title: Crohn's_Disease__patient2


title: ChIP-Seq: ARID1A-WT2 H3K27Ac rep3


title: ChIP-Seq: ARID1A-WT2 H3K27Ac rep1


title: Astrocyte_WT_Rep2_ATAC-seq

city: Atlanta

first: Isaac

last: Kremsky

state: GA

address: 1510 Clifton Rd

department: Biology

institute: Emory University

data_processing:
ATAC-seq raw reads were trimmed using pyadapter_trim.py.
Reads were aligned to the “MacaM_Rhesus_Genome_Annotation_v7.8.2” genome using Tophat2 v2.1.0 with the flags, “--no-mixed –no-discordant” for RNA-seq, and using bowtie version 2 2.2.6 with the flag, “-X 2000” for ATAC-seq.
Non-uniquely mapped reads were excluded from both RNA-seq and ATAC-seq samples, and duplicates were removed from ATAC-seq samples using picard-tools-2.1.7 MarkDuplicates.
For ATAC-seq, only fragments < 115 bp in length were kept, as those indicate transcription factor binding.
.bam files were converted to .bed using “bamToBed -split” for RNA-seq, and .bedpe using “bamToBed -bedpe” for ATAC-seq.  The ATAC-seq .bedpe file was converted to a bed file containing only the beginning and end of each fragment.
.bed files were converted to bedGraph using “bedtools genomecov -scale”, where the scale factor was the total number of uniquely mapped reads for RNA-seq, and the total number of uniquely mapped, non-duplicate fragments for ATAC-seq.  The result is an RPM-normalized .bedGraph file for each replicate. .bedGraph files were then converted to bigwig using “bedGraphToBigWig”
Genome_build: MacaM_Rhesus_Genome_Annotation_v7.8.2
Supplementary_files_format_and_content: bigwig files of RPM-normalized signal.

organism: Macaca mulatta

source_name: Astrocytes

extract_protocol:
ell cultures were harvested, washed in cold 1x PBS, and counted. One hundred thousand cells were resuspended in 50 µL cold resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2) containing 0.1% NP-40 (Sigma), 0.1% Tween-20 (Sigma), and 0.01% digitonin (Abcam ab141501) and incubated for 3 min on ice. Following lysis, 1 mL RSB with 0.01% Tween-20 was added to the samples. Samples were centrifuged for 10 min at 4°C/500 x g and the supernatant was carefully removed. Nuclei were then resuspended in the transposase reaction mix (25 µL 2x TD buffer, 2.5 µL Tn5 transposase, 0.5 µL 10% Tween-20, 2.5 µL 1% digitonin [0.05% final concentration], and 19.5 µL water) and incubated at 37°C for 30 min in a thermomixer with shaking at 600 r.p.m. Following the reaction, samples were treated with Proteinase K (Fisher 25530015) at 55°C for 2 hr and genomic DNA was isolated via phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation.
Library preparation was performed using 2x KAPA HiFi mix (KAPA BIOSYSTEMS INC #kk4604) and 1 mM indexed primers under the following PCR conditions: 72°C for 5 min; 98°C for 30 sec; and 8-12 cycles at 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min. ATAC-seq experiments were performed on two replicates

value: Astrocytes

tag: disease state

value: wild type


title: Astrocyte_WT_Rep1_ATAC-seq


title: ChIP-Seq: ARID1A-KO1 H3K27Ac rep3


title: Crohn's_Disease__patient1


title: ChIP-Seq: ARID1A-KO1 H3K27Ac rep2


title: Day3_WT_Rep2_ATAC-seq

source_name: Developing astrocytes

value: Developing astrocytes


title: Crohn's_Disease__patient3

value: intestinal mucosa


title: Astrocyte_HD_Rep2_ATAC-seq

value: Huntington’s Disease


title: ChIP-Seq: ARID1A-KO1 H3K27Ac rep1


title: NPC_WT_Rep2_ATAC-seq

source_name: Neural progenitor cells

value: Neural progenitor cells


title: Healthy_control_subject1

value: Control


title: ChIP-Seq: ARID1A-WT1 H3K27Ac rep3


title: Day3_WT_Rep1_ATAC-seq


title: NPC_WT_Rep1_ATAC-seq


title: ChIP-Seq: ARID1A-WT1 H3K27Ac rep2


title: ChIP-Seq: ARID1A-KO1 H3K9me3 rep3

value: Histone H3 trimethyl K9 (Abcam, #ab8898)


title: Healthy_control_subject2


title: ChIP-Seq: ARID1A-WT1 H3K27Ac rep1


title: ChIP-Seq: ARID1A-KO1 H3K9me3 rep2


title: NPC_HD_Rep2_ATAC-seq


title: NPC_HD_Rep1_ATAC-seq


title: ChIP-Seq: ARID1A-KO1 H3K9me3 rep1


title: Healthy_control_subject3


title: ChIP-Seq: ARID1A-WT1 H3K9me3 rep2


title: PSC_HD_Rep2_ATAC-seq

source_name: Pluripotent stem cells

value: Pluripotent stem cells


title: ChIP-Seq: ARID1A-WT1 H3K9me3 rep3


title: PSC_WT_Rep1_ATAC-seq


title: PSC_HD_Rep1_ATAC-seq


title: ChIP-Seq: ARID1A-KO1 H3K9Ac rep3

value: Acetyl-Histone H3 (Lys9) (CST, #9649)


title: ChIP-Seq: ARID1A-WT1 H3K9me3 rep1


title: ChIP-Seq: ARID1A-WT1 H3K9Ac rep2


title: ChIP-Seq: ARID1A-KO1 H3K9Ac rep2


title: PSC_HD_Rep2_RNA-seq

extract_protocol:
The RNA was extracted using Qiagen miRNeasy Mini Kit with DNase digestion. The RNA quantity and quality were validated using Nanodrop 2000 Spectrophotometer and Agilent’s 4200 Bioanalyzer Capillary electrophoresis.
Amplified mRNA was fragmented, and barcodes were added using Illumina’s Nextera XT kits. Amplified Libraries were validated by Agilent 4200 Tapestation and quantified using a Qubit fluorimeter. Libraries were normalized, pooled and clustered on an Illumina HiSeq 3000/4000 Flowcell using the Illumina cBOT. The libraries were sequenced on an Illumina HiSeq 3000 system in 101-base single-read reactions with multiplexing to achieve approximately 20 million reads per sample. RNA-seq experiments were performed in three different replicates.


title: Astrocyte_WT_Rep1_RNA-seq


title: ChIP-Seq: ARID1A-KO2 RNA Pol2 rep1

value: RNA Polymerase II (Abcam, #ab5095)


title: ChIP-Seq: ARID1A-KO2 RNA Pol2 rep3


title: ChIP-Seq: ARID1A-WT1 H3K9Ac rep1


title: ChIP-Seq: ARID1A-KO1 H3K9Ac rep1


title: Astrocyte_HD_Rep2_RNA-seq


title: Day3_HD_Rep1_RNA-seq


title: Day3_HD_Rep2_RNA-seq


title: ChIP-Seq: ARID1A-KO1 RNA Pol2 rep3


title: ChIP-Seq: ARID1A-WT2 RNA Pol2 rep3


title: PSC_HD_Rep3_RNA-seq


title: PSC_WT_Rep2_ATAC-seq


title: 97_eIF4B_42C_CHX_16min

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
97_eIF4B_42C_CHX_16min_NNNAGAGC
processed data file:
97_99_eIF4B_42C_CHX_16min_merged_minus_strand.bedgraph
97_99_eIF4B_42C_CHX_16min_merged_plus_strand.bedgraph

data_processing:
library strategy: CRAC-seq
Demultiplexing. Command: pyBarcodeFilter.py -f raw_file.fastq -b barcodes_file.txt
Adapter stripping and quality control. Command: flexbar -r file.fastq -a adapters.txt -ao 4 -m 11 -at RIGHT -u 2 -q TAIL -qf i1.8
Collapsing. Command: pyFastqDuplicateRemover.py -f file.fastq (Note that this step was used only for the CRAC analysis. RNAseq files were not collapsed)
Removal of low-complexity reads. Command: bbduk.sh in=file.fasta entropy=0.5 entropywindow=10 entropyk=6
Alignment. Command: novoalign -f file.fasta -r Random -o SAM -d genome.novoindex
samtools view -bS file.sam
samtools sort file.bam
Bedgraph files (+ strand). Command: bedtools genomecov -split -strand + -ibam sorted_file.bam -bg -scale variable > file_plus_strand.bedgraph
Bedgraph files (- strand). Command: bedtools genomecov -split -strand - -ibam sorted_file.bam -bg -scale variable > file_minus_strand.bedgraph
Read counting. Command: pyReadCounters.py -f file.bam --file_type=bam --sense --gtf=annotation_file.gtf
Genome_build: Saccharomyces cerevisiae EF4.74 with the introns artificially removed to improve mapping
Supplementary_files_format_and_content: The .txt files (generated using pyReadCounters.py) contain information on the number of reads mapping to each transcript. The bedgraph files show the distribution of reads across the genome. Individual replicates were merged into a single file to generate the bedgraph files.

organism: Saccharomyces cerevisiae

growth_protocol: For CRAC experiments (07-99), cells were cultured in SC -TRP medium containing 2% glucose to 0.4 OD. For the 'control', cells were then subjected to 100 mJ of 254nm UV-crosslinking (4-6 seconds), collected by filtration, resuspended in 50 mL of ice cold PBS, centrifuged to pellet, and frozen at -80°C. For all other conditions,  cells at 0.4 OD were first collected by filtration,  then transferred to the appropriate medium and cultured for either 30 seconds or 16 minutes prior to UV-crosslinking. All subsequent harvesting steps were identical to the control. For RNAseq experiments (A-F), we used the same approach as for CRAC but without the crosslinking step.

extract_protocol:
The CRAC protocol is based on Tuck and Tollervey, 2013.
Modifications are described in Bresson and Tollervey, 2020.

tag: cell/ploidy type

value: haploid cells

tag: genotype/variation

tag: molecule subtype

value: RNA crosslinked to protein


title: ChIP-Seq: ARID1A-WT1 RNA Pol2 rep3

value: endometrial epithelial cells


title: ChIP-Seq: ARID1A-KO2 RNA Pol2 rep2

value: ARID1A KO


title: ChIP-Seq: ARID1A-KO1 RNA Pol2 rep2


title: ChIP-Seq: ARID1A-WT1 RNA Pol2 rep2

value: ARID1A WT


title: 99_eIF4B_42C_CHX_16min

description:
99_eIF4B_42C_CHX_16min_NNNCACTAGC
processed data file:
97_99_eIF4B_42C_CHX_16min_merged_minus_strand.bedgraph
97_99_eIF4B_42C_CHX_16min_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-WT2 RNA Pol2 rep2


title: ChIP-Seq: ARID1A-WT2 RNA Pol2 rep1


title: PSC_WT_Rep1_RNA-seq


title: ChIP-Seq: ARID1A-WT1 H3K9Ac rep3


title: ChIP-Seq: ARID1A-KO1 RNA Pol2 rep1


title: 98_eIF4B_42C_16min

description:
98_eIF4B_42C_16min_NNNGTGAGC
processed data file:
23_56_75_98_eIF4B_42C_16min_merged_minus_strand.bedgraph
23_56_75_98_eIF4B_42C_16min_merged_plus_strand.bedgraph


title: 82_eIF4A_GE_30s

description:
82_eIF4A_GE_30s_NNNCACTAGC
processed data file:
51_79_82_eIF4A_GE_30s_merged_minus_strand.bedgraph
51_79_82_eIF4A_GE_30s_merged_plus_strand.bedgraph

value: GE


title: ChIP-Seq: ARID1A-WT1 RNA Pol2 rep1


title: 81_eIF4A_mock_16min

description:
81_eIF4A_mock_16min_NNNGTGAGC
processed data file:
17_53_77_81_eIF4A_mock_16min_merged_minus_strand.bedgraph
17_53_77_81_eIF4A_mock_16min_merged_plus_strand.bedgraph

value: mock


title: ChIP-Seq: ARID1A-KO2  BRG1 rep2


title: ChIP-Seq: ARID1A-WT2  BRG1 rep2


title: ChIP-Seq: ARID1A-WT2  BRG1 rep3


title: ChIP-Seq: ARID1A-WT2  BRG1 rep1


title: 80_eIF4A_control

description:
80_eIF4A_control_NNNATCACG
processed data file:
11_13_18_52_76_80_eIF4A_control_merged_minus_strand.bedgraph
11_13_18_52_76_80_eIF4A_control_merged_plus_strand.bedgraph

value: control


title: 73_eIF4B_GE_30s

description:
73_eIF4B_GE_30s_NNNGCGCAGC
processed data file:
72_73_eIF4B_GE_30s_merged_minus_strand.bedgraph
72_73_eIF4B_GE_30s_merged_plus_strand.bedgraph


title: 76_eIF4A_control

description:
76_eIF4A_control_NNNCGTGAT
processed data file:
11_13_18_52_76_80_eIF4A_control_merged_minus_strand.bedgraph
11_13_18_52_76_80_eIF4A_control_merged_plus_strand.bedgraph


title: 79_eIF4A_GE_30s

description:
79_eIF4A_GE_30s_NNNTAGTGC
processed data file:
51_79_82_eIF4A_GE_30s_merged_minus_strand.bedgraph
51_79_82_eIF4A_GE_30s_merged_plus_strand.bedgraph


title: 77_eIF4A_mock_16min

description:
77_eIF4A_mock_16min_NNNGCACTA
processed data file:
17_53_77_81_eIF4A_mock_16min_merged_minus_strand.bedgraph
17_53_77_81_eIF4A_mock_16min_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO2  BRG1 rep1


title: 72_eIF4B_GE_30s

description:
72_eIF4B_GE_30s_NNNATTAGC
processed data file:
72_73_eIF4B_GE_30s_merged_minus_strand.bedgraph
72_73_eIF4B_GE_30s_merged_plus_strand.bedgraph


title: 83_eIF4A_42C_16min

description:
83_eIF4A_42C_16min_NNNAGAGC
processed data file:
15_16_54_83_eIF4A_42C_16min_merged_minus_strand.bedgraph
15_16_54_83_eIF4A_42C_16min_merged_plus_strand.bedgraph


title: 74_eIF4B_mock_16min

description:
74_eIF4B_mock_16min_NNNCGCTTAGC
processed data file:
25_55_74_eIF4B_mock_merged_minus_strand.bedgraph
25_55_74_eIF4B_mock_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO1  BRG1 rep3


title: 71_eIF4B_control

description:
71_eIF4B_control_NNNTAAGC
processed data file:
08_21_26_71_eIF4B_control_merged_minus_strand.bedgraph
08_21_26_71_eIF4B_control_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO1  BRG1 rep2


title: ChIP-Seq: ARID1A-KO2 AR-CST rep3


title: ChIP-Seq: ARID1A-KO1  BRG1 rep1


title: 70_Ded1_GE_30s

description:
70_Ded1_GE_30sec_NNNATCACG
processed data file:
69_70_Ded1_GE_30sec_merged_minus_strand.bedgraph
69_70_Ded1_GE_30sec_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO2 AR-CST rep2


title: ChIP-Seq: ARID1A-WT1  BRG1 rep2


title: ChIP-Seq: ARID1A-WT1  BRG1 rep1


title: 69_Ded1_GE_30s

description:
69_Ded1_GE_30sec_NNNTAGTGC
processed data file:
69_70_Ded1_GE_30sec_merged_minus_strand.bedgraph
69_70_Ded1_GE_30sec_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO2  BRG1 rep3


title: ChIP-Seq: ARID1A-WT1  BRG1 rep3


title: 66_Ded1_mock_16min

description:
66_Ded1_mock_NNNCTAGC
processed data file:
58_66_Ded1_mock_merged_minus_strand.bedgraph
58_66_Ded1_mock_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO2 AR-CST rep1


title: 67_Ded1_GE_16min

description:
67_Ded1_GE_16min_NNNTGGAGC
processed data file:
59_62_67_Ded1_GE_16min_merged_minus_strand.bedgraph
59_62_67_Ded1_GE_16min_merged_plus_strand.bedgraph


title: 68_Ded1_42C_16min

description:
68_Ded1_42C_16min_NNNCGTGAT
processed data file:
60_63_68_Ded1_42C_16min_merged_minus_strand.bedgraph
60_63_68_Ded1_42C_16min_merged_plus_strand.bedgraph


title: 65_Ded1_control

description:
65_Ded1_control_NNNAGAGC
processed data file:
57_61_65_Ded1_control_merged_minus_strand.bedgraph
57_61_65_Ded1_control_merged_plus_strand.bedgraph


title: 63_Ded1_42C_16min

description:
63_Ded1_42C_16min_NNNGACTTAGC
processed data file:
60_63_68_Ded1_42C_16min_merged_minus_strand.bedgraph
60_63_68_Ded1_42C_16min_merged_plus_strand.bedgraph


title: 75_eIF4B_42C_16min

description:
75_eIF4B_42C_16min_NNNTCTCTAGC
processed data file:
23_56_75_98_eIF4B_42C_16min_merged_minus_strand.bedgraph
23_56_75_98_eIF4B_42C_16min_merged_plus_strand.bedgraph


title: 64_untagged

source_name: untagged

value: untagged


title: 62_Ded1_GE_16min

description:
62_Ded1_GE_16min_NNNACTCAGC
processed data file:
59_62_67_Ded1_GE_16min_merged_minus_strand.bedgraph
59_62_67_Ded1_GE_16min_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-WT2 AR-CST rep3


title: ChIP-Seq: ARID1A-WT2 AR-CST rep2


title: 61_Ded1_control

description:
61_Ded1_control_NNNTCTCTAGC
processed data file:
57_61_65_Ded1_control_merged_minus_strand.bedgraph
57_61_65_Ded1_control_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO1 AR-CST rep3


title: ChIP-Seq: ARID1A-WT2 AR-CST rep1


title: 60_Ded1_42C_16min

description:
60_Ded1_42C_16min_NNNCACTAGC
processed data file:
60_63_68_Ded1_42C_16min_merged_minus_strand.bedgraph
60_63_68_Ded1_42C_16min_merged_plus_strand.bedgraph


title: 59_Ded1_GE_16min

description:
59_Ded1_GE_16min_NNNGTGAGC
processed data file:
59_62_67_Ded1_GE_16min_merged_minus_strand.bedgraph
59_62_67_Ded1_GE_16min_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO1 AR-CST rep2


title: ChIP-Seq: ARID1A-KO1 AR-CST rep1


title: 58_Ded1_mock_16min

description:
58_Ded1_mock_16min_NNNATTAGC
processed data file:
58_66_Ded1_mock_merged_minus_strand.bedgraph
58_66_Ded1_mock_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-WT1 AR-CST rep2


title: 57_Ded1_control

description:
57_Ded1_control_NNNTAAGC
processed data file:
57_61_65_Ded1_control_merged_minus_strand.bedgraph
57_61_65_Ded1_control_merged_plus_strand.bedgraph


title: 56_eIF4B_42C_16min

description:
56_eIF4B_42C_16min_NNNCGTGAT
processed data file:
23_56_75_98_eIF4B_42C_16min_merged_minus_strand.bedgraph
23_56_75_98_eIF4B_42C_16min_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-WT1 AR-CST rep1


title: ChIP-Seq: ARID1A-KO2 Input rep2


title: ChIP-Seq: ARID1A-KO2 Input rep3


title: ChIP-Seq: ARID1A-WT2 Input rep3


title: 54_eIF4A_42C_16min

description:
54_eIF4A_42C_16min_NNNGACTTAGC
processed data file:
15_16_54_83_eIF4A_42C_16min_merged_minus_strand.bedgraph
15_16_54_83_eIF4A_42C_16min_merged_plus_strand.bedgraph


title: 55_eIF4B_mock_16min

description:
55_eIF4B_mock_16min_NNNATTAGC
processed data file:
25_55_74_eIF4B_mock_merged_minus_strand.bedgraph
25_55_74_eIF4B_mock_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-WT2 Input rep2


title: ChIP-Seq: ARID1A-KO2 Input rep1


title: 51_eIF4A_GE_16min

description:
51_eIF4A_GE_30s_NNNTCTCTAGC
processed data file:
51_79_82_eIF4A_GE_30s_merged_minus_strand.bedgraph
51_79_82_eIF4A_GE_30s_merged_plus_strand.bedgraph


title: 52_eIF4A_control

description:
52_eIF4A_control_NNNCGTGAT
processed data file:
11_13_18_52_76_80_eIF4A_control_merged_minus_strand.bedgraph
11_13_18_52_76_80_eIF4A_control_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO1 Input rep3


title: 28_untagged


title: 45_eIF4A_GE_16min

description:
45_eIF4A_GE_16min_NNNATTAGC
processed data file:
12_14_19_45_eIF4A_GE_16min_merged_minus_strand.bedgraph
12_14_19_45_eIF4A_GE_16min_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO1 Input rep2


title: ChIP-Seq: ARID1A-WT1 AR-CST rep3


title: 27_eIF4B_GE_16min

description:
27_eIF4B_GE_16min_NNNCACTGT
processed data file:
09_22_27_eIF4B_GE_16min_merged_minus_strand.bedgraph
09_22_27_eIF4B_GE_16min_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-WT1 Input rep2


title: 25_eIF4B_mock_16min

description:
25_eIF4B_mock_16min_NNNTAGTGC
processed data file:
25_55_74_eIF4B_mock_merged_minus_strand.bedgraph
25_55_74_eIF4B_mock_merged_plus_strand.bedgraph


title: 22_eIF4B_GE_16min

description:
22_eIF4B_GE_16min_NNNGACTTAGC
processed data file:
09_22_27_eIF4B_GE_16min_merged_minus_strand.bedgraph
09_22_27_eIF4B_GE_16min_merged_plus_strand.bedgraph


title: 26_eIF4B_control

description:
26_eIF4B_control_NNNATCACG
processed data file:
08_21_26_71_eIF4B_control_merged_minus_strand.bedgraph
08_21_26_71_eIF4B_control_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-WT1 Input rep3


title: ChIP-Seq: ARID1A-WT1 Input rep1


title: 21_eIF4B_control

description:
21_eIF4B_control_NNNACTCAGC
processed data file:
08_21_26_71_eIF4B_control_merged_minus_strand.bedgraph
08_21_26_71_eIF4B_control_merged_plus_strand.bedgraph


title: ATAC-Seq: ARID1A-KO2 rep3

data_processing:
For ATAC-seq data processing, we used the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). In detail, for each sample, ATAC-seq reads were first checked for adaptor contamination. Then, adaptor trimmed reads were aligned to hg19 using Bowtie2  (PMID: 20080505) under paired-end mode with parameter “-X2000”, which permits 2000 bp for the maximum allowable insert size between two paired ends of each read. Using the ENCODE ATAC-seq pipeline, duplicated reads were properly filtered out. ATAC-seq enriched peaks were called using MACS2 (PMID: 18798982) based on remaining unique reads with parameters “-f BAMPE -q 0.05 --nomodel”. In total, we collected 45,569 peaks for the ARID1AWT sample and 27,480 peaks for the ARID1AKO sample.
Genome_build: hg19

extract_protocol: ATAC-seq library construction was performed as previously described with minor modifications (PMID: 24097267) using 60,000 cells of two independent clones of human endometrial epithelial ARID1AWT and ARID1AKO cells. Transposed DNA was purified using a QIAgen MinElute PCR Purification kit, and was subsequently amplified using NEBNext High Fidelity 2x PCR master mix for 12 cycles. PCR products were purified using Agencourt AMPure XP, and sequencing was performed by JHMI Deep Sequencing and Microarray Core using a NextSeq500 platform with double-end reads of 75 bases.

treatment_protocol: wo biological pairs of wild-type (ARID1AWT) and knockout (ARID1AKO) cells were used (PMID: 26953344). These pairs of isogenic ARID1A wildtype and knockout cell lines were established from human endometrial using a CRISPR/Cas9 genome editing method.


title: ATAC-Seq: ARID1A-KO2 rep2


title: 20_untagged


title: ATAC-Seq: ARID1A-KO1 rep3


title: ATAC-Seq: ARID1A-KO2 rep1


title: 53_eIF4A_mock_16min

description:
53_eIF4A_mock_16min_NNNGCGCAGC
processed data file:
17_53_77_81_eIF4A_mock_16min_merged_minus_strand.bedgraph
17_53_77_81_eIF4A_mock_16min_merged_plus_strand.bedgraph


title: 19_eIF4A_GE_16min

description:
19_eIF4A_GE_16min_NNNTCTCTAGC
processed data file:
12_14_19_45_eIF4A_GE_16min_merged_minus_strand.bedgraph
12_14_19_45_eIF4A_GE_16min_merged_plus_strand.bedgraph


title: 18_eIF4A_control

description:
18_eIF4A_control_NNNCACTAGC
processed data file:
11_13_18_52_76_80_eIF4A_control_merged_minus_strand.bedgraph
11_13_18_52_76_80_eIF4A_control_merged_plus_strand.bedgraph


title: ATAC-Seq: ARID1A-KO1 rep2


title: ATAC-Seq: ARID1A-KO1 rep1


title: 16_eIF4A_42C_16min

description:
16_eIF4A_42C_16min_NNNAGAGC
processed data file:
15_16_54_83_eIF4A_42C_16min_merged_minus_strand.bedgraph
15_16_54_83_eIF4A_42C_16min_merged_plus_strand.bedgraph


title: 17_eIF4A_mock_16min

description:
17_eIF4A_mock_16min_NNNGTGAGC
processed data file:
17_53_77_81_eIF4A_mock_16min_merged_minus_strand.bedgraph
17_53_77_81_eIF4A_mock_16min_merged_plus_strand.bedgraph


title: ATAC-Seq: ARID1A-WT2 rep3


title: ChIP-Seq: ARID1A-WT2 Input rep1


title: 15_eIF4A_42C_16min

description:
15_eIF4A_42C_16min_NNNCGCTTAGC
processed data file:
15_16_54_83_eIF4A_42C_16min_merged_minus_strand.bedgraph
15_16_54_83_eIF4A_42C_16min_merged_plus_strand.bedgraph


title: ChIP-Seq: ARID1A-KO1 Input rep1


title: ATAC-Seq: ARID1A-WT2 rep1


title: ATAC-Seq: ARID1A-WT2 rep2


title: 14_eIF4A_GE_16min

description:
14_eIF4A_GE_16min_NNNGCGCAGC
processed data file:
12_14_19_45_eIF4A_GE_16min_merged_minus_strand.bedgraph
12_14_19_45_eIF4A_GE_16min_merged_plus_strand.bedgraph


title: 13_eIF4A_control

description:
13_eIF4A_control_NNNATTAGC
processed data file:
11_13_18_52_76_80_eIF4A_control_merged_minus_strand.bedgraph
11_13_18_52_76_80_eIF4A_control_merged_plus_strand.bedgraph


title: 23_eIF4B_42C_16min

description:
23_eIF4B_42C_16min_NNNCGTGAT
processed data file:
23_56_75_98_eIF4B_42C_16min_merged_minus_strand.bedgraph
23_56_75_98_eIF4B_42C_16min_merged_plus_strand.bedgraph


title: ATAC-Seq: ARID1A-WT1 rep3


title: 12_eIF4A_GE_16min

description:
12_eIF4A_GE_16min_NNNTGGAGC
processed data file:
12_14_19_45_eIF4A_GE_16min_merged_minus_strand.bedgraph
12_14_19_45_eIF4A_GE_16min_merged_plus_strand.bedgraph


title: ATAC-Seq: ARID1A-WT1 rep2


title: ATAC-Seq: ARID1A-WT1 rep1


title: 11_eIF4A_control

description:
11_eIF4A_control_NNNCTAGC
processed data file:
11_13_18_52_76_80_eIF4A_control_merged_minus_strand.bedgraph
11_13_18_52_76_80_eIF4A_control_merged_plus_strand.bedgraph


title: RN2 crAno9_e2.1 + crRosa2 rep2

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

data_processing:
Raw reads were mapped to the mouse (mm10) genome using Lexogen Quantseq 2.3.1 FWD platform. Briefly, low quality reads, poly (A) read-through and adapter contamination were removed with BBDuk, and raw reads were mapped into mm10 using STAR Aligner with modified ENCODE settings. HTSeq-count was used to generate gene read count files.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene read counts for each sample

source_name: MLL-AF9/NrasG12D murine cell line

growth_protocol: RN2 cells were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were harvested on day 6 post infection and total RNA were extracted following the Direct-zol RNA Miniprep Plus (ZYMO) protocol.
 RNA-seq libraries were prepared with QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina. Briefly, 500ng of total RNA were used as input and 12 cycles of PCR were applied for amplification. Quality of the RNA-seq libraries was checked by High Sensitivity DNA Bioanalyzer kit (Aligent).

treatment_protocol: Cells were infected with sgRNAs in lentiviral format and selected with 750μg/μl G418 for 4 days from day 2 post infection.

value: Acute myeloid leukemia


title: 07_untagged


title: 08_eIF4B_control

description:
08_eIF4B_control_NNNACTCAGC
processed data file:
08_21_26_71_eIF4B_control_merged_minus_strand.bedgraph
08_21_26_71_eIF4B_control_merged_plus_strand.bedgraph


title: RN2 crKat6a_e14.1 + crJmjd6_e3.2


title: CHLA-06 cells expressing SMARCB1 replicate 2

city: Montreal

first: Sidong

last: Huang

state: Quebec

address: 3655 promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

data_processing:
Sequencing reads were mapped to reference human genome sequence (hg19) downloaded from Illumina iGenomes using STAR (version 2.4.2).
The number of fragments was counted with HTSeq (version 0.6.1p1) based on known gene from RefSeq database on UCSC Genome Browser.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: ATRT patient tumor

growth_protocol: BT12 cells were cultured in Iscove’s Modified Dulbecco’s Medium plus 20% FBS, 4mM L-Glutamine, ITS (5 μg/mL insulin, 5 μg/mL transferrin and 5 ng/mL sodium selenite).  CHLA-06 cells were cultured in DMEM/F12 supplemented with 15mM HEPES, 110mg/L Sodium Pyruvate, 1.2g/L Sodium Bicarbonate, 1xB27(Invitrogen), 20ng/mL EGF (Invitrogen), 20ng/mL bFGF and 25μg/ml gentamycin.

extract_protocol:
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) by following the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with lentiviral vectors (Control and SMARCB1) for 8 hours followed by puromycin selection for 2 days before harvesting.

value: Atypical teratoid rhabdoid tumor (ATRT) cells

value: ectopic SMARCB1 expression

tag: cell line


title: CHLA-06 cells expressing SMARCB1 replicate 1

tag: cell type


title: CHLA-06 cells expressing SMARCB1 replicate 3


title: RN2 crRosa2 + crKat6a_e14.1


title: RN2 crRosa2 + crKat6a_e12.1


title: CHLA-06 cells expressing vector control replicate 2

value: Deficient


title: CHLA-06 cells expressing vector control replicate 3


title: RN2 crJmjd6_e3.1 + crKat6a_e12.1


title: RN2 crKat6a_e14.1 + crRosa2


title: CHLA-06 cells expressing vector control replicate 1


title: RN2 crJmjd6_e3.2 + crKat6a_e14.1


title: RN2 crKat6a_e12.1 + crRosa2


title: BT12 cells expressing SMARCB1 replicate 3


title: BT12 cells expressing SMARCB1 replicate 2


title: RN2 crKat6a_e12.1 + crJmjd6_e3.1


title: RN2 crRosa1 + crJmjd6_e3.2 rep2


title: BT12 cells expressing vector control replicate 3


title: BT12 cells expressing SMARCB1 replicate 1


title: RN2 crRosa1 + crJmjd6_e3.1 rep2


title: RN2 crJmjd6_e3.2 + crRosa1 rep2


title: BT12 cells expressing vector control replicate 2


title: BT12 cells expressing vector control replicate 1


title: RN2 crRosa2 + crAno9_e2.1 rep2


title: 09_eIF4B_GE_16min

description:
09_eIF4B_GE_16min_NNNGACTTAGC
processed data file:
09_22_27_eIF4B_GE_16min_merged_minus_strand.bedgraph
09_22_27_eIF4B_GE_16min_merged_plus_strand.bedgraph


title: 24hr_02_negative

description: repeat 2 pooled from 3 mice

data_processing:
Raw ATAC-seq reads were trimmed to remove adapter sequences and low-quality bases (Q < 20) using TrimGalore; reads with length < 20 bp after trimming were discarded.
Alignment to the mm10 genome was performed using bowtie2 (v2.3.5.1)(PMID: 22388286). Aligned reads were sorted with samtools, filtered to remove reads overlapping genomic regions with high, anomalous signal across multiple methods (ENCODE “blacklisted” regions) (PMID: 31249361) using bedtools (v2.29.0) (PMID: 20110278), and duplicates were marked for exclusion in downstream analyses using Picard markDuplicates (v2.20.6; Broad Institute).
RPKM-normalized bigWig files for visualization were created using the bamCoverage function from deepTools (v3.3.0) with the X, Y, and mitochondrial chromosomes excluded from normalization. ATAC-seq peaks were subsequently identified using MACS2, followed by filtering for peaks reproducibly identified in replicate samples using the irreproducible discovery rate (IDR) method with a threshold of 0.05 (as implemented by the Kundaje Lab)
Differential accessibility analysis was performed by first quantifying the number of reads overlapping ATAC-seq peaks using featureCounts with duplicate reads excluded (--ignoreDup) and reads overlapping multiple features assigned to the feature with the largest overlap (--largestOverlap). Raw read counts were then filtered to remove low-abundance features (logCPM >= 1 in at least 2 samples) and normalized for library size using edgeR (v3.26.8).
Principal component analysis of normalized read counts indicated a strong batch effect which segregated biological replicates from all conditions. Therefore, a batch term was included into the generalized linear model alongside experimental group for subsequent estimation of dispersion, model fitting, and differential analysis using the quasi-likelihood F-test framework in edgeR.
Genome_build: mm10 genome
Supplementary_files_format_and_content: RPKM-normalized bigWig files for visualization

extract_protocol:
Lungs were removed, single suspension cells were achieved by enzymatic digestion of tissue, and alveolar macrophage cells were harvested by FACS.
Omni-ATAC was performed on 50,000 cells from two biological replicates per AM subpopulation using Tn5 transposase from the Nextera DNA Library Prep Kit (FC-121-1030). Following transposition, the Qiagen MinElute Kit (28204) was used to purify the DNA. Based on qPCR amplification curves, samples were amplified for four additional cycles after the five-cycle preamplification (9 total cycles). For size selection and clean-up of amplified library, three rounds of AMPure beads-enabled purification were performed. 1X AMPure beads were used first to remove primer dimers, followed by 0.5X to remove large fragments >1,000 kb, and finally 1.8X to further clean up.

treatment_protocol: The animals were infected with Cryptococcus neoformans (oro-tracheally) for 9 hours and 24 hours

value: lung

value: alveolar macrophages

value: 6 weeks old

tag: phenotype

tag: time point

value: 24 hours


title: PH002_SJ_REMISSION

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
scRNA-seq
PolyA RNA
processed data file: barcodes.tsv
processed data file: features.tsv

data_processing:
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment were performed with 10x Genomics Cell Ranger software.
Indexed BAM files containing position-sorted reads aligned to the genome.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: barcodes.tsv: Raw barcodes.
Supplementary_files_format_and_content: features.tsv: Raw genes.
Supplementary_files_format_and_content: *matrix.mtx: Raw gene-barcode matrices.

source_name: bone marrow

extract_protocol:
Frozen BM specimens were rapidly thawed and transferred into 50 mL conical tubes. 20 mL Pre-warmed RPMI 1640 (Corning) supplemented with 5% Fetal Bovine Serum (FBS) (Sigma Aldrich) and 2-Mercaptoethanol (2-ME, 55nM) (Thermo Fisher Scientific) was added drop-wise to tubes. Cell suspensions were subjected to centrifugation at 400 x g for 5 min at 4°C and supernatant was discarded. Pellets were re-suspended in 5mL RPMI 1640 with 5% FBS and 2-ME, and filtered using a 70 μm nylon mesh (Thermo Fisher Scientific) with residual cell clumps discarded. After centrifuging at 400 x g at 4°C for 5 min, the supernatant was discarded, and the cell pellet was re-suspended in PBS (Corning) with 2% FCS and placed on ice prior to staining for FACS. Single-cell BM suspensions were re-suspended in PBS with 2% FCS and Human TruStain FcX Blocking Solution (BioLegend) and incubated on ice for 10 mins. Cell suspensions were centrifuged at 400 x g at 4°C for 5 min, and supernatant discarded. Cell pellets were re-suspended in PBS with 2% FCS, FITC-conjugated anti-human CD45 (1:200, BD Pharmingen), APC-conjugated anti-human CD19 (1:200 concentration, BioLegend) and PE-conjugated anti-human CD10 (1:200, BioLegend), and incubated on ice for 30 mins. Following incubation, cell suspensions were subjected to two wash cycles involving re-suspension of cell pellets in 3 mL PBS with 2% FCS, followed by centrifuging at 400 x g at 4°C for 5 min, followed by supernatant removal. Finally, samples were re-suspended in 300 mL of PBS with 2% FCS per 2 x 10e6 cells, supplemented with DAPI (0.5 mg/mL) for live/dead staining. Cell sorting was performed using the SY3200™ highly automated parallel sorting (HAPS) cell sorter (Sony).
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics).

value: B-ALL

tag: Stage

value: Remission

value: ratio of 1:5 CD19+:CD19-CD45+ bone marrow cells

tag: age (years)

tag: Sex

value: female

tag: source

tag: source institute

value: St. Jude


title: PH002_SJ_RELAPSE

value: Relapse


title: 24hr_02_positive

description: repeat 2 pooled from 3 mice

tag: strain

tag: tissue

tag: age


title: 9hr_02_negative

description: repeat 2 pooled from 3 mice

value: 9 hours


title: 9hr_02_positive

description: repeat 2 pooled from 3 mice


title: 24hr_01_negative

description: repeat 1 pooled from 3 mice


title: naive 02

description: repeat 2 pooled from 3 mice

value: naive


title: PH002_SJ_DIAGNOSIS

value: Diagnosis


title: PH001_COG_RELAPSE

value: male

value: PAUZUW

value: COG


title: 24hr_01_positive

description: repeat 1 pooled from 3 mice


title: PH001_COG_DIAGNOSIS


title: HEALTHY004_SC_CD45

value: Healthy

value: CD45+ bone marrow cells

value: STEMCELL


title: HEALTHY003_SC_CD45


title: 9hr_01_negative

description: repeat 1 pooled from 3 mice

value: lung

value: alveolar macrophages

value: 6 weeks old


title: HEALTHY002_WC4_CD45

value: WEILL CORNELL


title: 9hr_01_positive

description: repeat 1 pooled from 3 mice


title: naive 01

description: repeat 1 pooled from 3 mice


title: HEALTHY001_LONZA_CD45

value: LONZA


title: ETV005_COG_REMISSION

value: B-ALL

value: Remission

value: ratio of 1:5 CD19+:CD19-CD45+ bone marrow cells

value: PAWMMA


title: TAP_crb3-tap_grc3V70M_rep2

city: Boston

first: Danesh

last: Moazed

state: MA

address: 240 Longwood Avenue, LHRRB 517

department: Cell Biology

institute: Harvard Medical School

data_processing:
Pooled libraries were demultiplexed using Geneious and barcode sequences were trimmed from the reads.
Reads were aligned to the reference genome using bowtie with default parameters.
The mapped reads were normalized to counts per million using Deeptools and visualized in IGV.
Genome_build: ASM294v2
Supplementary_files_format_and_content: The mapped reads were normalized to counts per million using Deeptools, saved as bw files and visualized in IGV.

organism: Schizosaccharomyces pombe

growth_protocol: Yeast cultures were grown in rich (YES) medium to OD600 densities of 1-2.

extract_protocol:
50 OD600 units of cells per ChIP were fixed with 1% formaldehyde for 15min, quenched with glycine and collected. Cell pellets were resuspended in lysis buffer (50mM  Hepes/KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton-X-100, 0.1% Na Deoxycholate, 0.1% SDS, 1mM PMSF, supplemented with protease inhibitors) and cells were lysed by the glass bead method, using MagNA Lyser (Roche) (3 pulses of 90s at 4500rpm, 1 pulse of 45s at 5000rpm). The lysates were sonicated by 3 pulses of 20s (amplitude 40%) in a Branson microtip sonifier with intermittent cooling on ice, to a fragment distribution of 200-1000 bp. Cell debris were removed by centrifugation (16000xg) at 4*C for 15min and the cleared lysates were incubated for 2 hours at 4*C with magnetic beads coupled to antibodies against the targets of interest. For H3K9me2 30µl Protein A Dynabeads (Invitrogen) were coupled with 2µg anti-H3K9me2 antibody (Ab1220, Abcam). For H3K9me3 ChIPs, 30µl Streptavidin Dynabeads M280 (Invitrogen) were coupled to 2µg of anti-H3K9me3 antibody (Diagenode C15500003) and blocked with 5µM biotin. For Crb3-TAP ChIPs, 4.5µg Dynabeads M-270 Epoxy beads (Invitrogen) were coupled to 1.5µg rabbit IgG (Sigma, #15006) and incubated with the cleared lysate. The beads-protein complexes were washed three times with lysis buffer, once with chilled TE buffer (10mM Tris/HCl, 1 mM EDTA) and eluted in elution buffer (50mM Tris/HCl pH 8.0, 1mM EDTA, 1% SDS) with heating (65oC) for 20min. Crosslinks were reversed at 65*C overnight and the eluates were treated with RNase A and Proteinase K (Roche).
For ChIP-seq, reverse crosslinked DNA treated with RNase A and proteinase K was purified using the Qiagen PCR purification kit. The DNA was then sonicated in a QSonica water bath sonicator (5 min with 15s ON/OFF pulses, 20% amplitude) to a fragment size of ~200bp, concentrated and quantified using Qubit dsDNA high sensitivity kit. 1-10ng of DNA were used to prepare libraries as described previously (Wong et al, 2013). Libraries were pooled and sequenced on Illumina HiSeq 2500 and Illumina NextSeq 500 platforms.

tag: medium

value: YES

tag: antibody

value: TAP (rabbit IgG Sigma, #15006)


title: RN2 crJmjd6_e3.1+ crRosa1 rep2

value: Acute myeloid leukemia

tag: genotype


title: TAP_crb3-tap_rep1

tag: genotype/variation


title: TAP_untagged_rep2

value: untagged


title: Anti-NK1.1 3XTG-AD microglia-3

city: New Brunswick, NJ 089

first: Qi

last: Yang

state: New Jersey

address: 89 French St

institute: Rutgers

data_processing:
Single-end 75 bp high throughout sequencing was performed using a NextSeq 500 (Illumina)
Raw data was converted to fastq files using bcl2fastq v2.20.0.422 and quality checked using fastqc v 1.0.0.
RNA-seq reads were aligned to mm10 genome by the STAR  aligner V2.5.3a
Reads Per Kilobase of exon per Megabase  (RPKM) estimation of reference genes and transcripts using Cufflinks V2.0
Differential expression was calculated using DEseq2 (v1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Text file for processed data file, and Fastq files for each sample

source_name: microglia isolated from anti-Nk1.1 treated 3XTg-AD mice, replicate 3

extract_protocol:
Microglia were sorted by fluorescence activated cell sorting. Trizol-LS extraction of total RNA was performed according to the manufacturer's instructions.
cDNA was prepared using the SMART-seq v4 ultra input RNA kit (Takrara). Libraies were generated using Nextera XT DNA library prep kit (Illumina).
RNA-seq was performed with NextSeq 500, 75 bp , single end.

treatment_protocol: 7 month old 3XTg-AD mice treated with 25μg of anti-NK1.1 antibodies or isotype controls every 4 days for 4 weeks.

tag: treatment

value: Anti-NK1.1 antibody

value: microglia

value: 7 months


title: Input_crb3-tap_grc3V70M_rep2


title: Anti-NK1.1 3XTG-AD microglia-2

source_name: microglia isolated from anti-Nk1.1 treated 3XTg-AD mice, replicate 2


title: TAP_crb3-tap_rep2


title: ETV005_COG_RELAPSE

tag: disease state

value: Relapse

value: male

value: COG


title: PH001_COG_REMISSION

tag: cell type

value: PAUZUW


title: Anti-NK1.1 3XTG-AD microglia-1

source_name: microglia isolated from anti-Nk1.1 treated 3XTg-AD mice, replicate 1


title: Input_crb3-tap_grc3V70M_rep1


title: ETV005_COG_DIAGNOSIS

value: Diagnosis


title: Isotype 3XTG-AD micoglia-3

source_name: microglia isolated from isotype treated 3XTg-AD mice, replicate 3

value: Isotype antibody


title: Input_crb3-tap_rep1


title: Input_crb3-tap_rep2


title: adipose derived stromal cell from WT mice  inguinal fat pad

first: Jiajia

last: Xu

address: 720 Rutland Avenue

department: Pathology-Surgical Pathology

institute: The Johns Hopkins University School of Medicine

hyb_protocol: 17 hours at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted with the Partek GS 6.6 platform, excluding Affy's junction (JUC~) and unmapped (PRSUnmapped~) probes and their data. Values were then RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analysis.

label: biotin

source_name: inguinal fat tissue

label_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.

growth_protocol: 15%FBS DMEM growth medium

extract_protocol: RNA were extract with TRIZOL Reagent

treatment_protocol: Wisp1 gene on chromosome 15 exons 1 to 5 was inserted with flox and then mate with Cre-neo mouse and result in Wisp1 global knockout  offspring

value: inguinal fat tissue

tag: background strain

value: WT

value: 6-10 week old


title: TAP_crb3-tap_grc3V70M_rep1


title: Isotype 3XTG-AD micoglia-2

source_name: microglia isolated from isotype treated 3XTg-AD mice, replicate 2


title: adipose derived stromal cell from Wisp knowout mice inguinal fat pad

value: Wisp1 KO


title: Isotype 3XTG-AD micoglia-1

source_name: microglia isolated from isotype treated 3XTg-AD mice, replicate 1


title: Input_untagged_rep2

value: YES


title: ETV004_COG_RELAPSE

value: B-ALL

value: ratio of 1:5 CD19+:CD19-CD45+ bone marrow cells

value: PAUCIG


title: ETV004_COG_DIAGNOSIS


title: ETV003_SJ_REMISSION

value: Remission

value: female

value: St. Jude


title: Anti-NK1.1 microglia

description: microglia from 3XTg-AD mice treated with anti-NK1.1 depleting antibodies.

data_processing:
Library was generated using chromium 5' gene expression kit (10Xgenomincs) accoding to the manufacturer’s instruction.
The following Chromium i7 multiplex barcodes were used : B5 for sample Yang 1 (Isotype microglia) and D5 for sample Yang 2 (anti-NK1.1 microglia).
Primary analysis was performed using the Cellrange pipeline.
Reference genome mouse (mm10) was used for read alignment and gene expression quantification using Cellranger v3.1.0 pipelines.
The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines. These pipelines combine Chromium specific algorithms with the RNA-seq aligner STAR.
Genome_build: Reference genome mouse (mm10) was used for read alignment
Supplementary_files_format_and_content: tar archives contain matrix.mtx; features.tsv; barcodes.tsv

source_name: microglia isolated from anti-Nk1.1 treated 3XTg-AD mice

growth_protocol: Primary mouse cells

extract_protocol:
Microglia were sorted by fluorescence activated cell sorting. Total RNA extracted following the instructions of the 10X genomics kit.
Library was generated using chromium 5' gene expression kit (10Xgenomincs) accoding to the manufacturer’s instruction.

value: Anti-NK1.1 antibody

value: microglia


title: H3K9me3_clr4Δ_rep2

value: H3K9me3 (Diagenode C15500003)


title: H3K9me3_dhp1-1_rep2


title: Isotype microglia

description: Microglia from 3XTg-AD mice treated with control isotype antibodies.

source_name: microglia isolated from isotype treated 3XTg-AD mice


title: H3K9me3_dhp1-1_rep1


title: ETV003_SJ_RELAPSE

value: Relapse


title: ETV002_COG_REMISSION

value: male

value: PASFIF

value: COG


title: ETV003_SJ_DIAGNOSIS

value: Diagnosis


title: RN2 crBrd9 e6.1 + crJmjd6 e3.1

value: Acute myeloid leukemia


title: ETV002_COG_RELAPSE


title: RN2 crRosa 2 + crBrd9 e5.2


title: 3XTg-AD brain NK cells

description: 8 month old 3XTg-AD females

data_processing:
The following Chromium i7 multiplex barcodes were used : A3 for sample Yang-1 (wild type brain NK cells) and C3 for sample Yang-2 (3XTg-AD brain NK cells).
Primary analysis was performed using the Cellrange pipeline.
Reference genome mouse (mm10) was used for read alignment and gene expression quantification using Cellranger v3.1.0 pipelines.
The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines. These pipelines combine Chromium specific algorithms with the RNA-seq aligner STAR.
Genome_build: Reference genome mouse (mm10) was used for read alignment a
Supplementary_files_format_and_content: matrix.mtx; features.tsv; barcodes.tsv

source_name: NK cells isolated from the brains of 3XTg-AD mice

growth_protocol: primary mouse cells

extract_protocol:
NK cells were sorted by fluorescence activated cell sorting. Single cell libraries were generated using  following the instructions of the 10X genomics kit.
Library was generated using chromium 5' gene expression kit (10Xgenomincs) accoding to the manufacturer’s instructions.
Sequencing was performed on a Nextseq 5000, 75X2bp  paired end.

treatment_protocol: no treatment

tag: condition

value: 8 month old


title: H3K9me3_wt_rep2

value: wt

value: YES


title: ETV004_COG_REMISSION

value: B-ALL

tag: Stage

value: ratio of 1:5 CD19+:CD19-CD45+ bone marrow cells


title: ETV002_COG_DIAGNOSIS

tag: age (years)


title: RN2 crRosa 2 + crAno9 e2.1 rep1


title: H3K9me2_dhp1-1_rep2


title: H3K9me2_clr4Δ_rep2


title: ETV001_NYU_RELAPSE

tag: Sex

value: KM

value: NYU


title: ETV001_NYU_DIAGNOSIS

tag: source


title: RN2 crRosa 1 + crJmjd6 e3.1 rep1


title: RN2 crRosa 1 + crJmjd6 e3.2 rep1


title: H3K9me2_grc3V70M_rep2


title: RN2 crRosa 1 + crBrd9 e6.1


title: H3K9me2_grc3V70M_rep1


title: H3K9me3_grc3V70M_rep2


title: H3K9me3_grc3V70M_rep1


title: TAP_crb3-tap_grc3V70M_10xteto-ade6_rep2

value: TAP (rabbit IgG Sigma, #15006)


title: wild type brain NK cells

description: 8 month old C57BL/6 females

source_name: NK cells isolated from the brains of wildtype mice

value: Wildtype

value: Healthy

value: female


title: TAP_crb3-tap_10xteto-ade6_rep2


title: Chuong-87

city: Los Angeles

first: Ya-Chen

last: Liang

state: CA

address: 2011 Zonal Ave., HMR 304A

institute: University of Southern California

data_processing:
RNA-seq analysis. The RNA-seq analysis pipeline was adapted according to the publication (Trapnell et al., 2012). Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1) and fastq_trimmer_by_quality (window size 3; min score >= 20). Mapping. Tool: TopHat2 (Galaxy Version 2.1.1). Quantification and differentially expressed gene analysis. Tools: Cufflinks package (Trapnell et al., 2010)–including Cufflinks (Galaxy Version 2.2.1.2), Cuffmerge (Galaxy Version 2.2.1.1), Cuffquant (Galaxy Version 2.2.1.1), and Cuffdiff (Galaxy Version 2.2.1.3). Deeptools bamCoverage (Galaxy Version 3.1.2.0.0) was used to normalize the reads to 1X sequencing depth and wig_to_bigwig (Galaxy Version 1.1.1) was used to generate bigWig files of read coverages.
ChIP-seq analysis. Manipulation. Tools: fastq_groomer (Galaxy Version 1.1.1), fastq_quality_filter (Galaxy Version 1.0.2), fastq_trimmer_by_quality (Galaxy Version 1.1.1; window size 3; min score >= 20). Mapping. Tool: bowtie2 (Galaxy Version 2.3.4.2; genome: UCSC galGal4, --very-sensitive). Filtering. Tools: samtool_filter2 (Galaxy Version 1.8; -q 1), samtools_sort (Galaxy Version 2.0.1), samtools_rmdup (Galaxy Version 1.0.1; BAM is single-end). Peak-calling. Tools: MACS2 (Galaxy Version 2.1.1.20160309.4; for H3K27ac-ChIP, --gsize 1065365425 --nomodel --extsize 147 --bdg --broad --broad-cutoff 0.1; for CTCF/KLF-ChIP, --gsize 1065365425 --nomodel --extsize value obtained from macs2_predictd tool) and macs2_bdgcmp (Galaxy Version 2.1.1.20160309.0; -m FE and -m logLR -p 0.00001). To normalize MACS2 results from different libraries for comparison, we followed a “Build Signal Track” instruction from https://github.com/taoliu/MACS/wiki/Build-Signal-Track#Run_MACS2_bdgcmp_to_generate_foldenrichment_and_logLR_track.  Convert format. Tool: wig_to_bigWig (Galaxy Version 1.1.1).
NG Capture-C analysis. Double Capture-C results were analyzed according to the publication (Davies et al., 2016). The analysis pipeline was well documented and can be downloaded from “https://github.com/Hughes-Genome-Group/captureC/releases/download/VS2.0/UserManualforCaptureCanalysis.pdf". In brief, 1) download the CaptureC analyser package including CCanalyser3.pl, dpngenome3_1.pl, dpnII2E.pl from “https://github.com/Hughes-Genome-Group/captureC/releases", 2) generate in silico DpnII digested chicken genome ver. Ensemble galGal4 Release 72 with alpha and beta keratins, 3) perform adapter trimmer using the tool trim_galore (Dr. Felix Krueger at the Babraham Institute), 4) Merge overlapping reads by using the tool FLASH (Magoc and Salzberg, 2011), 5) in silico DpnII digest the FLASH-merged reads; 6) install Bowtie 1.2 (Langmead et al., 2009), 7) build up bowtie index using the original genome used in the Step 2, 8) align digested FLASH-merged reads (output of Step 5) using Bowtie1.2, and 9) run CCanalyser3.pl. wig_to_bigwig (Galaxy Version 1.1.1) was used to generate bigWig files from wig files of CCanalyser3 outputs.
Genome_build: UCSC Genome Browser assembly ID: galGal4
Supplementary_files_format_and_content: Bigwig files were generated using the wig/bedgraph_to_bigwig tool. Detail processes of RNA-seq, ChIP-seq, and NG Capture-C are described above.

organism: Gallus gallus

source_name: E14 leg scale skin

growth_protocol: White Leghorn chicken eggs were used. Eggs were incubated in a humidified egg incubator with an automatic egg turner.

extract_protocol:
Please find detailed protocols for ChIP and Capture-C DNA preparaion in Methods of this publication. RNA extraction for RNA-seq: Total RNAs of indicated tissues were extracted followed by the standard Trizol extraction protocol (Invitrogen, Cat.15596026). ChIPed-DNA preparation for ChIP-seq: The protocol was adapted from Dr. Ruchi Bajpai’s laboratory (Bajpai et al., 2010). 3C library preparation for NG Capture-C: The protocol was adapted from Dr. Wange Lu’s laboratory (Davies et al., 2016; Davies et al., 2017).
For RNA-seq library preparation: TruSeq RNA Prep Kit v2 (Illumina, RS-122-2001/-2002). For ChIP-seq library preparation: NEBNext Ultra End Repair/dA-Tailing Module (New England Biolabs, Cat. E7442S), NEBNext Ultra Ligation Module (New England Biolabs, Cat. E7445S), and KAPA HiFi HotStart ReadyMix (Kapa Biosystems, Cat. KK2601). For NG Capture-C library preparation: 5 µg of sheared 3C-DpnII DNA was used in adaptor ligation for pre-capture library using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB, Cat. E6040). Adaptors were from NEBNext Multiplex Oligos for Illumina (NEB, Cat. E7500). The indexed 3C DNA was amplified using a primer pair of P5 (5’-aatgatacggcgaccaccga) and P7 (5’-caagcagaagacggcatacgagat) and purified using 1.8X AMPure XP beads. To perform the first capture, SeqCap EZ Hybridization and Wash Kit (Roche, Cat. 05634261001) was used. For one library, the indexed sequencing library, 5 µg of a Cot-1 DNA equivalent chicken Hybloc DNA (Applied Genetics Lab, Cat. CHB), 1 µl of 1xGen Universal Blocking Oligo—TS-p5 (1 nmole/µl), and 1 µl of 1xGen Universal Blocking Oligo—TS-p7(6nt) (1 nmole/µl) were mixed well and dried completely in a low retention PCR tube (Axygen, Cat. PCR-02-L-C). The dried pellet was then resuspended in Nimblegen Hybridization Buffer and Component A, mixed with 2 µl of a capture probe pool (3 pmole in total), and incubated for hybridization at 47℃ for 72 hours. After the first hybridization, biotinylated-probe-hybridized DNA (captured DNA) was mixed with 40 µl of prepared streptavidin magnetic beads (Invitrogen, Cat. 65001) and incubated at 47℃ for 45 min. The mixture was further washed using the SeqCap Wash Kit. The captured DNA was then purified using 1.8X AMPure XP beads and eluted in final 44 µl of nuclease-free water and amplified using the P5/P7 primer pair for 12 cycles. This 1st-captured DNA was finally cleaned up with 1.8X AMPure XP beads and eluted in 25 µl of water. To perform the second capture, the 1st-captured DNA was mixed with components described in the first capture part and incubated for hybridization at 47℃ for 24 hours. The double-captured DNA was then washed, pulled down by using the streptavidin beads, purified, amplified, and cleaned up as described before.

treatment_protocol: No treatment

tag: chip antibody

tag: skin region

value: leg scutate scale

tag: skin/appendage layer

value: whole skin


title: Chuong-31

source_name: E9 leg scale epidermis

tag: age

value: epidermis


title: RN2 crJmjd6 e3.3 + crRosa 2

tag: strain


title: H3K9me2_wt_rep2

tag: medium

tag: antibody


title: RN2 crJmjd6 e3.3 + crBrd9 e5.2

tag: genotype


title: TAP_untagged_10xteto-ade6_rep2

tag: genotype/variation


title: RN2 crJmjd6 e3.2 + crRosa 1 rep1


title: Input_clr4Δ_rep2


title: TAP_crb3-tap_grc3V70M_10xteto-ade6_rep1


title: Input_dhp1-1_rep2


title: RN2 crJmjd6 e3.1 + crRosa 1 rep1


title: H3K9me2_dhp1-1_rep1


title: TAP_crb3-tap_10xteto-ade6_rep1


title: Input_dhp1-1_rep1


title: Chuong-188


title: Chuong-187

source_name: E14 non-keratinized feather filament

value: dorsal back

value: non-keratinized feather filament base (2 mm)


title: Chuong-86


title: RN2 crJmjd6 e3.1 + crBrd9 e6.1

source_name: MLL-AF9/NrasG12D murine cell line

value: Acute myeloid leukemia


title: H3K9me2_wt_10xteto-ura4-gfp_rep1


title: Input_crb3-tap_grc3V70M_10xteto-ade6_rep1


title: RN2 crBrd9 e6.1 + crRosa 1


title: Input_grc3V70M_rep2


title: Input_grc3V70M_rep1


title: Chuong-29

source_name: E9 dorsal back skin epidermis


title: RN2 crBrd9 e5.2 + crJmjd6 e3.3


title: Input_crb3-tap_10xteto-ade6_rep1


title: Chuong-33


title: Chuong-387


title: RN2 crBrd9 e5.2 + crRosa 2


title: RN2 crAno9 e2.1 + crRosa 2 rep1


title: Input_untagged_10xteto-ade6_rep1


title: Chuong-386


title: Chuong-13

source_name: E7 dorsal back skin epidermis


title: Chuong-1


title: HFD-5

city: Shanghai

first: dongsheng

last: xiao

address: No.151 Libing Road, Zhangjiang Hi-Tech Park Pudong, Shanghai 201203, P.R. China

country: China

institute: Shanghai Biotechnology Corporation

data_processing:
The main steps of applying Seqtk [1] for filtering are as follows:1) Remove the sequence of joints contained in reads；2) Remove bases with 3 'end mass Q less than 20, that is, the base error rate is less than 0.01, among, Q=-10logerror_ratio；3) Remove reads with length less than 25, 4) Remove ribosome RNA reads of the species.
Spliced mapping algorithm of TopHat (version:2.0.9) [2] was applied to Genome mapping of pre-processed reads，The alignment result generated by Mapping is BAM file
In order to make gene expression levels between different genes and samples comparable, reads were transformed into FPKM (Fragments Per Kilobase of exon model Per Million mapped reads) to standardize gene expression
Cufflinks (version:2.2.1)  was applied to quantitative gene mapping results of tophat
Cuffdiff was used for gene analysis of differences between samples, and multiple hypothesis test and correction were carried out after p-value was obtained. The threshold value of p-value was determined by controlling FDR (False Discovery Rate), and the p-value after correction was q-value.Meanwhile, we calculate Fold-change according to FPKM
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKM  and counts

organism: Rattus norvegicus

source_name: Liver

growth_protocol: All rats were acclimated for 1 week before initiation of the experiment and maintained on a 12/12 h light/dark cycle with free access to food and water.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using TAKARA RNAiso Plus#9109. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were randomly divided into two groups (n=12 each): Control group (ND group), received regular rodent chow diet (59.6% carbohydrate, 8.5% fat and 20.3% protein in total calories); HFD group, fed a high fat diet (43% carbohydrate, 41% fat and 17% protein in total calories) for 24 weeks.

value: Sprague-Dawley

tag: tissue

value: Liver

value: ~22 weeks

tag: diet

value: High Fat Diet

value: wild type


title: HFD-4