title: exosomes_unstress_rep1

city: Nanjing

first: Dongping

last: Li

state: Jiangsu

address: Zhilan Road 18

department: Department of State Key Laboratory of Natural Medicines

institute: China Pharmaceutical University

hyb_protocol: Resuspend the dried sample in 17μL of nuclease-free water,Add 1.0μL of the Hyb Spike-In solution (3rd Dilution) ,4.5μL of the 10× GE Blocking Agent and 22.5μL of 2× Hi-RPM Hybridization Buffer to each sample for a total of 45μL.Incubate them at 100°C for 5 minutes and immediately transfer to an ice water bath for 5 minutes. hybridized samples to Agilent Mouse miRNA, Release 21.0 (8*60K)for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.1(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: NK cells-derived exosomes

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and RNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM PARIS™ Kit (Ambion-1556 ) following the manufacturer's instructions.

value: exosomes

value: unstressed mice


title: exosomes_stress_rep1

status: Public on Oct 30 2019

type: RNA

country: China

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment

value: stress mice


title: exosomes_unstress_rep2


title: MCF7-ARID1A_KO_Clone_14_4-hydroxy_tamoxifen_rep 3

type: SRA

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description:
mcf7_arid1a_ko_clone_14_4_oht_c14.macs2.bed.gz
mcf7_arid1a_ko_clone_14_4_oht_c14.genrich.bed.gz

library_source: genomic

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library.
The peaks were called with MACS2, version 2.1.1.20160309, using following parameters:  -g hs -f BAM --nomodel --shift -100 --extsize 200.
For estimation of consistency in results of peak calling we used also Genrich, version 0.5, with parameters: -j  -y  -r -v.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: hg38
Supplementary_files_format_and_content: bed/text

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF7 cells were grown in DMEM High glucose media with 2 mM Glutamine, 10% FBS, Sodium pyruvate

extract_protocol:
Omni ATAC-seq protocol was performed from Corces et al., 2017, Nature Methods. Transposase and buffers were purchased from Illumina Nextera kits.
DNA was prepared for Illumina sequencing using Nextera indices on the HiSeq 4000 with paired end 150 bp.

treatment_protocol: Cells were treated with vehicle (DMSO) or 100 nM 4-Hydroxytamoxifen for 6 hours.

tag: genotype/variation

value: MCF7 ARID1A knockout clone 14

tag: cell type

value: ER+  Breast Cancer Cell Line

tag: passages

value: 4-hydroxy tamoxifen


title: MCF7-ARID1A_KO_Clone_14_4-hydroxy_tamoxifen_rep 4


title: MCF7-ARID1A_KO_Clone_14_4-hydroxy_tamoxifen_rep 2


title: exosomes_stress_rep3


title: exosomes_unstress_rep3


title: exosomes_stress_rep2


title: pp2a-b’γ sid2_apic_rep3

city: Turku

first: Guido

last: Durian

address: Tykistokatu 6A

department: Biochemistry, Molecular Plant Biology

country: Finland

institute: University of Turku

description: pool of 7 leaf halves

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2 software was used for basecalling; automatic adapter trimming was used.
Gene expression was analyzed using Strand NGS 3.11 software (Agilent). Sequence reads were aligned to the Arabidopsis thaliana TAIR10 reference genome with Ensembl gene and transcript annotation.
Aligned reads were normalized and quantified using DESeq Bioconductor package (R).
Replicate analysis was performed by a two-way ANOVA and a Shapiro-Wilk test of normality (cutoff p < 0.1).
The Benjamini-Hochberg procedure was applied to obtain corrected p values representing a false discovery rate (FDR) for each gene, in each comparisons (i.e. genotype; tissue; tissue-genotype)
Genome_build: Arabidopsis thaliana TAIR10 reference genome
Supplementary_files_format_and_content: Expression all mutant apices vs wild type.txt:  Tab-delimited text file including fold changes for given comparisons for each gene; containing gene identities and descriptions as well as corrected p-values (FDRs). 2way ANOVA p (Corr) (genotype) cut-off = 0.05

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: pp2a-b’γ sid2_apic

growth_protocol: Arabidopsis thaliana wild type (Col-0) and mutant pp2a-b’γ, double mutants pp2a-b’γ sid2 and pp2a-b’γζ and complementation line pp2a-b´γ P35S:PP2A-B’γ were grown for 7 weeks at 130 µmol photons m-2s-1, 22oC and 50% humidity at an 8 h light period.

extract_protocol:
RNA from the samples (pools of leaf halves) was isolated using the innuPREP Plant RNA kit (Analytik Jena; 845-KS-2060250) according to the manufacturer´s instructions.
RNA library preparation for sequencing was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047).

treatment_protocol: For each pair of basal-/apical-pools (e.g. "WT_basal_rep1" and "WT_apic_rep1") seven fully expanded rosette leaves from seven-week-old plants were split into apical and basal halves. In the case of pp2a-b´γ, this yielded pools of apical leaf halves that showed symptoms of yellowing and cell death and visually asymptomatic basal leaf halves. 5 biological replicates (i. e. 5 pairs of basal-/apical-pools) per genotype were analyzed.

tag: ecotype

value: apical (= distal) leaf halves of fully expanded leaves


title: pp2a-b’γ sid2_apic_rep2

description: pool of 7 leaf halves


title: pp2a-b’γζ_apic_rep2

description: pool of 7 leaf halves


title: pp2a-b’γζ_apic_rep5

description: pool of 7 leaf halves


title: pp2a-b’γζ_apic_rep3

description: pool of 7 leaf halves


title: pp2a-b’γζ_apic_rep4

description: pool of 7 leaf halves


title: pp2a-b’γ sid2_apic_rep5

description: pool of 7 leaf halves


title: pp2a-b’γ sid2_apic_rep4

description: pool of 7 leaf halves


title: pp2a-b’γζ_apic_rep1

description: pool of 7 leaf halves


title: pp2a-b’γ sid2_apic_rep1

description: pool of 7 leaf halves


title: MCF7-ARID1A_KO_Clone_14_4-hydroxy_tamoxifen_rep 1


title: pp2a-b´γ P35S:PP2A-B’γ_apic_rep5

description: pool of 7 leaf halves

source_name: pp2a-b´γ P35S:PP2A-B’γ_apic


title: pp2a-b´γ P35S:PP2A-B’γ_apic_rep4

description: pool of 7 leaf halves


title: MCF7-ARID1A_KO_Clone_14_Vehicle rep 4

description:
mcf7_arid1a_ko_clone_14_veh_c14.macs2.bed.gz
mcf7_arid1a_ko_clone_14_veh_c14.genrich.bed.gz

value: Vehicle


title: Peripheral-8mm-rpe-cho-donor-1

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

country: USA

institute: UNIVERSITY OF IOWA

description: Sample 4

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg19 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
Experiment 1:  Relates to donors 1-3 (Samples 1-6).  The six samples were collectively aggregated with the cellranger aggr function with the following parameter: --normalized=mapped.  Cells were then filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 300 (to remove cells with poor read quality) or greater than 6000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). Aggregated reads were normalized and clustered in Seurat (v3.0.2) with the following commands: seurat_obj <- NormalizeData(seurat_obj, normalization.method = "LogNormalize", scale.factor = 10000); seurat_obj <- FindVariableFeatures(seurat_obj, selection.method = "mvp", nfeatures = 2000); all.genes <- rownames(seurat_obj); seurat_obj <- ScaleData(seurat_obj, features = all.genes); seurat_obj <- RunPCA(Seurat_obj, features = VariableFeatures(object = seurat_obj)); seurat_obj <- FindNeighbors(seurat_obj, dims = 1:14); seurat_obj <- FindClusters(seurat_obj, resolution = 0.175).
Experiment 2:   Relates to donors 4-7 (Samples 7-14).  Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 500 (to remove cells with poor read quality) or greater than 7000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). For each of the eight libraries, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands: donor_x_region <- NormalizeData(donor_x_region, normalization.method = "LogNormalize", scale.factor = 10000); donor_x_region <- FindVariableFeatures(donor_x_region, selection.method = "vst", nfeatures = 2000).  Integration anchors from the first 20 dimensions of the canonical correlation analysis were used to integrate data with the following commands: CD31.anchors <- FindIntegrationAnchors(object.list = c(donor_4_macula, donor_5_macula, donor_6_macula, donor_7_macula, donor_4_peripheral, donoro_5_peripehral, donor_6_peripheral, donor_7_peripheral), dims=1:20); CD31.combined <- IntegrateData(anchorset = CD31.anchors, dims = 1:20).  Data scaling, principal component analysis, and clustering were performed with the following commands: CD31.combined <- ScaleData(CD31.combined, verbose = FALSE); CD31.combined <- RunPCA(CD31.combined, npcs = 30, verbose = FALSE); CD31.combined <- RunUMAP(CD31.combined, reduction = "pca", dims = 1:20); CD31.combined <- FindNeighbors(CD31.combined, reduction = "pca", dims = 1:20); CD31.combined <- FindClusters(CD31.combined, resolution = 0.5).
Genome_build: hg19
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format. Log-normalized expression values (from GetAssayData(object = seurat_object) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values.

source_name: RPE-choroid

extract_protocol:
In experiment 1, an 8-mm macular centered and an 8-mm peripheral punch of RPE/choroid from the inferotemporal region were acquired from three human donors (Donors 1-3). Tissue was dissociated using the Papain Dissociation System (Worthington Biochemical Corporation, Lakewood NJ). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Single-cell RNA libraries were prepared for sequencing using standard 10X genomics protocols. Briefly, cryopreserved samples from donors 1-3 were thawed, and single cells were captured and barcoded using the Chromium System with the v3 single cell-reagent kit (10x Genomics, Pleasanton CA). Cryopreserved cells from donors 4-7 were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) of the CD31+ cell fraction. The positive cell fraction was passed two times through a 40 mm filter to remove aggregates before immediate single cell capturing and barcoding as described above. Sequencing was performed on pooled libraries using the Illumina HiSeq 4000 platform (San Diego, CA), generating 150 base pair paired-end reads.

tag: enrichment

value: unenriched

tag: donor

value: RPE-choroid

tag: location

value: periphery

tag: punch-size


title: MCF7-ARID1A_KO_Clone_14_Vehicle rep 3


title: pp2a-b´γ P35S:PP2A-B’γ_apic_rep3

description: pool of 7 leaf halves


title: MCF7-ARID1A_KO_Clone_14_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_14_Vehicle rep 1


title: pp2a-b´γ P35S:PP2A-B’γ_apic_rep1

description: pool of 7 leaf halves


title: pp2a-b’γ_apic_rep5

description: pool of 7 leaf halves


title: MCF7-ARID1A_KO_Clone_11_4-hydroxy_tamoxifen_rep 2

description:
mcf7_arid1a_ko_clone_11_4_oht_c11.macs2.bed.gz
mcf7_arid1a_ko_clone_11_4_oht_c11.genrich.bed.gz

value: MCF7 ARID1A knockout clone 11


title: pp2a-b’γ_apic_rep4

description: pool of 7 leaf halves


title: MCF7-ARID1A_KO_Clone_11_4-hydroxy_tamoxifen_rep 4


title: MCF7-ARID1A_KO_Clone_11_4-hydroxy_tamoxifen_rep 1


title: MCF7-ARID1A_KO_Clone_11_4-hydroxy_tamoxifen_rep 3


title: MCF7-ARID1A_KO_Clone_11_Vehicle rep 4

description:
mcf7_arid1a_ko_clone_11_veh_c11.macs2.bed.gz
mcf7_arid1a_ko_clone_11_veh_c11.genrich.bed.gz


title: MCF7-parental_4-hydroxy tamoxifen rep 4

description:
mcf7_ecacc_4_oht_parental_wt.macs2.bed.gz
mcf7_ecacc_4_oht_parental_wt.genrich.bed.gz

value: MCF7 cells


title: MCF7-ARID1A_KO_Clone_11_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_11_Vehicle rep 1


title: MCF7-parental_4-hydroxy tamoxifen rep 3


title: pp2a-b’γζ_basal_rep4

description: pool of 7 leaf halves

value: basal (= proximal) halves of fully expanded leaves


title: WT_apic_rep5

description: pool of 7 leaf halves


title: WT_apic_rep2

description: pool of 7 leaf halves


title: WT_apic_rep1

description: pool of 7 leaf halves


title: WT_apic_rep3

description: pool of 7 leaf halves


title: pp2a-b’γζ_basal_rep5

description: pool of 7 leaf halves


title: WT_apic_rep4

description: pool of 7 leaf halves


title: MCF7-parental_Vehicle rep 4

description:
mcf7_ecacc_veh_parental_wt.macs2.bed.gz
mcf7_ecacc_veh_parental_wt.genrich.bed.gz


title: pp2a-b´γ P35S:PP2A-B’γ_apic_rep2

description: pool of 7 leaf halves


title: pp2a-b’γζ_basal_rep3

description: pool of 7 leaf halves


title: pp2a-b’γ_apic_rep1

description: pool of 7 leaf halves


title: pp2a-b’γ_apic_rep2

description: pool of 7 leaf halves


title: pp2a-b’γ_apic_rep3

description: pool of 7 leaf halves


title: MCF7-ARID1A_KO_Clone_11_Vehicle rep 3


title: MCF7-parental_Vehicle rep 2


title: pp2a-b’γζ_basal_rep1

description: pool of 7 leaf halves


title: MCF7-parental_4-hydroxy tamoxifen rep 1


title: MCF7-parental_Vehicle rep 1


title: pp2a-b’γ sid2_basal_rep5

description: pool of 7 leaf halves

source_name: pp2a-b’γ sid2_basal


title: MCF7-parental_4-hydroxy tamoxifen rep 2


title: pp2a-b’γ sid2_basal_rep3

description: pool of 7 leaf halves


title: ZR-75-1-siFOXA1_DCDT__Input_rep_1

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-3 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

growth_protocol: MCF7 cells were grown in DMEM High glucose media with 2 mM Glutamine, 10% FBS, Sodium pyruvate. ZR-75-1 cells were grown in RPMI media with 2 mM Glutamine, 10% FBS, Sodium pyruvate. Charcoal stripping was performed in phenol red free media with 5% of double times charcoal stripped FBS.

extract_protocol:
Nuclear lysates were prepared and antibody-bound chromatin was purified using appropriate antibodies. Antibodies used: ARID1A HPA005456, BRG1 ab215998, SNF5 Bethyl A301-087A, ERα ab3575 and Merck Millipore 06-935 antibody mix, H3K27ac Diagenode C15410196 Premium, HDAC1 Diagenode Premium C15410325, ARID2 Bethyl A302-229A, BRD4 from Cheng Ming Chiang's lab.
DNA was prepared for Illumina sequencing on the HiSeq 4000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: Cells were treated, without any serum deprivation, for 6 hours with vehicle (DMSO) or 100 nM 4-Hydroxytamoxifen.

tag: cell line

tag: chip antibody

value: Charcoal stripped serum containing media

value: ZR-75-1 cells


title: pp2a-b’γ sid2_basal_rep4

description: pool of 7 leaf halves


title: ZR-75-1-siFOXA1_DCDT__ARID1A_rep_1


title: ZR-75-1-siFOXA1_DCDT__ARID1A_rep_3


title: pp2a-b´γ P35S:PP2A-B’γ_basal_rep5

description: pool of 7 leaf halves

source_name: pp2a-b´γ P35S:PP2A-B’γ_basal


title: ZR-75-1-siCont_DCDT__ARID1A_rep_2


title: MCF7-parental_Vehicle rep 3


title: ZR-75-1-siCont_DCDT__ARID1A_rep_3


title: pp2a-b’γ sid2_basal_rep2

description: pool of 7 leaf halves


title: pp2a-b´γ P35S:PP2A-B’γ_basal_rep2

description: pool of 7 leaf halves


title: ZR-75-1-siFOXA1_DCDT__ARID1A_rep_2


title: pp2a-b´γ P35S:PP2A-B’γ_basal_rep3

description: pool of 7 leaf halves


title: pp2a-b´γ P35S:PP2A-B’γ_basal_rep1

description: pool of 7 leaf halves


title: pp2a-b’γ sid2_basal_rep1

description: pool of 7 leaf halves


title: ZR-75-1-siFOXA1_DCDT__BRG1_rep_3

value: Abcam ab215998


title: ZR-75-1-siCont_DCDT__Input_rep_1


title: pp2a-b’γ_basal_rep5

description: pool of 7 leaf halves


title: ZR-75-1-siFOXA1_DCDT__BRG1_rep_2


title: ZR-75-1-siFOXA1_DCDT__BRG1_rep_1


title: ZR-75-1-siCont_DCDT__BRG1_rep_3


title: pp2a-b’γ_basal_rep3

description: pool of 7 leaf halves


title: pp2a-b’γ_basal_rep4

description: pool of 7 leaf halves


title: ZR-75-1-siCont_DCDT__BRG1_rep_2


title: pp2a-b´γ P35S:PP2A-B’γ_basal_rep4

description: pool of 7 leaf halves


title: ZR-75-1-siCont_DCDT__ARID1A_rep_1


title: MCF7-siCont_DCDT__Input_rep_1


title: WT_basal_rep4

description: pool of 7 leaf halves


title: MCF7-siFOXA1_DCDT__Input_rep_1


title: WT_basal_rep2

description: pool of 7 leaf halves


title: WT_basal_rep5

description: pool of 7 leaf halves


title: MCF7-siFOXA1_DCDT__ARID1A_rep_2


title: WT_basal_rep3

description: pool of 7 leaf halves


title: pp2a-b’γ_basal_rep1

description: pool of 7 leaf halves


title: ZR-75-1-siCont_DCDT__BRG1_rep_1


title: MCF7-siFOXA1_DCDT__ARID1A_rep_1


title: MCF7-siCont_DCDT__ARID1A_rep_2


title: WT_basal_rep1

description: pool of 7 leaf halves


title: MCF7-siCont_DCDT__ARID1A_rep_3


title: 10 spleen mouse WT-3

city: Salt Lake City

first: Matt

last: Bettini

state: Utah

address: 15 North Medical Drive East, EEJMRB RM 1820

institute: University of Utah

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 using TopHat Alignment v1.0.0
Fragment per kilobase million of library size (FPKM) were calculated using Cufflinks Assembly & DE v1.1.0
Genome_build: RefSeq mm9
Supplementary_files_format_and_content: abundance measurements

source_name: 10 spleen mouse WT-3

growth_protocol: CD4+ T cells were expanded from the spleens of 6-8-week-old female NOD or NOD.InsY16A Tg mice immunized with Insulin C19A. T cell lines were generated by plating 5x10^6 splenocytes per well in a 24 well plate with complete RPMI containing 10% FCS and 10uM peptide. After two weeks, CD4+ T cells were MACs purified using the manufactures protocol.  The purified average purity was >95% and <1% Foxp3+. Five million purified CD4+ T cells were transferred to 8-10 week old NOD.scid female recipients.

extract_protocol:
TritonX-100 cell lysis, reverse transcription, cDNA amplification
Nextera XT

tag: strain

value: NOD

value: pancreatic spleen

tag: age

value: 8-10 weeks

tag: genotype


title: MCF7-siCont_DCDT__ARID1A_rep_1


title: 12 spleen mouse Y16A-2

source_name: 12 spleen mouse Y16A-2


title: MCF7-siFOXA1_DCDT__BRG1_rep_3


title: pp2a-b’γ_basal_rep2

description: pool of 7 leaf halves


title: 9 spleen mouse Y16A-3

source_name: 9 spleen mouse Y16A-3


title: 8 spleen mouse WT-2

source_name: 8 spleen mouse WT-2


title: MCF7-siFOXA1_DCDT__BRG1_rep_2


title: MCF7-siCont_DCDT__BRG1_rep_3


title: 7 spleen mouse WT-1

source_name: 7 spleen mouse WT-1


title: 6 pancreas mouse Y16A-2

source_name: 6 pancreas mouse Y16A-2

value: pancreatic islets


title: MCF7-siFOXA1_DCDT__BRG1_rep_1

value: ER+  Breast Cancer Cell Line


title: MCF7-siFOXA1_DCDT__ARID1A_rep_3


title: pp2a-b’γζ_basal_rep2

description: pool of 7 leaf halves


title: MCF7-siCont_DCDT__BRG1_rep_2


title: 5 pancreas mouse Y16A-1

source_name: 5 pancreas mouse Y16A-1


title: MCF7-siCont_DCDT__BRG1_rep_1


title: 11 spleen mouse Y16A-1

source_name: 11 spleen mouse Y16A-1


title: 4 pancreas mouse WT-3

source_name: 4 pancreas mouse WT-3


title: 3 pancreas mouse Y16A-3

source_name: 3 pancreas mouse Y16A-3


title: MCF7-ARID1A_KO_Clone_14_H4K12ac_4-hydroxy tamoxifen rep 2

source_name: MCF7-ARID1A KO Clone 14_H4K12ac ChIP-seq_4-hydroxytamoxifen

value: 100 nM 4-hydroxy tamoxifen for 6 hours

value: MCF7 ARID1A knockout clone 14


title: 1 pancreas mouse WT-1

source_name: 1 pancreas mouse WT-1


title: 2 pancreas mouse WT-2

source_name: 2 pancreas mouse WT-2


title: MCF7-ARID1A_KO_Clone_14_H4K12ac_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 14_H4K12ac ChIP-seq_Vehicle

value: Vehicle


title: Pla2g4a_rep2

city: Boston

first: Chun-Cheih

last: Chao

state: MA

address: 60 Fenwood road BTM 10032

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
DGE libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
Reads were first demulitplex using Picard (v.2.17.11) IlluminaBaseCallsToSam; with well indices CCGGCA (F4), CGCACC (F7), CGGACG (F10), CGTCCG (G1), GACGCC (G4), and GCCCAG (G7).
Reads were aligned using GRCh38 mouse genome with STAR (v2.4.2a) with default parameters
Duplicate reads are marked with Picard UmiAwareMarkDuplicatesWithMateCigar to identify duplicate reads based on UMI sequence and alignment start site.
Gene are then quantified using RSEM v1.2.21 with paired-end option and accessed for quality using RNA-SeQC.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format with gene ID, symbol, and RPKM

source_name: Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the 3' DGE protocol as described (Soumillon et al., bioRxiv 2014)

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: WT NOD/ShiLtJ

tag: Sex

value: Female


title: Pla2g4a_rep1


title: Pla2g4a_rep3


title: Cers6_rep3


title: MCF7-ARID1A_KO_Clone_14_H4K12ac_Vehicle rep 1


title: MCF7-ARID1A_KO_Clone_11_H4K12ac_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 11_H4K12ac ChIP-seq_4-hydroxytamoxifen


title: MCF7-ARID1A_KO_Clone_14_H4K12ac_4-hydroxy tamoxifen rep 1


title: MCF7-ARID1A_KO_Clone_11_H4K12ac_4-hydroxy tamoxifen rep 2


title: MCF7-ARID1A_KO_Clone_11_H4K12ac_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 11_H4K12ac ChIP-seq_Vehicle


title: MCF7-ARID1A_KO_Clone_11_H4K12ac_4-hydroxy tamoxifen rep 1


title: MCF7-ARID1A_KO_Clone_11_H4K12ac_Vehicle rep 1


title: Cers6_rep1


title: Cers5_rep2


title: Cers5_rep3


title: MCF7-parental_H4K12ac_4-hydroxy tamoxifen rep 3


title: Cers6_rep2


title: MCF7-ARID1A_KO_Clone_14_H4K12ac_4-hydroxy tamoxifen rep 3


title: MCF7-parental_H4K12ac_4-hydroxy tamoxifen rep 2


title: Ugcg_rep2

value: Ugcg


title: Cers5_rep1


title: MCF7-ARID1A_KO_Clone_14_H4K12ac_Vehicle rep 2


title: Ugcg_rep3


title: B4galt6_rep3


title: Ugcg_rep1


title: MCF7-parental_H4K12ac_Vehicle rep 3

source_name: MCF7-parental_H4K12ac ChIP-seq_Vehicle


title: MCF7-parental_H4K12ac_Vehicle rep 2


title: MCF7-parental_H4K12ac_4-hydroxy tamoxifen rep 1


title: B4galt6_rep1


title: MCF7-parental_H4K12ac_Vehicle rep 1


title: Control_rep3

value: Control


title: MCF7-ARID1A_KO_Clone_14_H4K8ac_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 14_H4K8ac ChIP-seq_4-hydroxytamoxifen

value: Abcam ab15823


title: MCF7-ARID1A_KO_Clone_14_H4K8ac_4-hydroxy tamoxifen rep 2


title: Control_rep1


title: MCF7-ARID1A_KO_Clone_11_H4K12ac_Vehicle rep 2

value: MCF7 ARID1A knockout clone 11


title: Control_rep2


title: MCF7-ARID1A_KO_Clone_14_H4K8ac_4-hydroxy tamoxifen rep 1


title: MCF7-ARID1A_KO_Clone_14_H4K8ac_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 14_H4K8ac ChIP-seq_Vehicle


title: MCF7-ARID1A_KO_Clone_14_H4K8ac_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_14_H4K8ac_Vehicle rep 1


title: Tg_mTEC

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

data_processing:
Basecalling by RTA 1.12.4.2, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 2.17, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq reads were aligned to mouse genome (mm10) using STAR (STAR_2.5.1b)
10x genomics data analysis was performed with the Cellranger v2.0.1 software using the default parameters. Cells with extremely low number of UMI counts were filtered out.
Genome_build: mm10

source_name: Tg Adult_mTEC

growth_protocol: samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol: 10x Genomics Single Cell Chromium v2 mRNA libraries were made and sequenced on the NextSeq with v2 chemistry

value: FoxN1+/- Myc Tg+/-

value: Thymus

tag: sorting profile

value: DAPI- EpCAM+ CD45- Ly51- UEA-1+


title: MCF7-ARID1A_KO_Clone_11_H4K8ac_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 11_H4K8ac ChIP-seq_4-hydroxytamoxifen


title: MCF7-ARID1A_KO_Clone_11_H4K8ac_4-hydroxy tamoxifen rep 2


title: Tg_cTEC

source_name: Tg Adult_cTEC

tag: tissue

value: DAPI- EpCAM+ CD45- Ly51+ UEA-1-


title: WT_mTEC

value: WT


title: E17_5-cTEC

source_name: E17_5 cTEC


title: MCF7-ARID1A_KO_Clone_11_H4K8ac_4-hydroxy tamoxifen rep 1

tag: treatment


title: MCF7-ARID1A_KO_Clone_11_H4K8ac_Vehicle rep 2

source_name: MCF7-ARID1A KO Clone 11_H4K8ac ChIP-seq_Vehicle

tag: genotype/variation


title: WT_cTEC


title: E13_5_TEC

value: DAPI- EpCAM+ CD45-


title: MCF7-ARID1A_KO_Clone_11_H4K8ac_Vehicle rep 1

tag: cell type


title: Adult_mTEC


title: B4galt6_rep2


title: E15_5_cTEC


title: MCF7-ARID1A_KO_Clone_11_H4K8ac_Vehicle rep 3

tag: passages


title: MCF7-parental_H4K8ac_4-hydroxy tamoxifen rep 3

value: MCF7 cells


title: MCF7-parental_H4K8ac_Vehicle rep 3

source_name: MCF7-parental_H4K8ac ChIP-seq_Vehicle

value: ER+  Breast Cancer Cell Line


title: Adult_cTEC


title: MCF7-parental_H4K8ac_Vehicle rep 1


title: Cdk2-HET

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
barcodes.tsv.gz: BC-2
matrix.mtx.gz: BC-2

data_processing:
10X Genomics cellranger(v2.1.0) mkfastq was used to generate demultiplexed fastq files.
10X Genomics cellranger(v2.1.0) count was used to map reads to the reference genome and generate gene-BC matrices.
10X Genomics cellranger(v2.1.0) aggr was used to generate the final combined, filtered gene-BC matrix provided as processed data files (barcodes.tsv, genes.tsv, matrix.mtx).
Seurat was used to extract germ-cell cluster and to filter cell barcodes with less than 200 detected genes and less than 10,000 UMIs.
Expression data from Cdk2-WT and Cdk2-Y15S samples (used for all analyses) were further filtered to remove genes that are detected in less than 10% of cell barcodes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited; cell barcodes/genes/matrix.tsv output files from cellranger aggr containing UMI counts for filtered barcodes; Cell barcodes with suffix "-1" are from Cdk2-W, "-2" from Cdk2-HET, and "-3" from Cdk2-Y15S.
Supplementary_files_format_and_content: tab-delimited; germline_finalUMICounts.tsv and cell_cluster_mapping.tsv are germ-cell-cluster specific files; Cell barcodes with suffix "-1" are from Cdk2-WT and "-3" from Cdk2-Y15S.

source_name: Testis

growth_protocol: Mice used were maintained on a mixed genetic background (FVB/NJ and B6(Cg)-Tyrc-2J/J) maintained under a protocol (2004-0038) approved by Cornell’s Animal Care and Use Committee. Cdk2<+/YS>  animals were bred to get the P3 males of indicated genotypes for sample preparation.

extract_protocol:
3.5 DPP testes were decapsulated in HBSS (Mediatech Inc.) and digested with 0.642 ml of Trypsin/EDTA (0.25%, Invitrogen Inc.) and 0.071 ml DNase I (1 mg/ml in HBSS, Sigma Inc.) at 37 °C for 3-5 min min. Digestion was stopped by adding 0.5 ml of media (HBSS + 10% FBS), the cells were filtered through a 70-µm cell strainer and resuspended in HBSS with 0.04% FBS.
10X Genomics Single Cell 3' RNAseq v2

treatment_protocol: No treatment

tag: sample type

value: Single cell suspension

value: post-natal day 3


title: Cdk2-Y15S

description:
barcodes.tsv.gz: BC-3
matrix.mtx.gz: BC-3
germline_finalUMICounts.tsv: BC-3
cell_cluster_mapping.tsv: BC-3


title: MCF7-parental_H4K8ac_4-hydroxy tamoxifen rep 2

value: 100 nM 4-hydroxy tamoxifen for 6 hours


title: Cdk2-WT

description:
barcodes.tsv.gz: BC-1
matrix.mtx.gz: BC-1
germline_finalUMICounts.tsv: BC-1
cell_cluster_mapping.tsv: BC-1


title: MCF7-parental_H4K8ac_Vehicle rep 2

value: Vehicle


title: SKBR3 small RNA

first: yue

last: huang

state: 江苏省

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the analysis.
Trimmed reads (with 5’, 3’-adaptor bases removed) were aligned to mature-tRNA and pre-tRNA reference sequences getting from GtRNAdb using NovoAlign software (v2.07.11).
The alignment statistical analysis was applied to retain the valid sequences for subsequent tDR expression profiling and differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: TagCount

source_name: breast

growth_protocol: Human breast cancer cell lines MCF-7 and SKBR-3 were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). Human normal breast epithelial cell line HBL-100 was obtained from Cell bank of Chinese Academy of Sciences (Shanghai, China). SKBR-3 cells were cultured in RPMI-1640 (Multicell, USA), MCF-7 and HBL-100 cells were cultured in DMEM (Gibco, UK) supplemented with 10% Fetal Bovine Serum (FBS, Gibco), 100 U/ml penicillin and 100 μg/ml streptomycin (Multicell, USA). Cells were cultured at 37°C in a humidified atmosphere containing 5% CO2 and the cell medium was replaced every 48 h.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Life Technologies, USA). We do the following treatments before library preparation for total RNA samples: 3’-aminoacyl (charged) deacylation to 3’-OH for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription.  Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HER2/ERBB2 amplified cells

value: breast adenocarcinoma


title: HBL-100 small RNA

value: normal breast epithelial cells

value: breast epithelial


title: MCF7-ARID1A_KO_Clone_14_H4K5ac_4-hydroxy tamoxifen rep 1 Input

source_name: MCF7-ARID1A KO Clone 14_H4K5ac ChIP-seq_4-hydroxytamoxifen Input

value: MCF7 ARID1A knockout clone 14


title: NB_cTEC


title: MCF-7 small RNA

value: estrogen-sensitive cells


title: MCF7-ARID1A_KO_Clone_14_H4K5ac_Vehicle rep 1 Input

source_name: MCF7-ARID1A KO Clone 14_H4K5ac ChIP-seq_Vehicle Input


title: MCF7-ARID1A_KO_Clone_11_H4K5ac_4-hydroxy tamoxifen rep 1 Input

source_name: MCF7-ARID1A KO Clone 11_H4K5ac ChIP-seq_4-hydroxytamoxifen Input

value: MCF7 ARID1A knockout clone 11


title: MCF7-ARID1A_KO_Clone_11_H4K5ac_Vehicle rep 1 Input

source_name: MCF7-ARID1A KO Clone 11_H4K5ac ChIP-seq_Vehicle Input


title: HFF_Input_Rep1

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
Library strategy: PIRCh-seq
Raw reads were uniquely mapped to mm9/hg19 using Tophat with default parameter
Samtools and BedTools were used to transform the mapped bam file into bedGraph and bigwig file for visualization on UCSC genome browser. RPKM and raw reads count were calculated by self-designed scripts with ensemble annotation, Homo_sapiens.GRCh37.75.gtf and Mus_musculus.NCBIM37.67.gtf for human and mouse samples respectively. Gene with RPKM >0.1 in input or any PIRCh-seq profiles were defined as expressed and used for downstream analysis
To further investigate the detailed mechanism behind RNA-histone binding, we perform peak calling on PIRCh-seq result. We merged two replicates of each gene to minimize experimental deviation bias, and smoothed the normalized count on each base through a 5 bp width window, along with 2 bp step size. Smoothed signal per window was used for peak calling through home-made code. Significant peak filter was based on fold change of input signal and enrichment P-value. At last, PIRCh-seq peak list was intergraded with RNA structure and modification information for next-step analysis.
Genome_build: mm9/ hg19
Supplementary_files_format_and_content: mouse_merge_rpkm.txt

source_name: Human Female fibroblast

extract_protocol:
To harvest the cells for PIRCh-seq. Approximately 4x107 cells were trypsinized and pooled into 50ml falcon tube. After wash with 40ml of cold PBS once. Make fresh 1% glutaraldehyde in room temperature PBS from 25% stock, discard remaining stock. Resuspend cell pellet in 1ml of glutaraldehyde solution and use a p1000 pipette to resuspend well, and top up to 40ml (1ml 1% glutaraldehyde / 1 milion cells). After invert a couple times, shake gently for 10 min, and then quench with 1/10 volume of 1.25M glycine. Invert a couple times, shake gently for 5 min, spin down 2000g, 4 min. Wash pellet once with 40ml cold PBS. Resuspend pellet in 1ml/20million cells of cold PBS. Aliquot 1ml to each fresh eppendorf tube, spin down 2000g, 4 min. Last, aspirate carefully, flash freeze cell pellets, store at -80C if necessary.For sonication, prepared cell pellets were spined down 2000g 4 min and remove any remaining PBS. Lysis per 20 million cells with 1ml of lysis buffer (1% SDS, 50mM Tris 7.0, 10mM EDTA, 1mM PMSF, 0.1U/ul Superase-in (Ambion), 1x Proteinase inhibitor (Roche)). After that, sonicate till chromatin size is ~300-2000bp and lysate is clear. Then spin down lysates at 16000g for 10 min. After that, we can flash freeze the supernate and store in -80℃ if necessary.
For PIRCh-seq library construction, Add 400ul dilution buffer to each reaction and H3 or specific Histone modification antibody (Dilution buffer: 0.01% SDS, 1.1% Triton X 100, 1.2 mM EDTA, 16.7 mM Tris 7.0, 167 mM NaCl, 1mM PMSF, 0.1U/ul Superase-in (Ambion), 1x Proteinase inhibitor (Roche)). Shake the reaction end-to-end at 4℃ overnight. Use 50ul Protein A dynabeads per 5ug antibody IP. Wash beads with 5 times original volume of dilution buffer 4 times. Notice that do not exceed 200ul original volume of beads per tube. At last wash, aliquot beads to 1 tube per reaction. Aspirate buffer, resuspend and transfer beads to your IP using 200ul of the IP sample. End to end shake at room temperature for 2 hours. Wash with 1ml wash buffer 4 times, resuspend beads in 50ul IP elution buffer, vortex at setting 1 for 15 min. Then transfer supernatant to a fresh tube. Repeat elution on beads for once more. Combine supernatant for a total of 100ul. Immediatley add 5ul 3M NaOAc to neutralize pH. Add 10ul TurboDnase buffer and 1ul TurboDnase (Ambion), 37C for 30min. Add 3ul 500mM EDTA to eliminate divalent ions. Add 5ul Proteinase K (Ambion), 50C 45 min. For making sequencing libraryies, extract RNA using Trizol/chloroform, and precipitate with equal volume of isopropanol. Wash RNA pellet in 1ml ul 70% EtOH, resuspend pellets in 10ul H2O. Add 1ul TurboDnase buffer, Add 1ul TurboDnase, 1.2ul TurboDnase inactivating reagents. Vortex for 3', spin down. Save the 10ul supernatant, heat at 75C for 10' to kill Dnase. Use 5ul in Nugen Ovation v2 kit.

tag: cell-type

value: Human Female fibroblast

tag: antibody

value: Input


title: HFF_H3_PIRCh_Rep1


title: MCF7-parental_H4K8ac_4-hydroxy tamoxifen rep 1

value: Abcam ab15823


title: MCF7-parental_H4K5ac_4-hydroxy tamoxifen rep 1 Input


title: H9_H3K4me3_PIRCh_Rep2

source_name: Human Embryonic stem cells

value: Human Embryonic stem cells


title: MCF7-parental_H4K5ac_Vehicle rep 1 Input

value: MCF7 cells


title: MCF7-ARID1A_KO_Clone_14_H4K5ac_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 14_H4K5ac ChIP-seq_4-hydroxytamoxifen

value: ER+  Breast Cancer Cell Line

value: Abcam ab51997


title: MCF7-ARID1A_KO_Clone_14_H4K5ac_4-hydroxy tamoxifen rep 1


title: H9_H3_PIRCh_Rep1


title: H9_H3K4me3_PIRCh_Rep1


title: H9_H3K4me1_PIRCh_Rep1


title: H9_Input_Rep2


title: MCF7-ARID1A_KO_Clone_14_H4K5ac_4-hydroxy tamoxifen rep 2


title: H9_Input_Rep1


title: MCF7-ARID1A_KO_Clone_14_H4K5ac_Vehicle rep 1

source_name: MCF7-ARID1A KO Clone 14_H4K5ac ChIP-seq_Vehicle


title: H9_H3_PIRCh_Rep2


title: MCF7-ARID1A_KO_Clone_14_H4K5ac_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_11_H4K5ac_4-hydroxy tamoxifen rep 1

source_name: MCF7-ARID1A KO Clone 11_H4K5ac ChIP-seq_4-hydroxytamoxifen


title: MCF7-ARID1A_KO_Clone_11_H4K5ac_4-hydroxy tamoxifen rep 2


title: MCF7-ARID1A_KO_Clone_11_H4K5ac_4-hydroxy tamoxifen rep 3


title: MCF7-ARID1A_KO_Clone_11_H4K5ac_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 11_H4K5ac ChIP-seq_Vehicle


title: H9_H3K4me1_PIRCh_Rep2


title: MCF7-ARID1A_KO_Clone_11_H4K5ac_Vehicle rep 2


title: F3-HFHS+Veh25.6

city: stockholm

first: yu

last: pei

address: Karolinska Vägen 6

country: Sweden

institute: karolinska institutet

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were aligned to assembly mm10 using STAR 2.4.2a (https://github.com/alexdobin/STAR)
Aligned reads were counted per gene, and RPKM values were generated, using rpkmforgenes.py of https://github.com/danielramskold/S3_species-specific_sequencing with the options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and RefSeq gene annotation
Raw counts were normalized by Seurat R package V2.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts and normalized expression counts (Only 137 sample were used for analyses, and all downstream analyses were based on the normalised expression file)

source_name: MII oocytes

extract_protocol:
Smartseq2
Smartseq2

value: MII oocytes

tag: generation and lineage

tag: female f0 diet

value: high fat and high sugar

tag: female f0 hormone treatment

value: vehicle


title: F3-HFHS+Veh25.5


title: F3-HFHS+Veh25.7


title: F3-HFHS+Veh25.3


title: F3-HFHS+Veh25.4


title: F3-HFHS+Veh25.2


title: F3-HFHS+Veh25.1


title: MCF7-ARID1A_KO_Clone_14_H4K5ac_Vehicle rep 3

tag: cell line

tag: chip antibody

value: Vehicle


title: F3-HFHS+Veh25.8

tag: strain


title: F3-CD+DHT23

value: control

value: dihydrotestosterone


title: F3-CD+DHT22


title: F3-CD+DHT21


title: F3-CD+DHT20


title: MCF7-parental_H4K5ac_4-hydroxy tamoxifen rep 3

value: 100 nM 4-hydroxy tamoxifen for 6 hours


title: MCF7-parental_H4K5ac_Vehicle rep 2

source_name: MCF7-parental_H4K5ac ChIP-seq_Vehicle


title: MCF7-parental_H4K5ac_Vehicle rep 3


title: MCF7-parental_H4K5ac_4-hydroxy tamoxifen rep 1


title: F3-CD+DHT19


title: MCF7-parental_H4K5ac_4-hydroxy tamoxifen rep 2


title: MCF7-parental_H4K5ac_Vehicle rep 1


title: jc4901_mcf7_vehicle_wild_type Clone 221 rep 3

data_processing:
STAR, version 2.5.1a, was used to align reads against hg38 reference genome.
The read counting was performed using intrinsic function of STAR.
For normalized measurement of mRNA expression the read counts were converted into RPKM values.
Differential gene expression analysis was performed using DESeq2 workflow.
Genome_build: GRCh38
Supplementary_files_format_and_content: text

extract_protocol:
RNA was extracted using Qiagen RNeasy kit.
RNAseq libraries were prepared using Illumina’s TruSeq mRNA Stranded Sample prep kit.

treatment_protocol: Cells were treated, without any serum deprivation, for 6 hours with vehicle (DMSO) or 100 nM 4-Hydroxytamoxifen, 250 nM JQ1 and 10 nM Fulvestrant.

value: breast cancer cell line

value: DMSO Vehicle for 6 hours


title: jc4900_mcf7_vehicle_wild_type Clone 221 rep 2


title: F3-CD+DHT18


title: F3-CD+DHT17


title: MCF7-ARID1A_KO_Clone_11_H4K5ac_Vehicle rep 1

value: MCF7 ARID1A knockout clone 11


title: F3-CD+DHT16


title: jc4899_mcf7_vehicle_wild_type Clone 221 rep 1


title: F3-CD+DHT15


title: F3-CD+DHT13


title: jc4884_mcf7_vehicle_wild_type Clone 219 rep 2


title: jc4885_mcf7_vehicle_wild_type Clone 219 rep 3


title: jc4886_mcf7_vehicle_wild_type Clone 219 rep 4


title: F3-CD+DHT24


title: F3-CD+DHT12


title: jc4883_mcf7_vehicle_wild_type Clone 219 rep 1


title: F3-CD+DHT11


title: jc4870_mcf7_vehicle_wild_type Clone 216 rep 4


title: jc4902_mcf7_vehicle_wild_type Clone 221 rep 4


title: jc4869_mcf7_vehicle_wild_type Clone 216 rep 3


title: F3-CD+DHT10


title: jc4868_mcf7_vehicle_wild_type Clone 216 rep 2


title: F3-CD+DHT9


title: F3-CD+DHT6


title: F3-CD+DHT7


title: jc4918_mcf7_vehicle_parental_cell_line  rep 4

description: jc4918_MCF7_Vehicle_Parental_cell_line_CRI03


title: jc4917_mcf7_vehicle_parental_cell_line  rep 3

description: jc4917_MCF7_Vehicle_Parental_cell_line_CRI03


title: jc4867_mcf7_vehicle_wild_type Clone 216 rep 1


title: jc4916_mcf7_vehicle_parental_cell_line  rep 2

description: jc4916_MCF7_Vehicle_Parental_cell_line_CRI03


title: F3-CD+DHT8


title: F3-CD+DHT4


title: jc4915_mcf7_vehicle_parental_cell_line  rep 1

description: jc4915_MCF7_Vehicle_Parental_cell_line_CRI03


title: F3-CD+DHT3


title: jc4949_mcf7_vehicle_arid1a Clone 14 rep 3


title: F3-CD+DHT2


title: F3-CD+DHT1


title: jc4948_mcf7_vehicle_arid1a Clone 14 rep 2


title: F3-CD+Veh24


title: F3-CD+Veh23


title: jc4932_mcf7_vehicle_arid1a Clone 11 rep 2


title: jc4933_mcf7_vehicle_arid1a Clone 11 rep 3


title: F3-CD+DHT14


title: F3-CD+Veh22


title: jc4931_mcf7_vehicle_arid1a Clone 11 rep 1


title: jc4934_mcf7_vehicle_arid1a Clone 11 rep 4


title: jc4947_mcf7_vehicle_arid1a Clone 14 rep 1


title: F3-CD+Veh20


title: jc4906_mcf7_jq1_wild_type Clone 221 rep 4

value: 250 nM JQ1 for 6 hours


title: F3-CD+Veh17


title: F3-CD+Veh18


title: jc4903_mcf7_jq1_wild_type Clone 221 rep 1


title: F3-CD+Veh21


title: jc4890_mcf7_jq1_wild_type Clone 219 rep 4


title: jc4905_mcf7_jq1_wild_type Clone 221 rep 3


title: F3-CD+DHT5


title: jc4950_mcf7_vehicle_arid1a Clone 14 rep 4


title: F3-CD+Veh19


title: jc4904_mcf7_jq1_wild_type Clone 221 rep 2


title: F3-CD+Veh15


title: F3-CD+Veh16


title: jc4889_mcf7_jq1_wild_type Clone 219 rep 3


title: F3-CD+Veh14


title: F3-CD+Veh13


title: F3-CD+Veh11


title: F3-CD+Veh12


title: jc4887_mcf7_jq1_wild_type Clone 219 rep 1


title: F3-CD+Veh10


title: jc4888_mcf7_jq1_wild_type Clone 219 rep 2


title: F3-CD+Veh9


title: jc4922_mcf7_jq1_parental_cell_line  rep 4

description: jc4922_MCF7_JQ1_Parental_cell_line_CRI03


title: jc4872_mcf7_jq1_wild_type Clone 216 rep 2


title: F3-CD+Veh8


title: jc4871_mcf7_jq1_wild_type Clone 216 rep 1


title: jc4873_mcf7_jq1_wild_type Clone 216 rep 3


title: F3-CD+Veh7


title: jc4921_mcf7_jq1_parental_cell_line  rep 3

description: jc4921_MCF7_JQ1_Parental_cell_line_CRI03


title: F3-CD+Veh6


title: F3-CD+Veh5


title: jc4919_mcf7_jq1_parental_cell_line  rep 1

description: jc4919_MCF7_JQ1_Parental_cell_line_CRI03


title: jc4952_mcf7_jq1_arid1a Clone 14 rep 2


title: jc4953_mcf7_jq1_arid1a Clone 14 rep 3


title: jc4954_mcf7_jq1_arid1a Clone 14 rep 4


title: jc4951_mcf7_jq1_arid1a Clone 14 rep 1


title: jc4920_mcf7_jq1_parental_cell_line  rep 2

description: jc4920_MCF7_JQ1_Parental_cell_line_CRI03


title: F3-CD+Veh4


title: F3-HFHS+Veh26.8


title: F3-CD+Veh3


title: F3-HFHS+Veh26.7


title: jc4937_mcf7_jq1_arid1a Clone 11 rep 3


title: F3-CD+Veh2


title: jc4874_mcf7_jq1_wild_type Clone 216 rep 4


title: F3-HFHS+Veh26.5


title: F3-HFHS+Veh26.4


title: jc4935_mcf7_jq1_arid1a Clone 11 rep 1


title: jc4938_mcf7_jq1_arid1a Clone 11 rep 4


title: F3-HFHS+Veh26.6


title: F3-HFHS+Veh26.3


title: jc4913_mcf7_fulvestrant_wild_type Clone 221 rep 3

value: 10 nM Fulvestrant for 6 hours


title: jc4936_mcf7_jq1_arid1a Clone 11 rep 2


title: F3-HFHS+Veh26.2


title: jc4911_mcf7_fulvestrant_wild_type Clone 221 rep 1


title: F3-CD+Veh1


title: F3-HFHS+Veh26.1


title: jc4912_mcf7_fulvestrant_wild_type Clone 221 rep 2


title: jc4914_mcf7_fulvestrant_wild_type Clone 221 rep 4


title: jc4898_mcf7_fulvestrant_wild_type Clone 219 rep 4


title: F3-HFHS+Veh22.7


title: F3-HFHS+Veh22.6


title: jc4897_mcf7_fulvestrant_wild_type Clone 219 rep 3


title: F3-HFHS+Veh22.5


title: jc4896_mcf7_fulvestrant_wild_type Clone 219 rep 2


title: jc4895_mcf7_fulvestrant_wild_type Clone 219 rep 1


title: jc4882_mcf7_fulvestrant_wild_type Clone 216 rep 4


title: F3-HFHS+Veh22.8


title: F3-HFHS+Veh22.2


title: F3-HFHS+Veh22.3


title: F3-HFHS+Veh22.1


title: F3-HFHS+Veh22.4


title: jc4880_mcf7_fulvestrant_wild_type Clone 216 rep 2


title: jc4930_mcf7_fulvestrant_parental_cell_line  rep 4

description: jc4930_MCF7_Fulvestrant_Parental_cell_line_CRI03


title: jc4879_mcf7_fulvestrant_wild_type Clone 216 rep 1


title: F2-CD+DHT7.2


title: F2-CD+DHT7.3


title: jc4928_mcf7_fulvestrant_parental_cell_line  rep 2

description: jc4928_MCF7_Fulvestrant_Parental_cell_line_CRI03


title: F2-CD+DHT7.1


title: F2-CD+DHT7.4


title: jc4961_mcf7_fulvestrant_arid1a Clone 14 rep 3


title: F2-CD+DHT6.5


title: jc4960_mcf7_fulvestrant_arid1a Clone 14 rep 2


title: F2-CD+DHT6.2


title: jc4959_mcf7_fulvestrant_arid1a Clone 14 rep 1


title: F2-CD+DHT6.3


title: jc4946_mcf7_fulvestrant_arid1a Clone 11 rep 4


title: F2-CD+DHT6.1


title: jc4945_mcf7_fulvestrant_arid1a Clone 11 rep 3


title: jc4944_mcf7_fulvestrant_arid1a Clone 11 rep 2


title: jc4881_mcf7_fulvestrant_wild_type Clone 216 rep 3


title: F2-CD+DHT9.4


title: F2-CD+DHT9.3


title: jc4910_mcf7_4_hydroxy_tamoxifen_wild_type Clone 221 rep 4

description: jc4910_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: F2-CD+DHT7.5


title: jc4929_mcf7_fulvestrant_parental_cell_line  rep 3

description: jc4929_MCF7_Fulvestrant_Parental_cell_line_CRI03


title: jc4927_mcf7_fulvestrant_parental_cell_line  rep 1

description: jc4927_MCF7_Fulvestrant_Parental_cell_line_CRI03


title: jc4909_mcf7_4_hydroxy_tamoxifen_wild_type Clone 221 rep 3

description: jc4909_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4962_mcf7_fulvestrant_arid1a Clone 14 rep 4


title: jc4894_mcf7_4_hydroxy_tamoxifen_wild_type Clone 219 rep 4

description: jc4894_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4907_mcf7_4_hydroxy_tamoxifen_wild_type Clone 221 rep 1

description: jc4907_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4908_mcf7_4_hydroxy_tamoxifen_wild_type Clone 221 rep 2

description: jc4908_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: F2-CD+DHT6.4


title: jc4893_mcf7_4_hydroxy_tamoxifen_wild_type Clone 219 rep 3

description: jc4893_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4892_mcf7_4_hydroxy_tamoxifen_wild_type Clone 219 rep 2

description: jc4892_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4891_mcf7_4_hydroxy_tamoxifen_wild_type Clone 219 rep 1

description: jc4891_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: F2-CD+DHT9.5


title: jc4878_mcf7_4_hydroxy_tamoxifen_wild_type Clone 216 rep 4

description: jc4878_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4943_mcf7_fulvestrant_arid1a Clone 11 rep 1


title: jc4875_mcf7_4_hydroxy_tamoxifen_wild_type Clone 216 rep 1

description: jc4875_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4876_mcf7_4_hydroxy_tamoxifen_wild_type Clone 216 rep 2

description: jc4876_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4877_mcf7_4_hydroxy_tamoxifen_wild_type Clone 216 rep 3

description: jc4877_MCF7_4_hydroxy_Tamoxifen_Wild_type_CRI03


title: jc4926_mcf7_4_hydroxy_tamoxifen_parental_cell_line  rep 4

description: jc4926_MCF7_4_hydroxy_Tamoxifen_Parental_cell_line_CRI03


title: F2-CD+Veh14.3


title: F2-CD+Veh14.4


title: jc4925_mcf7_4_hydroxy_tamoxifen_parental_cell_line  rep 3

description: jc4925_MCF7_4_hydroxy_Tamoxifen_Parental_cell_line_CRI03


title: F2-HFHS+Veh4.1


title: F2-HFHS+Veh4.4


title: F2-HFHS+Veh4.2


title: F2-HFHS+Veh4.3


title: F2-CD+DHT9.2


title: F2-CD+DHT9.1


title: F2-HFHS+Veh5.4


title: F2-CD+Veh14.1


title: F2-CD+Veh14.5


title: F2-CD+Veh14.2


title: jc4924_mcf7_4_hydroxy_tamoxifen_parental_cell_line  rep 2

description: jc4924_MCF7_4_hydroxy_Tamoxifen_Parental_cell_line_CRI03


title: jc4923_mcf7_4_hydroxy_tamoxifen_parental_cell_line  rep 1

description: jc4923_MCF7_4_hydroxy_Tamoxifen_Parental_cell_line_CRI03


title: F2-HFHS+Veh5.3


title: F2-HFHS+Veh5.2


title: F2-HFHS+Veh5.1


title: F2-HFHS+Veh5.5


title: F2-HFHS+Veh10.5


title: F2-HFHS+Veh4.5


title: F2-HFHS+Veh10.4


title: jc4955_mcf7_4_hydroxy_tamoxifen_arid1a Clone 14 rep 1

description: jc4955_MCF7_4_hydroxy_Tamoxifen_ARID1A_CRI03


title: jc4957_mcf7_4_hydroxy_tamoxifen_arid1a Clone 14 rep 3

description: jc4957_MCF7_4_hydroxy_Tamoxifen_ARID1A_CRI03


title: jc4958_mcf7_4_hydroxy_tamoxifen_arid1a Clone 14 rep 4

description: jc4958_MCF7_4_hydroxy_Tamoxifen_ARID1A_CRI03


title: jc4956_mcf7_4_hydroxy_tamoxifen_arid1a Clone 14 rep 2

description: jc4956_MCF7_4_hydroxy_Tamoxifen_ARID1A_CRI03


title: F2-HFHS+Veh10.2


title: F2-HFHS+Veh10.3


title: jc4942_mcf7_4_hydroxy_tamoxifen_arid1a Clone 11 rep 4

description: jc4942_MCF7_4_hydroxy_Tamoxifen_ARID1A_CRI03


title: jc4941_mcf7_4_hydroxy_tamoxifen_arid1a Clone 11 rep 3

description: jc4941_MCF7_4_hydroxy_Tamoxifen_ARID1A_CRI03


title: F2-HFHS+Veh10.1


title: F2-CD+DHT17.4


title: F2-CD+DHT17.2


title: F2-CD+DHT17.3


title: F2-CD+DHT17.5


title: MCF7-ARID1A_KO_Clone_11_BRD4_Vehicle rep 3

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

source_name: MCF7-ARID1A KO Clone 11_BRD4 ChIP-seq_Vehicle

treatment_protocol: Cells were treated, without any serum deprivation, for 6 hours with vehicle (DMSO) or 100 nM 4-Hydroxytamoxifen, 250 nM JQ1 and 10 nM Fulvestrant. For estrogen treatment, cells were treated with media containing double times charcoal stripped serum (DCDT) for 72 hours prior to Vehicle or b-estradiol treatment for 6 hours.

value: N-terminal antibody from Cheng Ming Chiang


title: jc4939_mcf7_4_hydroxy_tamoxifen_arid1a Clone 11 rep 1

description: jc4939_MCF7_4_hydroxy_Tamoxifen_ARID1A_CRI03


title: MCF7-ARID1A_KO_Clone_11_BRD4_4-hydroxy tamoxifen rep 1

source_name: MCF7-ARID1A KO Clone 11_BRD4 ChIP-seq_4-hydroxytamoxifen


title: MCF7-ARID1A_KO_Clone_11_BRD4_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_11_BRD4_4-hydroxy tamoxifen rep 2


title: F2-HFHS+DHT5


title: F2-HFHS+DHT4


title: F2-HFHS+DHT3


title: MCF7-ARID1A_KO_Clone_11_BRD4_Vehicle rep 1


title: MCF7-parental_BRD4_4-hydroxy tamoxifen rep 3


title: F2-HFHS+DHT1


title: F2-HFHS+DHT2


title: F2-CD+Veh3.5


title: MCF7-parental_BRD4_Vehicle rep 3

source_name: MCF7-parental_BRD4 ChIP-seq_Vehicle


title: F2-CD+Veh3.2


title: F2-CD+Veh3.4


title: F2-CD+Veh3.3


title: MCF7-parental_BRD4_Vehicle rep 1


title: jc4940_mcf7_4_hydroxy_tamoxifen_arid1a Clone 11 rep 2

description: jc4940_MCF7_4_hydroxy_Tamoxifen_ARID1A_CRI03


title: MCF7-parental_BRD4_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_14_ARID2_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 14_ARID2 ChIP-seq_4-hydroxytamoxifen

value: Bethyl A302-229A


title: MCF7-ARID1A_KO_Clone_11_BRD4_4-hydroxy tamoxifen rep 3


title: F2-CD+Veh3.1


title: MCF7-ARID1A_KO_Clone_14_ARID2_4-hydroxy tamoxifen rep 2


title: F2-CD+DHT17.1


title: F2-CD+Veh2.4


title: F2-CD+Veh2.5


title: MCF7-ARID1A_KO_Clone_14_ARID2_4-hydroxy tamoxifen rep 1


title: F2-CD+Veh2.3


title: F2-CD+Veh2.2


title: MCF7-ARID1A_KO_Clone_14_ARID2_Vehicle rep 2

source_name: MCF7-ARID1A KO Clone 14_ARID2 ChIP-seq_Vehicle


title: F2-CD+Veh2.1


title: MCF7-ARID1A_KO_Clone_11_ARID2_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 11_ARID2 ChIP-seq_4-hydroxytamoxifen


title: MCF7-ARID1A_KO_Clone_14_ARID2_Vehicle rep 3


title: MCF7-parental_BRD4_4-hydroxy tamoxifen rep 2


title: F2-HFHS+Veh19.5


title: MCF7-ARID1A_KO_Clone_14_ARID2_Vehicle rep 1


title: F2-HFHS+Veh19.4


title: MCF7-parental_BRD4_4-hydroxy tamoxifen rep 1


title: MCF7-ARID1A_KO_Clone_11_ARID2_4-hydroxy tamoxifen rep 1


title: MCF7-ARID1A_KO_Clone_11_ARID2_4-hydroxy tamoxifen rep 2


title: F2-HFHS+Veh19.3


title: MCF7-ARID1A_KO_Clone_11_ARID2_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 11_ARID2 ChIP-seq_Vehicle


title: MCF7-ARID1A_KO_Clone_11_ARID2_Vehicle rep 1


title: F2-CD+Veh13.5


title: F2-HFHS+Veh19.2


title: F2-HFHS+Veh19.1


title: MCF7-parental_ARID2_4-hydroxy tamoxifen rep 3


title: F2-CD+Veh13.3


title: MCF7-ARID1A_KO_Clone_11_ARID2_Vehicle rep 2


title: MCF7-parental_ARID2_4-hydroxy tamoxifen rep 2


title: MCF7-parental_ARID2_4-hydroxy tamoxifen rep 1


title: F2-CD+Veh13.4


title: MCF7-parental_ARID2_Vehicle rep 3

source_name: MCF7-parental_ARID2 ChIP-seq_Vehicle


title: F2-CD+Veh13.1


title: F2-CD+DHT8.4


title: F2-CD+DHT8.1


title: MCF7-ARID1A_KO_Clone_14_BRG1_4-hydroxy tamoxifen rep 1

source_name: MCF7-ARID1A KO Clone 14_BRG1 ChIP-seq_4-hydroxytamoxifen


title: MCF7-parental_ARID2_Vehicle rep 1


title: F2-CD+DHT8.5


title: F2-CD+DHT8.3


title: F1-HFHS+DHT14


title: MCF7-ARID1A_KO_Clone_14_BRG1_4-hydroxy tamoxifen rep 3


title: F2-CD+DHT8.2


title: F1-HFHS+DHT15


title: MCF7-ARID1A_KO_Clone_14_BRG1_Vehicle rep 2

source_name: MCF7-ARID1A KO Clone 14_BRG1 ChIP-seq_Vehicle


title: MCF7-parental_ARID2_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_14_BRG1_Vehicle rep 3


title: F1-HFHS+DHT13


title: MCF7-ARID1A_KO_Clone_11_BRG1_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 11_BRG1 ChIP-seq_4-hydroxytamoxifen


title: MCF7-ARID1A_KO_Clone_14_BRG1_Vehicle rep 1


title: F1-HFHS+DHT12


title: F2-CD+Veh13.2


title: MCF7-ARID1A_KO_Clone_11_BRG1_4-hydroxy tamoxifen rep 1


title: F1-HFHS+DHT10


title: MCF7-ARID1A_KO_Clone_11_BRG1_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 11_BRG1 ChIP-seq_Vehicle


title: MCF7-ARID1A_KO_Clone_11_BRG1_Vehicle rep 2


title: F1-HFHS+DHT9


title: MCF7-ARID1A_KO_Clone_14_BRG1_4-hydroxy tamoxifen rep 2


title: MCF7-ARID1A_KO_Clone_11_BRG1_Vehicle rep 1


title: F1-HFHS+DHT8


title: F1-HFHS+DHT6


title: F1-HFHS+DHT7


title: MCF7-parental_BRG1_Vehicle rep 3

source_name: MCF7-parental_BRG1 ChIP-seq_Vehicle


title: F1-HFHS+DHT4


title: F1-HFHS+DHT5


title: MCF7-parental_BRG1_4-hydroxy tamoxifen rep 1


title: MCF7-parental_BRG1_4-hydroxy tamoxifen rep 2


title: MCF7-ARID1A_KO_Clone_14_HDAC1_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 14_HDAC1 ChIP-seq_4-hydroxytamoxifen

value: Diagenode Premium C15410325


title: F1-HFHS+DHT2


title: MCF7-ARID1A_KO_Clone_14_HDAC1_4-hydroxy tamoxifen rep 2

value: ER+  Breast Cancer Cell Line


title: MCF7-parental_BRG1_Vehicle rep 2


title: F1-HFHS+DHT3


title: F1-HFHS+Veh14


title: F1-HFHS+DHT1


title: MCF7-ARID1A_KO_Clone_14_HDAC1_4-hydroxy tamoxifen rep 1


title: F1-HFHS+Veh15


title: F1-HFHS+Veh13


title: MCF7-ARID1A_KO_Clone_11_BRG1_4-hydroxy tamoxifen rep 2


title: MCF7-ARID1A_KO_Clone_14_HDAC1_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 14_HDAC1 ChIP-seq_Vehicle


title: F1-HFHS+DHT11

source_name: MII oocytes


title: MCF7-ARID1A_KO_Clone_14_HDAC1_Vehicle rep 2


title: F1-HFHS+Veh11


title: F1-HFHS+Veh10


title: MCF7-ARID1A_KO_Clone_14_HDAC1_Vehicle rep 1


title: MCF7-ARID1A_KO_Clone_11_HDAC1_4-hydroxy tamoxifen rep 2

source_name: MCF7-ARID1A KO Clone 11_HDAC1 ChIP-seq_4-hydroxytamoxifen


title: F1-HFHS+Veh12


title: MCF7-ARID1A_KO_Clone_11_HDAC1_4-hydroxy tamoxifen rep 3


title: MCF7-parental_BRG1_Vehicle rep 1


title: F1-HFHS+Veh9


title: MCF7-ARID1A_KO_Clone_11_HDAC1_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 11_HDAC1 ChIP-seq_Vehicle


title: F1-HFHS+Veh7


title: F1-HFHS+Veh8


title: F1-HFHS+Veh5


title: MCF7-parental_HDAC1_4-hydroxy tamoxifen rep 2


title: MCF7-ARID1A_KO_Clone_11_HDAC1_Vehicle rep 1


title: F1-HFHS+Veh6


title: F1-HFHS+Veh4


title: F1-HFHS+Veh3


title: MCF7-parental_HDAC1_4-hydroxy tamoxifen rep 1


title: MCF7-parental_HDAC1_Vehicle rep 2

source_name: MCF7-parental_HDAC1 ChIP-seq_Vehicle


title: F1-HFHS+Veh2


title: F1-HFHS+Veh1


title: MCF7-parental_HDAC1_Vehicle rep 3


title: F1-CD+DHT15


title: MCF7-ARID1A_KO_Clone_14_H3K27ac_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 14_H3K27ac ChIP-seq_4-hydroxytamoxifen

value: Diagenode C15410196 Premium


title: MCF7-parental_HDAC1_Vehicle rep 1


title: MCF7-ARID1A_KO_Clone_14_H3K27ac_4-hydroxy tamoxifen rep 2


title: MCF7-ARID1A_KO_Clone_14_H3K27ac_4-hydroxy tamoxifen rep 1


title: F1-CD+DHT11

value: MII oocytes


title: F1-CD+DHT12


title: F1-CD+DHT13


title: F1-CD+DHT10


title: MCF7-ARID1A_KO_Clone_11_HDAC1_4-hydroxy tamoxifen rep 1


title: MCF7-ARID1A_KO_Clone_11_HDAC1_Vehicle rep 2


title: F1-CD+DHT9


title: F1-CD+DHT8


title: MCF7-ARID1A_KO_Clone_11_H3K27ac_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 11_H3K27ac ChIP-seq_4-hydroxytamoxifen


title: MCF7-ARID1A_KO_Clone_14_H3K27ac_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 14_H3K27ac ChIP-seq_Vehicle


title: F1-CD+DHT7


title: MCF7-ARID1A_KO_Clone_14_H3K27ac_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_14_H3K27ac_Vehicle rep 1


title: MCF7-parental_HDAC1_4-hydroxy tamoxifen rep 3


title: MCF7-ARID1A_KO_Clone_11_H3K27ac_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 11_H3K27ac ChIP-seq_Vehicle


title: F1-CD+DHT6


title: MCF7-ARID1A_KO_Clone_11_H3K27ac_4-hydroxy tamoxifen rep 1


title: F1-CD+DHT4


title: F1-CD+DHT14


title: F1-CD+DHT3


title: F1-CD+DHT5


title: MCF7-ARID1A_KO_Clone_11_H3K27ac_Vehicle rep 1


title: MCF7-ARID1A_KO_Clone_11_H3K27ac_Vehicle rep 2


title: F1-CD+DHT2


title: F1-CD+DHT1


title: MCF7-parental_H3K27ac_4-hydroxy tamoxifen rep 2


title: F1-CD+Veh15


title: MCF7-parental_H3K27ac_4-hydroxy tamoxifen rep 1


title: F1-CD+Veh14


title: F1-CD+Veh13


title: MCF7-parental_H3K27ac_Vehicle rep 2

source_name: MCF7-parental_H3K27ac ChIP-seq_Vehicle


title: MCF7-parental_H3K27ac_Vehicle rep 3


title: F1-CD+Veh12


title: F1-CD+Veh11


title: MCF7-parental_H3K27ac_Vehicle rep 1


title: F1-CD+Veh10


title: MCF7-ARID1A_KO_Clone_14_4-hydroxy tamoxifen rep 1 Input

source_name: MCF7-ARID1A KO Clone 14_ER ChIP-seq_4-hydroxytamoxifen Input


title: MCF7-ARID1A_KO_Clone_14_Vehicle rep 2 Input

source_name: MCF7-ARID1A KO Clone 14_ER ChIP-seq_Vehicle Input


title: MCF7-ARID1A_KO_Clone_14_Vehicle rep 1 Input


title: F1-CD+Veh8


title: MCF7-parental_H3K27ac_4-hydroxy tamoxifen rep 3


title: F1-CD+Veh6


title: F1-CD+Veh9


title: MCF7-ARID1A_KO_Clone_11_4-hydroxy tamoxifen rep 1 Input

source_name: MCF7-ARID1A KO Clone 11_ER ChIP-seq_4-hydroxytamoxifen Input


title: F1-CD+Veh5


title: MCF7-ARID1A_KO_Clone_11_H3K27ac_4-hydroxy tamoxifen rep 2


title: MCF7-ARID1A_KO_Clone_11_Vehicle rep 2 Input

source_name: MCF7-ARID1A KO Clone 11_ER ChIP-seq_Vehicle Input


title: F1-CD+Veh4


title: F1-CD+Veh3


title: MCF7-ARID1A_KO_Clone_11_4-hydroxy tamoxifen rep 2 Input


title: MCF7-ARID1A_KO_Clone_11_Vehicle rep 1 Input


title: MCF7-parental_4-hydroxy tamoxifen rep 1 Input


title: F1-CD+Veh7


title: MCF7-parental_4-hydroxy tamoxifen rep 2 Input


title: F1-CD+Veh2


title: MCF7-parental_Vehicle rep 2 Input

source_name: MCF7-parental_ER ChIP-seq_Vehicle Input


title: MCF7-parental_Vehicle rep 1 Input


title: F1-CD+Veh1


title: MCF7-ARID1A_KO_Clone_14_4-hydroxy tamoxifen rep 2 Input


title: MCF7-ARID1A_KO_Clone_14_ER_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 14_ER ChIP-seq_4-hydroxytamoxifen

value: Abcam ab3575 and Millipore 06-935 antibody mix


title: Myc.cTEC.3

data_processing:
Basecalling by RTA 1.18.64, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 1.8.4, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq fastq reads were aligned to mouse genome (mm10) using STAR (v. 2.5.2b) on 2-pass mode with mouse gencode (release 12) gtf
Genes were subsequently counted using Rsubread and further normalized using limma-voom with quantile normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Genes were subsequently counted using Rsubread and further normalized using limma-voom with quantile normalization and Combat for batch removal.

source_name: cTEC

growth_protocol: samples were isolated by cell sorting from thymus single cell suspensions

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen)
mRNA sequencing libraries were prepared using the SMARTer Ultra Low Input RNA Kit v3 (Clontech) and Nextera XT DNA library preparation kit (Illumina)

tag: genotype

value: FoxN1+ MycTg+

value: Thymus

value: cTEC

value: DAPI- EpCAM+ CD45- Ly51+ UEA-1-

tag: batch


title: Myc.mTEC.2

source_name: mTEC

value: mTEC

tag: sorting profile

value: DAPI- EpCAM+ CD45- Ly51- UEA-1+


title: Myc.mTEC.1

tag: tissue


title: Myc.mTEC.3


title: MCF7-ARID1A_KO_Clone_14_ER_4-hydroxy tamoxifen rep 1

tag: treatment

value: 100 nM 4-hydroxy tamoxifen for 6 hours


title: MCF7-ARID1A_KO_Clone_14_ER_4-hydroxy tamoxifen rep 2


title: Myc.cTEC.2


title: 9M.mTEC.5

value: WT


title: MCF7-ARID1A_KO_Clone_14_ER_Vehicle rep 3

source_name: MCF7-ARID1A KO Clone 14_ER ChIP-seq_Vehicle

value: Vehicle


title: MCF7-ARID1A_KO_Clone_14_ER_Vehicle rep 2


title: MCF7-ARID1A_KO_Clone_14_ER_Vehicle rep 1


title: Myc.cTEC.1


title: MCF7-ARID1A_KO_Clone_11_ER_4-hydroxy tamoxifen rep 3

source_name: MCF7-ARID1A KO Clone 11_ER ChIP-seq_4-hydroxytamoxifen


title: 9M.mTEC.4


title: MCF7-ARID1A_KO_Clone_11_ER_4-hydroxy tamoxifen rep 2


title: 9M.mTEC.1


title: 9M.mTEC.3


title: 9M.mTEC.2


title: MCF7-ARID1A_KO_Clone_11_ER_4-hydroxy tamoxifen rep 1


title: MCF7-ARID1A_KO_Clone_11_ER_Vehicle rep 2

source_name: MCF7-ARID1A KO Clone 11_ER ChIP-seq_Vehicle


title: MCF7-ARID1A_KO_Clone_11_ER_Vehicle rep 1


title: 4W.mTEC.6


title: 4W.mTEC.7


title: 4W.mTEC.8


title: MCF7-parental_ER_4-hydroxy tamoxifen rep 3


title: 4W.mTEC.5


title: MCF7-parental_ER_4-hydroxy tamoxifen rep 2


title: 4W.mTEC.4


title: MCF7-parental_ER_4-hydroxy tamoxifen rep 1


title: 4W.mTEC.2


title: MCF7-parental_ER_Vehicle rep 2

source_name: MCF7-parental_ER ChIP-seq_Vehicle


title: 4W.mTEC.3


title: 4W.mTEC.1


title: MCF7-parental_ER_Vehicle rep 3


title: MCF7-parental_ER_Vehicle rep 1


title: NB.mTEC.4


title: NB.mTEC.3


title: MCF7-SNF5_estrogen rep 2

source_name: SNF5 ChIP-seq Estrogen

value: Charcoal stripped serum for 72 hours, 10 nM B-estradiol for 6 hours

value: Bethyl A301-087A


title: NB.mTEC.2


title: MCF7-SNF5_estrogen rep 3


title: MCF7-ARID1A_KO_Clone_11_ER_Vehicle rep 3


title: MCF7-SNF5_estrogen rep 1


title: MCF7-SNF5_DCDT_Vehicle rep 3

source_name: SNF5 ChIP-seq DCDT Vehicle

value: Charcoal stripped serum for 72 hours - vehicle


title: MCF7-SNF5_DCDT_Vehicle rep 2


title: NB.mTEC.1


title: E17.5.mTEC.3


title: E17.5.mTEC.1


title: MCF7-SNF5_DCDT_Vehicle rep 1


title: E17.5.mTEC.2


title: MCF7-SNF5_JQ1  rep 3

source_name: SNF5 ChIP-seq JQ1

value: 250 nM JQ1 for 6 hours


title: E15.5.mTEC.3


title: MCF7-SNF5_JQ1  rep 2

value: ER+  Breast Cancer Cell Line


title: E15.5.mTEC.1


title: MCF7-SNF5_Fulvestrant  rep 3

source_name: SNF5 ChIP-seq Fulvestrant

value: 10 nM Fulvestrant for 6 hours


title: MCF7-SNF5_JQ1  rep 1


title: MCF7-SNF5_Fulvestrant  rep 2


title: 9M.cTEC.5


title: 9M.cTEC.4


title: MCF7-SNF5_Fulvestrant  rep 1


title: HC2_hi

first: Julia

last: Marschallinger

address: 1201 Welch Road

data_processing:
Sequencing of isolated microglia was carried out with Illumina HiSeq 2000/2500, paired end, 2x 100 bp depth sequencer.
The quality of fastq files was assessed using FASTQC (v 0.11.4).
Reads were mapped to mouse mm9 reference genome using STAR (v 2.5.1b).
Raw read counts were generated with STAR using the GeneCounts function.
Differential expression analysis was performed using DESeq2 with standard settings.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

extract_protocol:
Primary microglia were isolated by gentle dounce homogenization of the brain, Percoll-based myelin removal, and FACS-purification of ~10,000 live CD11b+CD45lo cells. BODIPYlo (=lipid droplet-low) and BODIPYhi (=lipid droplet-high) microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according to the manufacturer’s protocol.
cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina).

tag: age

value: 18 month old

tag: Sex

value: male

value: BODIPY-high microglia (lipid-droplet rich)


title: HC3_lo

value: BODIPY-low microglia (lipid-droplet low)


title: MCF7-SNF5_4-hydroxytamoxifen rep 3

source_name: SNF5 ChIP-seq 4-hydroxy Tamoxifen

tag: cell type

tag: passages


title: 9M.cTEC.2

value: Thymus

value: cTEC


title: HC1_lo

tag: sample type


title: HC2_lo


title: MCF7-SNF5_4-hydroxytamoxifen rep 2


title: MCF7-SNF5_4-hydroxytamoxifen rep 1


title: 4W.cTEC.5

value: DAPI- EpCAM+ CD45- Ly51+ UEA-1-


title: MEF_Igg_Rep2

data_processing:
Library strategy: PIRCh-seq
Raw reads were uniquely mapped to mm9/hg19 using Tophat with default parameter
Samtools and BedTools were used to transform the mapped bam file into bedGraph and bigwig file for visualization on UCSC genome browser. RPKM and raw reads count were calculated by self-designed scripts with ensemble annotation, Homo_sapiens.GRCh37.75.gtf and Mus_musculus.NCBIM37.67.gtf for human and mouse samples respectively. Gene with RPKM >0.1 in input or any PIRCh-seq profiles were defined as expressed and used for downstream analysis
To further investigate the detailed mechanism behind RNA-histone binding, we perform peak calling on PIRCh-seq result. We merged two replicates of each gene to minimize experimental deviation bias, and smoothed the normalized count on each base through a 5 bp width window, along with 2 bp step size. Smoothed signal per window was used for peak calling through home-made code. Significant peak filter was based on fold change of input signal and enrichment P-value. At last, PIRCh-seq peak list was intergraded with RNA structure and modification information for next-step analysis.
Genome_build: mm9/ hg19
Supplementary_files_format_and_content: LncNr2f1_filter.bed

source_name: Mouse Embryonic fibroblasts

value: Mouse Embryonic fibroblasts

tag: antibody

value: Igg control


title: E15.5.mTEC.2

value: WT

value: mTEC

value: DAPI- EpCAM+ CD45- Ly51- UEA-1+


title: NPC_H3K27me3_PIRCh_Rep2

source_name: Mouse Neuronal precursor cells

tag: cell-type

value: Mouse Neuronal precursor cells


title: NPC Lnc-Nr2f1 ChIRP odd

tag: probe

value: Odd


title: 4W.cTEC.4


title: 9M.cTEC.1


title: NPC Lnc-Nr2f1 ChIRP even

value: Even


title: MCF7-SNF5_Vehicle rep 2

source_name: SNF5 ChIP-seq Vehicle

value: ER+  Breast Cancer Cell Line

value: Vehicle

value: Bethyl A301-087A


title: HC3_hi

value: 18 month old

value: male


title: MCF7-SNF5_Vehicle rep 1


title: Chrom-associated RNAs from ovaries of CCR4/+ rep2

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

description:
CCR4_chrom-seq_het_rep2
ccr4_het.chromseq.rep2

data_processing:
Small RNAs: The reads with clipped 3'-adapter were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Chrom-bound RNAs: After removal of Illumina 3’adapter, rRNA reads were filtered out; the remaining reads were mapped on the genome assembly of Drosophila (BDGP assembley R6/dm6) by bowtie 2.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited files include the frequencies of clipped read occurrences in each library.

organism: Drosophila melanogaster

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
small RNAs: Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt); chromatin bound RNA: Nuclear RNA was extractred as descirbed in (Chen et al 2016, PMID: 27292797).
small RNAs: Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012); chromatin bound RNAs: cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Reaction of tagmentation was performed in according to previously published protocol (Picelli et al. 2014) using in-house produced Tn5 charged with oligonucleotides compatible with the Illumina system. Reaction products were cleaned using Clean Mini (Evrogen), PCR amplified and sequenced on the Illumina HiSeq 2500.

tag: genotype/variation

value: twin +/-

value: ovaries

tag: biological replica

tag: technical replica

tag: molecule subtype

value: nuclear RNA


title: NPC Lnc-Nr2f1 ChIRP Input

value: Input


title: 4W.cTEC.3

tag: strain

tag: genotype

value: Thymus

value: cTEC

value: DAPI- EpCAM+ CD45- Ly51+ UEA-1-


title: 4W.cTEC.2

value: WT

tag: sorting profile

tag: batch


title: Chrom-associated RNAs from ovaries of CCR4/CCR4 rep2

description:
CCR4_chrom-seq_homo_rep2
ccr4_homo.chromseq.rep2

tag: tissue


title: HC1_hi

tag: age

value: BODIPY-high microglia (lipid-droplet rich)


title: NPC_H3K27ac_PIRCh_Rep2

value: Mouse Neuronal precursor cells


title: MCF7-BRG1_estrogen rep 3

source_name: BRG1 ChIP-seq Estrogen

tag: cell line

tag: treatment

value: Charcoal stripped serum for 72 hours, 10 nM B-estradiol for 6 hours

tag: chip antibody


title: 9M.cTEC.3

tag: cell type


title: MEF_Igg_Rep1

value: Mouse Embryonic fibroblasts

tag: antibody

value: Igg control


title: MCF7-BRG1_estrogen rep 2

value: ER+  Breast Cancer Cell Line

tag: passages


title: Chrom-associated RNAs from ovaries of CCR4/+ rep1

description:
CCR4_chrom-seq_het_rep1
ccr4_het.chromseq


title: NB.cTEC.3


title: NPC_H3K27ac_PIRCh_Rep1

tag: cell-type


title: MCF7-SNF5_Vehicle rep 3

value: Vehicle

value: Bethyl A301-087A


title: MCF7-BRG1_estrogen rep 1


title: NB.cTEC.2


title: NPC_H3K27me3_PIRCh_Rep1


title: NB.cTEC.1


title: MCF7-BRG1_DCDT_Vehicle rep 2

source_name: BRG1 ChIP-seq DCDT Vehicle

value: Charcoal stripped serum for 72 hours - vehicle


title: 604_50: TAM-NeuT

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on May 2015
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DeSeq2 normalized counts for each Sample.

source_name: Mammary Gland

growth_protocol: The generation and characterization of K14cre;Cdh1F/F;Trp53F/F mice have been previously described in detail. The mice were backcrossed onto the FVB/N background  and genotype was confirmed by PCR. MMTV-NeuT mice on a Balb/c background were purchased from Charles River Laboratories  and were bred in house. Female K14cre;Cdh1F/F;Trp53F/F and MMTV-NeuT mice were monitored twice every week for the onset of mammary tumor formation by caliper and palpation measurement starting at 2 or 4 months of age, respectively. Mice were kept in open cages with food and water provided ad libitum at a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted using the RNeasy Mini and Micro Kits (Qiagen)
Ovation RNA-Seq system V2 and Encore Rapid library systems protocols (NuGEN)
50 bp single-end run was performed on a HiSeq1500

treatment_protocol: Mammary glands or mammary tumors (size±225mm2), spleen and bone marrow were harvested from 4 month old K14cre;Cdh1F/F;Trp53F/F female mice containing early lesions, 8 months old tumor-bearing K14cre;Cdh1F/F;Trp53F/F, 4 month old tumor-bearing MMTV-NeuT female mice and age- and sex-matched FVB/N and Balb/c mice. Tumors and mammary glands were mechanically chopped with a McIlwain Tissue Chopper (Ted Pella, Inc, CA, USA) and were enzymatically digested for 1 hour at 37°C with 3 mg/ml collagenase type A (Roche) and 1.5 mg/ml porcine pancreatic trypsin (BD Biosciences) in serum-free DMEM medium. Digestion was stopped by the addition of DMEM supplemented with 8% FBS and the suspension was disaggregated through a 70 μm cell strainer. Spleens and bone marrow cells from tibiae and femora were harvested and disaggregated through a 70 μm cell strainer. Splenic suspensions were subsequently treated twice with NH4Cl erythrocyte lysis buffer for 3 min at room temperature. All single-cell suspensions were stained for 20 min at 4°C in the dark with anti-mouse F4/80 (1:200; BM8; eBioscience) and anti-mouse CD11b (1:200; M1/70; eBioscience) in IMDM supplemented with 2% FBS, 0.5% beta-mercaptoethanol, 0.5mM EDTA, Pen/Strep. Cells were then washed and incubated with magnetic anti-APC MicroBeads (Miltenyi Biotec) following the manufacturer’s guidelines. Isolation of F4/80+ cells from the CD11b+-enriched fraction was performed on a BD FACS ARIA II sorter with Diva software (BD Biosciences).

tag: strain background

value: Balb/c

value: TUM

value: Mammary Gland


title: NPC_H3K4me3_PIRCh_Rep1


title: 605_50: TAM-NeuT


title: 603_50: TAM-NeuT


title: E17.5.cTEC.3

source_name: cTEC


title: Chrom-associated RNAs from ovaries of CCR4/CCR4 rep1

description:
CCR4_chrom-seq_homo_rep1
ccr4_homo.chromseq

tag: genotype/variation

value: ovaries

tag: biological replica

value: nuclear RNA


title: MEF_H4K16ac_PIRCh_Rep2


title: MCF7-BRG1_DCDT_Vehicle rep 1


title: 601_50: TUM-SPL-NeuT

source_name: Spleen

value: Spleen


title: NPC_Input_Rep1

value: Input


title: MCF7-BRG1_JQ1  rep 3

source_name: BRG1 ChIP-seq JQ1

value: 250 nM JQ1 for 6 hours


title: 4W.cTEC.1

value: WT

value: Thymus

value: cTEC

value: DAPI- EpCAM+ CD45- Ly51+ UEA-1-


title: E17.5.cTEC.1


title: E17.5.cTEC.2


title: MCF7-BRG1_JQ1  rep 2


title: NPC_H3K4me3_PIRCh_Rep2

value: Mouse Neuronal precursor cells


title: E15.5.cTEC.3


title: MCF7-BRG1_JQ1  rep 1

value: ER+  Breast Cancer Cell Line


title: E15.5.cTEC.2


title: MCF7-BRG1_DCDT_Vehicle rep 3


title: NPC_Input_Rep2


title: MCF7-BRG1_Fulvestrant  rep 3

source_name: BRG1 ChIP-seq Fulvestrant

value: 10 nM Fulvestrant for 6 hours


title: MEF_H3K9me3_PIRCh_Rep2

value: Mouse Embryonic fibroblasts


title: MEF_H4K16ac_PIRCh_Rep1


title: MEF_H3K9me3_PIRCh_Rep1


title: 600_50: TUM-SPL-NeuT


title: 599_50: TUM-BM-NeuT

source_name: Bone Marrow

value: Bone Marrow


title: E15.5.cTEC.1


title: 596_50: WT-MG-NeuT

value: Balb/c


title: E13.5.TEC.3

source_name: TEC

value: TEC

value: DAPI- EpCAM+ CD45-


title: 598_50: TUM-BM-NeuT

value: TUM


title: 597_50: TUM-BM-NeuT


title: MEF_H3K27me3_PIRCh_Rep2


title: MCF7-BRG1_Fulvestrant  rep 1


title: MEF_H3K27me3_PIRCh_Rep1


title: MCF7-BRG1_Fulvestrant  rep 2


title: E13.5.TEC.2


title: MEF_H3K27ac_PIRCh_Rep2


title: E13.5.TEC.1


title: MEF_H3K27ac_PIRCh_Rep1


title: 594_50: WT-MG-NeuT

value: Mammary Gland


title: MCF7-BRG1_4-hydroxytamoxifen rep 2

source_name: BRG1 ChIP-seq 4-hydroxy Tamoxifen

value: 100 nM 4-hydroxy tamoxifen for 6 hours


title: 593_50: WT-SPL-NeuT

value: Spleen


title: Unbound Fraction vGluT2 #3 (Batch 2)

city: Tübingen

first: Vikas

last: Bansal

state: BW

address: Otfried Müller Strasse 23

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

description:
Second batch (rRNA reads filtered out)
Unbound_VU14

data_processing:
Basecalls performed using CASAVA version 1.8.2
Ribosomal RNA reads were first removed from FASTQ files using BBDuk with "maxcalledquality=96 mincalledquality=-5 qin=33 qout=33 ignorebadquality ref=rRNA.mmu.fa k=25 mink=25 hdist=1 statscolumns=5 maxns=0" and cleaned RNA-seq reads were aligned to the mouse reference genome (mm10) with Bowtie2 (v2.0.2) using RSEM (v1.2.29) with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: The mouse reference genome was indexed using the Ensembl annotations (v84) with rsem-prepare-reference from RSEM software. Next, rsem-calculate-expression was used to align the reads and quantify the gene abundance. The raw count from rsem-calculate-expression is used.

source_name: Unbound Fraction vGluT2 #3

extract_protocol:
Mix post nuclear supernatant with Trizol. Biotinylating RNA and capture of biotinylated RNA with Streptavidin C1 Dynabeads
4-TU labeled RNA-seq libraries were prepared using the ScriptSeq RNA-Seq Library Preparation Kit (Illumina # SSV21124) following the manufacturer protocol. In brief, rRNA depleted RNA was fragmented and cDNA was synthesized. 3' end was tagged, cDNA was purified, indexes was added and samples were amplified. The final product was again purified with Agencourt AMPure XP (Beckman Coulter, #A63881) and libraries were validated using High sensitivity DNA bioanalyzer (Agilent).

tag: condition

value: vGluT2 UB

value: Whole brain

tag: molecule subtype

value: Cytoplasmic RNA


title: MEF_H3K4me3_PIRCh_Rep2


title: 592_50: WT-SPL-NeuT

tag: genotype

value: WT


title: MEF_H3K4me3_PIRCh_Rep1


title: Unbound Fraction vGluT2 #1 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Unbound_VU11

source_name: Unbound Fraction vGluT2 #1


title: Unbound Fraction vGluT2 #2 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Unbound_VU13

source_name: Unbound Fraction vGluT2 #2


title: MCF7-BRG1_Vehicle rep 3

source_name: BRG1 ChIP-seq Vehicle

value: Vehicle


title: 591_50: WT-SPL-NeuT


title: MEF_H3K4me1_PIRCh_Rep2

source_name: Mouse Embryonic fibroblasts


title: MCF7-BRG1_Vehicle rep 2


title: Unbound Fraction Gad2 #3 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Unbound_GU17

source_name: Unbound Fraction Gad2 #3

value: Gad2 UB


title: 595_50: WT-MG-NeuT


title: 589_50: WT-BM-NeuT


title: MCF7-BRG1_Vehicle rep 1

value: ER+  Breast Cancer Cell Line


title: MEF_H3_PIRCh_Rep2


title: MEF_H3K4me1_PIRCh_Rep1


title: MCF7-BRG1_4-hydroxytamoxifen rep 3


title: Unbound Fraction Gad2 #2 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Unbound_GU16

source_name: Unbound Fraction Gad2 #2


title: 588_50: WT-BM-NeuT


title: MCF7-ARID1A_estrogen rep 1 Input

source_name: ARID1A ChIP-seq Estrogen Input

value: Charcoal stripped serum for 72 hours, 10 nM B-estradiol for 6 hours


title: 391_50: TAM-KEP

value: FVB


title: Affinity Purified vGluT2 #3 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Glut_TUVA14

source_name: Affinity Purified vGluT2 #3

value: TU-Tag

value: vGluT2 AP

value: Affinity-purified metabolically labeled RNA


title: MCF7-ARID1A_estrogen rep 2 Input


title: MEF_H3_PIRCh_Rep1

value: Mouse Embryonic fibroblasts


title: MEF_Input_Rep2

value: Input


title: MCF7-ARID1A_DCDT_Vehicle rep 2 Input

source_name: ARID1A ChIP-seq DCDT Vehicle Input

value: Charcoal stripped serum for 72 hours - vehicle


title: MCF7-BRG1_4-hydroxytamoxifen rep 1

value: 100 nM 4-hydroxy tamoxifen for 6 hours


title: Affinity Purified vGluT2 #2 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Glut_TUVA13

source_name: Affinity Purified vGluT2 #2


title: 390_50: TAM-KEP

source_name: Mammary Gland

value: TUM

value: Mammary Gland


title: MEF_Input_Rep1


title: MCF7-ARID1A_DCDT_Vehicle rep 1 Input


title: 590_50: WT-BM-NeuT

value: Balb/c

value: Bone Marrow


title: V6.5_H4K16ac_PIRCh_Rep2

source_name: Mouse Embryonic stem cells

value: Mouse Embryonic stem cells


title: MCF7-ARID1A_JQ1  rep 2 Input

source_name: ARID1A ChIP-seq JQ1 Input

value: 250 nM JQ1 for 6 hours


title: 389_50: TAM-KEP


title: Affinity Purified vGluT2 #1 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Glut_TUVA11

source_name: Affinity Purified vGluT2 #1

value: Whole brain


title: Affinity Purified Gad2 #3 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Gad2_TUGA17

source_name: Affinity Purified Gad2 #3

value: Gad2 AP


title: 388_50: TUM-SPL-KEP

source_name: Spleen

value: Spleen


title: Unbound Fraction Gad2 #1 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Unbound_GU15

source_name: Unbound Fraction Gad2 #1

value: Gad2 UB

value: Cytoplasmic RNA


title: MCF7-ARID1A_JQ1  rep 1 Input

value: ER+  Breast Cancer Cell Line


title: MCF7-ARID1A_Fulvestrant  rep 2 Input

source_name: ARID1A ChIP-seq Fulvestrant Input

value: 10 nM Fulvestrant for 6 hours


title: Affinity Purified Gad2 #1 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Gad2_TUGA15

source_name: Affinity Purified Gad2 #1

value: TU-Tag

value: Affinity-purified metabolically labeled RNA


title: Affinity Purified Gad2 #2 (Batch 2)

description:
Second batch (rRNA reads filtered out)
Gad2_TUGA16

source_name: Affinity Purified Gad2 #2


title: 386_50: TUM-SPL-KEP

value: FVB


title: MCF7-ARID1A_Fulvestrant  rep 1 Input


title: 387_50: TUM-SPL-KEP


title: Unbound Fraction vGluT2 #2 (Batch 1)

description:
First batch (rRNA reads filtered out)
Unbound_VU2

source_name: Unbound Fraction vGluT2 #2

value: vGluT2 UB


title: MCF7-ARID1A_4-hydroxytamoxifen rep 2 Input

source_name: ARID1A ChIP-seq 4-hydroxy Tamoxifen Input

value: 100 nM 4-hydroxy tamoxifen for 6 hours


title: Unbound Fraction vGluT2 #1 (Batch 1)

description:
First batch (rRNA reads filtered out)
Unbound_VU1

source_name: Unbound Fraction vGluT2 #1


title: 384_50: TUM-BM-KEP

source_name: Bone Marrow

value: TUM


title: V6.5_H4K16ac_PIRCh_Rep1


title: V6.5_H3K9me3_PIRCh_Rep2


title: 383_50: TUM-BM-KEP


title: V6.5_H3K9me3_PIRCh_Rep1


title: V6.5_H3K27me3_PIRCh_Rep1


title: MCF7-ARID1A_4-hydroxytamoxifen rep 1_Input

source_name: ARID1A ChIP-seq 4-hydroxy Tamoxifen_Input


title: MCF7-ARID1A_Vehicle rep 2_Input

source_name: ARID1A ChIP-seq Vehicle_Input

value: Vehicle


title: V6.5_H3K27ac_PIRCh_Rep1


title: MCF7-ARID1A_Vehicle rep 1_Input


title: Affinity Purified vGluT2 #2 (Batch 1)

description:
First batch (rRNA reads filtered out)
Glut_TUVA2

source_name: Affinity Purified vGluT2 #2

value: vGluT2 AP


title: Unbound Fraction Gad2 #1 (Batch 1)

description:
First batch (rRNA reads filtered out)
Unbound_GU1


title: MCF7-ARID1A_estrogen rep 3

source_name: ARID1A ChIP-seq Estrogen

value: Charcoal stripped serum for 72 hours, 10 nM B-estradiol for 6 hours

value: ARID1A HPA005456


title: 381_50: PRE-MG-KEP

source_name: Mammary Gland

value: PRE

value: Mammary Gland


title: V6.5_H3K4me3_PIRCh_Rep2

source_name: Mouse Embryonic stem cells

value: Mouse Embryonic stem cells


title: Unbound Fraction Gad2 #2 (Batch 1)

description:
First batch (rRNA reads filtered out)
Unbound_GU2

source_name: Unbound Fraction Gad2 #2

value: Gad2 UB

value: Whole brain


title: V6.5_H3K27ac_PIRCh_Rep2


title: V6.5_H3K27me3_PIRCh_Rep2


title: V6.5_H3K4me3_PIRCh_Rep1


title: MCF7-ARID1A_estrogen rep 2

value: ER+  Breast Cancer Cell Line


title: 382_50: PRE-MG-KEP


title: Affinity Purified Gad2 #2 (Batch 1)

description:
First batch (rRNA reads filtered out)
Gad2_TUGA2

value: Gad2 AP


title: 385_50: TUM-BM-KEP

value: Bone Marrow


title: 379_50: PRE-SPL-KEP

value: Spleen


title: MCF7-ARID1A_estrogen rep 1


title: 378_50: PRE-SPL-KEP

value: FVB


title: Affinity Purified Gad2 #1 (Batch 1)

description:
First batch (rRNA reads filtered out)
Gad2_TUGA1

value: TU-Tag

value: Affinity-purified metabolically labeled RNA


title: V6.5_H3K4me1_PIRCh_Rep1


title: V6.5_H3K4me1_PIRCh_Rep2


title: 377_50: PRE-SPL-KEP


title: PV_total_I4

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the mouse reference genome (mm10) with Bowtie2 (v2.0.2) using RSEM (v1.2.29) with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: The mouse reference genome was indexed using the Ensembl annotations (v84) with rsem-prepare-reference from RSEM software. Next, rsem-calculate-expression was used to align the reads and quantify the gene abundance. The raw count from rsem-calculate-expression is used.

extract_protocol:
Centrifuge the brain tissue sample to prepare supernatant and mix with Qiazol aliquot. This is total RNA sample usied for immunoprecipitation.
Ribosome-associated mRNA libraries were prepared using TruSeq® Stranded Total RNA Library Prep (Illumina # RS-122-2201) following the manufacturer protocol. In brief, 0.5ug of total RNA was treated with Ribo-zero rRNA removal and cleaned with RNACleanXP. Both cDNA strands were synthesized, Adenylation of 3' end was done and indexing adapters were ligated. Libraries were amplified and the final product was purified using Agencourt AMPure XP (Beckman Coulter, #A63881). Libraries were validated using High sensitivity DNA bioanalyzer (Agilent).

value: PV Input RNA

value: Cytoplasmic RNA


title: Affinity Purified vGluT2 #1 (Batch 1)

description:
First batch (rRNA reads filtered out)
Glut_TUVA1

source_name: Affinity Purified vGluT2 #1

value: vGluT2 AP


title: PV_total_I2


title: PV_total_I3


title: V6.5_H3_PIRCh_Rep2


title: 380_50: PRE-MG-KEP


title: PV_total_I1


title: MCF7-ARID1A_JQ1  rep 2

source_name: ARID1A ChIP-seq JQ1

value: 250 nM JQ1 for 6 hours


title: MCF7-ARID1A_JQ1  rep 3

value: ARID1A HPA005456


title: V6.5_H3_PIRCh_Rep1


title: 374_50: PRE-BM-KEP

value: PRE


title: MCF7-ARID1A_DCDT_Vehicle rep 1

source_name: ARID1A ChIP-seq DCDT Vehicle

value: Charcoal stripped serum for 72 hours - vehicle


title: V6.5_Input_Rep2

value: Mouse Embryonic stem cells

value: Input


title: 359_50: WT-MG-KEP

value: WT

value: Mammary Gland


title: MCF7-ARID1A_DCDT_Vehicle rep 2

value: ER+  Breast Cancer Cell Line


title: WT_ventricle tissue_rep1

first: Long-Sheng

last: Song

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

data_processing:
Raw files were uploaded into Illumina's BaseSpace hub (basespace.illumina.com) and aligned to mus musculus mm10 genome using the TopHat Alignment Version 1.0.0 App and selecting "Trim TruSeq Adapters" option.
Transcripts were assembled and differential expression was determined using the BaseSpace Cufflinks Assembly and DE Version 1.1.0 App selecting mm10 reference genome and "Stranded" polyA enriched sequences.
FPKM tables and CuffDiff results of differential gene expression of were downloaded and significantly expressed genes (FDR<0.05, FPKM>5) were used for analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files contain FPKM values for each sample and summary differential gene expression data.

source_name: WT_ventricle tissue

extract_protocol:
Ventricles were removed, flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent.
polyA RNA was enriched and TruSeq RNA stranded libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: post natal day 21

value: Ventricle Tissue


title: 376_50: PRE-BM-KEP

value: FVB

value: Bone Marrow


title: 375_50: PRE-BM-KEP


title: WT_total_F4

value: WT Input RNA

value: Whole brain


title: WT_total_F5

value: Cytoplasmic RNA


title: MCF7-ARID1A_JQ1  rep 1


title: 358_50: WT-MG-KEP


title: WT_ventricle tissue_rep2


title: WT_total_F3


title: MCF7-ARID1A_Fulvestrant  rep 3

source_name: ARID1A ChIP-seq Fulvestrant

value: 10 nM Fulvestrant for 6 hours


title: Cdk8Tg_ventricle tissue_rep2

source_name: Cdk8Tg_ventricle tissue

value: Cdk8Tg;  cardiac specific Cdk8 overexpressing


title: 357_50: WT-MG-KEP


title: MCF7-ARID1A_Fulvestrant  rep 2

value: ARID1A HPA005456


title: V6.5_Input_Rep1


title: WT_total_F1


title: 356_50: WT-SPL-KEP

source_name: Spleen

value: Spleen


title: Cdk8Tg_ventricle tissue_rep1


title: MCF7-ARID1A_Fulvestrant  rep 1


title: vGlut_total_E5

value: vGluT2 Input RNA


title: MCF7-ARID1A_4-hydroxytamoxifen rep 3

source_name: ARID1A ChIP-seq 4-hydroxy Tamoxifen

value: 100 nM 4-hydroxy tamoxifen for 6 hours


title: 354_50: WT-SPL-KEP


title: MCF7-ARID1A_4-hydroxytamoxifen rep 2


title: vGlut_total_E2


title: vGlut_total_E1


title: vGlut_total_E3


title: MCF7-ARID1A_4-hydroxytamoxifen rep 1


title: 352_50: WT-BM-KEP


title: 353_50: WT-BM-KEP


title: 351_50: WT-BM-KEP


title: Input DNA

data_processing:
Raw sequences reads were pre-processed using TrimGalore and aligned to the mm10 mouse reference genome with Bowtie with at most 2 mismathes. Reads that appeared more than twice at the same position on the same strand were discarded to remove PCR duplication.
BigWig files were generated from the coverage for visualization purposes.
Gzip compressed Fastq files were split into multiple files if more than 1.25GB in size to aid customer downloading.
ChIP-seq peaks were dertermined using EaSeq software v1.05 (easeq.net; Lerdrup M, et al. Nat Struct Mol Biol. 2016;23:349–357) using default settings with minor modification. Peaks were identified using adaptive local thresholding with the most abundant DNA-fragment size determined according to the Phantom Peak Coefficient method.
Thresholds from the input control was scaled according with the NCIS normalization factor to define border regions. Shoulders were excluded at values below µ + 2SD.
After border refinement and peak-merging, peaks were positively selected for a FDR value of 1E-05 or better and minimum a NCIS normalized log2 fold difference of two.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for peak visualization in a genomic browser

source_name: cardiac tissue

growth_protocol: Med1 fl/fl mice backrossed into C57Bl6 were crossed with Med1 fl/+ mice expressing Cre from the Myh6 promoter to generate cardiac specific Med1 KO mice and control littermates

extract_protocol:
Hearts from euthanized three-week-old male mice were rapidly harvested, rinsed in cold phosphate buffered saline, and snap frozen in liquid nitrogen. Genomic DNA was extracted from frozen tissue using the Zymo-Spin ChIP Kit according to manufacturer's directions.
Chromatin was immunoprecipitated in triplicate using antibodies against RNA Pol-II (Bethyl Laboratories #9201012), H3K27ac (Abcam #ab4729), H3K27me3 (Abcam #ab6002), and normal mouse IgG (Diagenode #C15410206 and Millipore #12-371B).
Libraries were prepared from pooled ChIP DNA and constructed by Zymo Research using EpiQuest services and proprietary methods.

value: cardiac tissue

value: input

tag: strain

value: mixed

tag: gender

value: male


title: vGlut_rpl22_D5

value: vGluT2 RiboTag IP

value: RiboTag

tag: tissue


title: vGlut_total_E4


title: MCF7-ARID1A_Vehicle rep 1

source_name: ARID1A ChIP-seq Vehicle

extract_protocol:
Nuclear lysates were prepared and antibody-bound chromatin was purified using appropriate antibodies. Antibodies used: ARID1A HPA005456, BRG1 ab215998, SNF5 Bethyl A301-087A, ERα ab3575 and Merck Millipore 06-935 antibody mix, H3K27ac Diagenode C15410196 Premium, HDAC1 Diagenode Premium C15410325, ARID2 Bethyl A302-229A, BRD4 from Cheng Ming Chiang's lab.
DNA was prepared for Illumina sequencing on the HiSeq 4000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

tag: cell line

value: ER+  Breast Cancer Cell Line

value: Vehicle


title: Med1 cKO K27me3 ChIP

value: tri-metylated H3K27

value: post natal day 21

value: Med1 cKO


title: MCF7-ARID1A_Vehicle rep 2

tag: treatment


title: vGlut_rpl22_D4

value: Whole brain


title: vGlut_rpl22_D3


title: MCF7 Cas9 Fulvestrant rep 2

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3246_MCF7_None_ICI_B_CRI01_1

data_processing:
library strategy: CRISPR gRNA-seq
Short reads were depleted from low-quality sequences and aligned to human gRNA sequence library (GRC_h37) using BLAT v. 34
Exact-matching reads were counted and treated as a measurement of gRNA abundance.
MAGecK was performed to rank the genes and DESeq2 was used to get log2 fold changes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files with counts for each sample.

source_name: MCF7 Cas9 Fulvestrant gRNA-seq

growth_protocol: MCF7-Cas9 expressing cells were grown in DMEM High glucose media with 2 mM Glutamine, 10% FBS, Sodium pyruvate with blasticidin.

extract_protocol:
Qiagen Blood and Cell culture Maxi kit was used to extract genomic DNA. Viral vector covering DNA were amplified with Illumina adapters containing primers.
Viral vector covering DNA were amplified with Illumina adapters containing primers. Libraries were made using Illumina Truseq HT and Thruplex dual indices.

treatment_protocol: Cells were infected with pooled gRNA libraries for 9 days and treated with drugs for 26 days.

value: MCF7 Cas9 expressing cells

tag: time point

value: Fulvestrant treated for 26 days after 9 days of infection


title: MCF7_None_CRISPR_lib_plasmid library_rep1

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3247_MCF7_None_CRISPR_lib_CRI01_1

source_name: Plasmid library gRNA-seq

tag: cell type

value: Pooled gRNA library without infecting cells


title: vGlut_rpl22_D2


title: vGlut_rpl22_D1


title: MCF7 Cas9 Fulvestrant rep 1

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3245_MCF7_None_ICI_A_CRI01_1


title: Bone Marrow proB and preB cells from WT mouse, biological replicate 3

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from WT bone marrow proB and preB cells.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

label: biotin

source_name: WT 22

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion).

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens. All the animals are females.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were given a cocktail of antibiotics (ampicillin, 1 g/L, Ratiopharm; vancomycin, 500 mg/L, Cell Pharm; ciprofloxacin, 200 mg/L, Bayer Vital; imipenem, 250 mg/L, MSD; metronidazole, 1 g/L, Fresenius) added to the drinking water ad libitum for a period of eight weeks.

value: WT

tag: Sex

value: Female

value: Bone marrow proB and preB


title: PV_rpl22_G4

value: PV RiboTag IP


title: Bone Marrow proB and preB cells from WT mouse, biological replicate 1

source_name: WT 20


title: Med1 cKO Pol-II ChIP

value: cardiac tissue

tag: antibody

value: RNA Pol-II


title: Med1 cKO K27ac ChIP

value: acetylated H3K27

value: male