title: dE4 J2 RIP 1

city: Philadelphia

first: Matthew

middle: Darrell

last: Weitzman

address: 4050 CTRB, 3501 Civic Center Blvd

department: Pathology & Laboratory Medicine

institute: Children's Hospital of Philadelphia

description: dE4 J2 RIP 1

data_processing:
Illumina basecall (BCL) files were demultiplexed to bam files with unique molecular identifiers (UMIs) using Picard Tools (version 2.25.1-1). Then, raw reads were extracted from the bam files to store in the fastq formatted files.
Then the reads were mapped to the hg38 genome assembly and the Ad5 genome using STAR (version 2.7.6a).
The alignment files were merged with bam files from the BCL to get UMI information.
Uniquely mapped reads were de-duplicated using umi_tools (version 1.0.1. Reads count on each gene was calculated at the same time of STAR mapping with the parameter --quantMode GeneCounts.
Splicing junction reads were extracted and annotated the from the above results using RegTools (version 0.5.2). The read counts were normalized to the total number of unique mapped de-duplicated reads per library.
Genome_build: hg18, Ad5
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage from deeptools 3.5.1;  Scores represent normalized read counts, counts per million (CPM)

source_name: J2-Enriched dsRNA

growth_protocol: A549 cells were grown in F12K media dupplemented with 10% FBS

extract_protocol:
Total RNA was harvested from WT Ad5 or E4-infected cells 48 hpi by TRIzol extraction. RNA was diluted to 500 ng/L in NET2 Buffer (50 mM Tris HCl pH 7.6, 150 mM NaCl, 3 mM MgCl2) and divided into immunoprecipitated fractions (IP, 50 g RNA) or 1% input RNA (0.5 g RNA). IP samples were treated with 2 Units of diluted single-strand specific RNase I (Thermo AM2294, 100 U/L) and 2 L TURBO DNase (Thermo AM2238) at 37 °C for ten minutes before the addition of 10 L SuperAse RNase inhibitor (Thermo AM2696) and placement on ice. 5 g J2 anti-dsRNA antibody (Scicons) was added to IP fraction to a final volume of 200 L and incubated overnight at 4 °C with end over end rotation. Protein G Dynabeads (Thermo 10004D) were washed twice with NET2 before being blocked with 1 mg/mL BSA and 10 g/mL linear acrylamide (Thermo AM9520) for thirty minutes. Blocked beads were added to J2/RNA mixture and allowed to continue rotating for an additional two hours. RNA-bound beads were subsequently washed using ice-cold NET2 buffer thrice for five minutes each before RNA was extracted using TRIzol LS (Thermo 10296010). Aqueous-phase TRIzol was subsequently extracted using RNA Clean and Concentrator (Zymo Research R1015) and eluted into 11 L elution buffer.
Input or dsRNA-enriched RNA from above was converted into Illumina sequencing libraries using the NEBNext Ultra II Directional RNA library kit (NEB E7760S) following manufacturers instructions with the following modifications. Ribosomal RNA was depleted using NEBNext rRNA depletion kit v2 (NEB E7405S). Input RNA was chemically fractionated for 15 minutes, while dsRNA IP RNA was fractionated for 7 minutes as directed for partially degraded RNA due to prior RNase I digestion. IDT xGen UDI-UMI Adapters 1-8 (Integrated DNA Technologies 10006913) were ligated to resulting cDNA after second-strand synthesis and end-prepping. All library purification steps used NEBNext RNA Sample Purification Beads (Beckman Coulter Agencourt RNAClean XP) or SPRISelect (Beckman Coulter B23317). After initial library quantification via qPCR, final libraries were amplified using xGen Library Amplification Primer Mix (Integrated DNA Technologies 1076775) and NEBNext Ultra II Q5 master mix for 4 cycles (input libraries) or 10 cycles (IP libraries). Libraries were quantified using Thermo Qubit fluorometric quantification, Agilent Bioanalyzer DNA Chip, and qPCR quantification relative to a standard curve. Eight total libraries were pooled in equimolar ratios and loaded onto an Illumina NextSeq 500 High Output flow cell (Illumina FC-404-2005) and ran for 150 cycles in single end mode.

treatment_protocol: A549 cells were infected with wildtype Ad5 or Ad5dE4 (dl1004) at a MOI of 10 for 48 hours

tag: virus infection

tag: rna type

value: dsRNA-enriched


title: dE4 J2 RIP 2

status: Public on Jul 15 2021

type: SRA

state: PA

country: USA

description: dE4 J2 RIP 2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: WT J2 RIP 2

description: WT J2 RIP 2

value: WT Ad5


title: WT J2 RIP 1

description: WT J2 RIP 1


title: dE4 Input 2

description: dE4 Input 2

source_name: Total RNA

value: Input


title: Barcoded, pooled single B cells [J_9]

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

data_processing:
mRNA sequencing data was demultiplexed into individual FASTQ files followed by alignment to the human reference genome hg38 using STAR (version 2.5.2).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Endometrial Cancer

extract_protocol:
Tumours were cut into ca. 1cm3, enzymatically digested in RPMI medium (Gibco, Paisley, UK) with 1 mg/µL collagenase type IV (Gibco Life Technologies, Grand Island, USA) and 12,6 µg/mL recombinant human DNase (Pulmozyme, Roche, Woerden, the Netherlands) for 30 minutes at 37 °C or overnight at room temperature. Digests were filtered using 70 µm cell strainers (Falcon) and enriched for peripheral blood mononuclear cells (PBMCs) using Ficoll-Paque PLUS (GE Healthcare Life Sciences, Marlborough, MA, USA). Cells were stored in liquid nitrogen until cell sorting. For cell sorting, tumour digests were thawed and washed with PBS and incubated with Zombie Aqua (1:100, Biolegend, San Diego, USA) for 15 minutes at room temperature. Samples were washed and stained with anti-CD27 APC-efluor 780 (clone O323; 47-0279-42; eBioscience) and either CD19-PE (clone HIB19; 12-0199-41; eBioscience), CD19-BV421 (clone HIB19; 562440; BD Biosciences), CD19-APC (clone HIB19; 17-0199-41; eBioscience) or CD19-PE-cy7 (clone HIB19; 25-0199-41; eBioscience) for 45 minutes at 4°C. Cells were washed and filtered using a 35 µm strainer (Falcon). Patient samples were pooled to minimize differences due to plate effects and sorted on a Beckman Coulter MoFlo Astrios. Each well contained 2 µl lysis buffer (0,2% Triton X-100 (Sigma-Aldrich) and 2U RNase inhibitor (Takara)) with 1 µl 10 µM oligo-dT primer and 1 µl 10 mM dNTP mix (Thermo Scientific). After sorting, the plate was spun down and incubated at 72°C for 3 minutes.
SmartScribe reverse transcriptase (Westburg-Clontech) and a template switching oligo (BC-TSO) were used to generate cDNA. Next, an exonuclease step was performed using 1:400 dilution of Exonuclease I.  A PCR preamplification step was done with KAPA HiFi HotStart Ready Mix (Roche Diagnostics, 23 cycles in experiment 1 and 25 cycles in experiment 2) and a custom-made PCR primer. The cDNA samples were purified using Ampure XP beads (Beckman Coulter) in a ratio of 0,8:1 (Ampure bead : cDNA). Samples were analysed on a 2100 Bioanalyzer using a PerkinElmer LabChip GX high-sensitivity DNA chip (Agilent) and on a Qubit™ 4 Fluorometer (ThermoFisher Scientific) according to manufacturer's instructions. 500 pg of each sample was tagmented and N7xx and S5xx index adapters were used for barcoding according to the Illumina Nextera XT DNA sample preparation kit (Illumina). Thereafter, samples were purified with Ampure XP beads (ratio 0,6 Ampure : 1 cDNA) and analysed on a 2100 Bioanalyzer. Samples were equimolar pooled (4 nM) and samples were sequenced on an Illumina Nextseq500 2500 using 75 bp paired end reads.
Modified SMARTseq2

tag: patient

tag: cell type

value: B cells

tag: disease

value: Endometrial Cancer


title: Barcoded, pooled single B cells [J_14]


title: Barcoded, pooled single B cells [J_10]


title: Barcoded, pooled single B cells [J_5]


title: dE4 Input 1

description: dE4 Input 1


title: WT Input 2

description: WT Input 2


title: RNA-seq_batch2_MT2_rep1

city: Charlottesville

first: Bi

last: Shi

state: Virginia

address: 1340 JPA Pinn Hall Room 6017

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
RNA-seq reads were aligned to the human genome assembly GRCH38/hg38 or mouse genome assembly GRCm38/mm10 using STAR. RNA-seq counts were annotated using RSEM. Differentially expressed genes were calculated using DESeq2.
ChIP-seq and PRO-seq sequence reads were aligned to the human genome assembly GRCH38/hg38 using BWA. Sam files were converted into bam files using Samtools. MACS2 was used to call peaks under the FDR threshold of 0.01.
H3K4me3/H3K27ac HiChIP data were performed with MAPS.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Peak file, loop bedpe or gene count

source_name: THP-1 cells

growth_protocol: For THP-1 cell transduction, 1 × 106 THP-1 cells were transduced with 500 μl of 30-fold concentrated lentivirus through spin-inoculation at 25°C at 2200 rpm for 2 hours each for 3 times with 24 hours interval, and were cultured with 500 μg/ml of G418 (Invivogen) for selection for 12-14 days.

extract_protocol:
For Chip-seq, genomic DNA were pulled down by antibodies. For RNA-seq, RNA was extracted with Qiagen miRNA-ease RNA extraction kit. HICHIP DNA was collected with Arima HICHIP kit.
For ChIP-seq and HICHIP, library preparation using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. For RNA-seq, NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina was used for library prepapration.
Library quality was assessed by Tapstation and Qubit concentration measurement.

treatment_protocol: Media with 100 ng/ml of doxycycline was added

value: Cultured THP-1 cells


title: RNA-seq_batch2_MT2_rep2


title: RNA-seq_batch2_WT_rep2


title: RNA-seq_batch2_Vector_rep2


title: HiChIP_H3K27ac_eIFIDR

library_source: genomic

data_processing:
library strategy: HiChIP
RNA-seq reads were aligned to the human genome assembly GRCH38/hg38 or mouse genome assembly GRCm38/mm10 using STAR. RNA-seq counts were annotated using RSEM. Differentially expressed genes were calculated using DESeq2.
ChIP-seq and PRO-seq sequence reads were aligned to the human genome assembly GRCH38/hg38 using BWA. Sam files were converted into bam files using Samtools. MACS2 was used to call peaks under the FDR threshold of 0.01.
H3K4me3/H3K27ac HiChIP data were performed with MAPS.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Peak file, loop bedpe or gene count

molecule: genomic DNA

tag: antibody

value: anti-H3K27ac (abcam, ab4729)


title: HiChIP_H3K27ac_del-TRP


title: HiChIP_H3K27ac_del-cIDR


title: HiChIP_H3K27ac_WT


title: HiChIP_H3K27ac_Vector


title: HiChIP_H3K4me3_batch2_del-TRP

value: anti-H3K4Me3 (Millipore, 05-745R)


title: HiChIP_H3K4me3_batch2_WT


title: HiChIP_H3K4me3_batch1_eIFIDR_rep2


title: HiChIP_H3K4me3_batch2_del-cIDR


title: HiChIP_H3K4me3_batch2_Vector


title: HiChIP_H3K4me3_batch1_eIFIDR_rep1


title: RNA-seq_batch2_Vector_rep1


title: HiChIP_H3K4me3_batch1_del-cIDR_rep2


title: HiChIP_H3K4me3_batch2_eIFIDR


title: HiChIP_H3K4me3_batch1_WT_rep2


title: HiChIP_H3K4me3_batch1_WT_rep1


title: HiChIP_H3K4me3_batch1_Vector_rep1


title: HiChIP_H3K4me3_batch1_Vector_rep2


title: ChIP-seq_MLL4_WT

value: anti-MLL4 (Santa Cruz, SC293217)


title: ChIP-seq_MLL4_del-cIDR


title: HiChIP_H3K4me3_batch1_del-cIDR_rep1


title: ChIP-seq_MLL4_Vector


title: WT Input 1

description: WT Input 1


title: RNA-seq_batch2_WT_rep1


title: ChIP-seq_H3K27me3_MT2

value: anti-H3K27Me3(Millipore 07-449)


title: ChIP-seq_H3K27me3_del-cIDR


title: ChIP-seq_H3K27me3_Vector


title: ChIP-seq_H3K27ac_MT2


title: ChIP-seq_H3K27ac_del-cIDR


title: ChIP-seq_H3K27me3_WT


title: ChIP-seq_H3K4me2_Vector

value: anti-H3K4Me2(Millipore 07-030)


title: ChIP-seq_H3K4me1_del-cIDR

value: anti-H3K4Me1(Abcam ab8895)


title: ChIP-seq_H3K4me3_del-cIDR


title: ChIP-seq_H3K4me1_Vector


title: ChIP-seq_H3K4me1_WT


title: ChIP-seq_H3K4me3_WT


title: ChIP-seq_H3K4me2_del-cIDR


title: ChIP-seq_H3K4me2_WT


title: PRO-seq_del-cIDR_rep1

data_processing:
library strategy: Pro-seq
RNA-seq reads were aligned to the human genome assembly GRCH38/hg38 or mouse genome assembly GRCm38/mm10 using STAR. RNA-seq counts were annotated using RSEM. Differentially expressed genes were calculated using DESeq2.
ChIP-seq and PRO-seq sequence reads were aligned to the human genome assembly GRCH38/hg38 using BWA. Sam files were converted into bam files using Samtools. MACS2 was used to call peaks under the FDR threshold of 0.01.
H3K4me3/H3K27ac HiChIP data were performed with MAPS.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Peak file, loop bedpe or gene count


title: PRO-seq_WT_rep1


title: PRO-seq_del-cIDR_rep2


title: RNA-seq_FUSIDR_rep2


title: ChIP-seq_UTX_Vector

value: anti-UTX (CST 33510)


title: PRO-seq_Vector_rep2


title: PRO-seq_WT_rep2


title: RNA-seq_del-TRP_rep2


title: RNA-seq_FUSIDR_rep1


title: RNA-seq_del-TRP_rep1


title: RNA-seq_eIFIDR_rep2


title: ChIP-seq_H3K4me3_Vector

value: anti-H3K4Me3(Millipore 07-449)


title: ChIP-seq_H3K27ac_WT


title: ChIP-seq_H3K4me1_MT2


title: RNA-seq_del-cIDR_rep1


title: RNA-seq_del-cIDR_rep2


title: RNA-seq_eIFIDR_rep1


title: ChIP-seq_UTX_WT


title: ChIP-seq_H3K27ac_Vector


title: RNA-seq_WT_rep1


title: PRO-seq_Vector_rep1


title: RNA-seq_WT_rep2


title: RNA-seq_Vector_rep1


title: SK-MEL-28 control polysome fraction rep 3

city: Leuven

first: Eleonora

last: Leucci

address: Herestraat 49, bus 818 room 06.423

department: Oncology

country: Belgium

institute: KU Leuven

data_processing:
Library strategy: Ribo-seq
Quality control of raw reads was performed with FastQC v0.11.5.
Adapters were filtered with eautils v1.2.2.18.
Splice- aware alignment was performed with STAR against the human hg19 human genome assembly. The number of allowed mismatches was 2. Reads that mapped to more than one site to the reference genome were discarded. The minimal score of align- ment quality to be included in count analysis was 10. Resulting SAM and BAM alignment files were handled with Samtools v0.1.19.24.
Quantification of reads per gene was performed with HT-Seq count v0.5.3p3.
Count-based differential expres- sion analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq.
Genome_build: human hg19 human genome assembly
Supplementary_files_format_and_content: Count files from HT-Seq count v0.5.3p3 containing quantification of genes per sample.

source_name: SK-MEL-28 melanoma cell line

growth_protocol: Sk-MEL-28 were grown in RPMI 1640 (Gibco, Invitrogen) supplemented with 10% FBS (Gibco, Invitrogen).

extract_protocol:
Cells were treated with 100 µg mL-1 of Cycloheximide (CHX, Sigma-Aldrich) for 12 min at 37 °C and resuspended in lysis buffer.  Lysates were then loaded on a sucrose gradient (the linear sucrose gradient 5-20%). Samples were then centrifugated in an SW41Ti rotor (Beckman Coulter) at 37.000 rpm for 170 min at 4 °C. The fractions were obtained with a BioLogic LP System (Bio-Rad). 14 fractions were collected from each sample, with each fraction having a final volume of 600 µL. From the initial 14 fractions, 4 final samples were obtained (by pulling together some of them): 40S, 60S, 80S and polysomes.
Libraries were prepared with TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were on treatment with salubrin for 72h before polysome preparation

tag: fraction

value: Polysome

tag: treatment

value: Untreated


title: SK-MEL-28 control polysome fraction rep 1


title: SK-MEL-28 control polysome fraction rep 2


title: SK-MEL-28 control 80S fraction rep 1


title: SK-MEL-28 control 60S fraction rep 1


title: SK-MEL-28 treated with salubrinal 60S fraction rep 3

value: Salubrinal


title: SK-MEL-28 control 80S fraction rep 2


title: SK-MEL-28 treated with salubrinal 80S fraction rep 3


title: SK-MEL-28 control 60S fraction rep 3


title: SK-MEL-28 control 80S fraction rep 3


title: SK-MEL-28 treated with salubrinal 80S fraction rep 2


title: SK-MEL-28 control 60S fraction rep 2


title: SK-MEL-28 treated with salubrinal polysome fraction rep 3


title: SK-MEL-28 treated with salubrinal polysome fraction rep 2


title: SK-MEL-28 control 40S fraction rep 2


title: RNA-seq_Vector_rep2


title: SK-MEL-28 control 40S fraction rep 3


title: SK-MEL-28 control 40S fraction rep 1


title: SK-MEL-28 treated with salubrinal 40S fraction rep 3


title: SK-MEL-28 treated with salubrinal 40S fraction rep 2


title: SK-MEL-28 control input fraction

value: input


title: ChIP-seq_UTX_del-cIDR


title: SK-MEL-28 treated with salubrinal 60S fraction rep 2


title: Single cell measurements of RNA & nuclear proteins in HeLa nuclei (n=1 non-treated, n=1 TNFalpha treated)

city: Cambridge

first: Hattie

last: Chung

state: MA

address: 415 Main St

institute: Broad Institute

description: HeLa nuclei extracted from non-treated (n=1) and TNFα (n=1) treated HeLa cells, pooled with nucleus-hashing antibodies, loaded on a single 10x channel, and computationally demultiplexed with DemuxEM

data_processing:
Raw bcl files were converted to fastq, and aligned to either hg19_premrna or mm10_premrna genomes using cellranger v4.0.0 running on Cumulus version 1.0
Genome_build: hg19_premrna or mm10_premrna
Supplementary_files_format_and_content: csv files for creating anndata object. Contains gene expression data, nucleus hashtag HTO counts, protein ADT counts, and pooled batches (if applicable). Load as anndata object.

source_name: HeLa cell line

growth_protocol: HeLa cells expressing a p65-mNeonGreen reporter construct were cultured at 37C and 5% CO2 in DMEM with high glucose, pyruvate, GlutaMax, heat-inactivated fetal bovine serum, and 100 U/mL penicillin-streptomycin. For TNFα treatment, cells were stimulated with 30 ng/mL TNFα at 37C for 40 min, then washed with PBS.

extract_protocol:
nuclei extraction with EZ prep
3' polyA RNA seq
10X Genomics Chromium Prep V3 3'

treatment_protocol: Non-treated (NT) and TNFα treated, combined

value: HeLa cell line

tag: mixed sample

value: (n=1 non-treated, n=1 TNFα treated)

tag: sample type

value: p65 protein


title: SK-MEL-28 treated with salubrinal input fraction


title: MV4-11_short-pino_H3K79me2

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

institute: University of Chicago

data_processing:
For ChIP-seq analyses, analysis of histone methylation density (HMD) was carried out using the scripts and workflow from (Grzybowski et al. Nat Protoc. 2019;14(12)).
For RNA-seq analyses, reads were aligned to the index using HISAT2 (v 2.0.1) (Pertea et al., 2016). Cufflinks was used for differential gene expression analysis between the three DMSO-treated samples vs. the 10 nM pinometostat-treated samples.
Genome_build: hg38
Supplementary_files_format_and_content: BED files represent read locations genome-wide
Supplementary_files_format_and_content: BEDGRAPH files represent basepair depth or normalized depth
Supplementary_files_format_and_content: BIGWIG files represent basepair depth or normalized depth for genome browsers
Supplementary_files_format_and_content: FPKM_TRACKING files represent gene abundances for transcripts in RNA-seq experiment

source_name: Cell culture

growth_protocol: Exponentially growing MV4;11 cells were grown in 150 mm2 tissue culture-treated plates (Corning cat # 0877224) in 30 ml media ± 10 nM pinometostat for 4 or 7 days. Every 2 days cells were spun down at 500 x g 5 min. then resuspended in media ± 10 nM pinometostat. Cells were harvested on day 4 or 7.

extract_protocol:
Native, internally calibrated ICeChIP-seq was carried out as described previously for H3K4me3, H3K27me3 and H3K36me3 (Grzybowski et al Mol Cell. 2015;58(5):886-899, Grzybowski et al. Nat Protoc. 2019;14(12)). A modified protocol was used for H3K79me2 that included cross-linking and denaturation. After 7 days of treatment, 2 x 107 cells were spun down at 500 x g 5 min. at 4 °C, the supernatant was discarded and the cells were washed 2x with 10 ml ice cold PBS. The cells were resuspended in 5 mL Buffer N then spun down at 500 x g 5 min. at 4 °C and the supernatant was discarded. The cells were resuspended in 2 packed cell volumes (PCV) of Buffer N into a single-cell suspension. 1 volume of the 2x Lysis Buffer was added and the cells were incubated for 10 minutes at 4 °C. The nuclei were pelleted by spinning them at 500 x g 5 min. at 4 °C and the supernatant was discarded. The pellet was resuspended in 6 PCV of Buffer N and carefully added to the top of 7.5 mL of the Sucrose Cushion in a 50 mL centrifuge tube. The nuclei were pelleted by spinning them at 500 x g 5 min. at 4 °C and the supernatant was discarded. Then the nuclei were resuspended in 2 PCV of Buffer N and then the chromatin concentrations was adjusted to 1 μg/μl through addition of buffer N. 100 μg of chromatin was then carried forward for ChIP and 2 μl of each of the semisynthetic nucleosome standards was added. The nuclei were prewarmed for 1-2 min at 37 °C and then 1.5 ul 15 U/μl MNase  per 100 μg chromatin was added and incubated at 37 °C for 12 minutes at 900 rpm agitation. The digestion was stopped with 13 μl (1/10 vol.) MNase stop buffer and immediately placed on ice. 17 μl 5M NaCl (up to 0.6 M) was slowly added while vortexing on the slowest setting that would allow effective mixing (setting 3.5 on VWR standard mini vortexer). The sample was spun down at 18,000 x g for 1 min. at 4 °C and the soluble fraction, including the chromatin, was transferred to a new tube. 66 mg of Hydroxyapatite (HAP) (Bio-Rad Ceramic Hydroxyapatite Type I 20 μm) was then rehydrated with 200 μL of HAP buffer 1 and the fragmented chromatin was mixed with the resin and incubated on a rotator for 10 minutes at 4°C. The HAP mixture was added to a centrifugal filter unit (Millipore Ultrafree MC-HV Centrifugal Filter, 0.45 um) and spun down at 600 x g for 30 sec at 4 °C. 200 μL of HAP buffer 1 was added and spun down at 600 x g for 30 sec at 4 °C. This step was repeated three more times for a total of four washes with HAP buffer 1. 200 μL of HAP buffer 2 was added and spun down at 600 x g for 30 sec at 4 °C. This step was repeated three more times for a total of four washes with HAP buffer 2. 100 μL of HAP elution was added and spun down at 600 x g for 30 sec at 4 °C. This was repeated two more times for a total of three elutions. 30 μl of 280 μl total HAP-purified chromatin was diluted to 20 μg/ml with ChIP buffer 1 for H3K4me3, H3K27me3 and H3K36me3 native ICeChIP. The remaining 150 μl of HAP-purified chromatin for H3K79me2 denaturative ICeChIP was crosslinked in 0.25% formaldehyde for 8 min. on a nutator at RT, then quenched by adding 1M Tris pH 7.5 to 200 mM and incubated for 5 min. at RT on a nutator. 50 μl of cross-linked chromatin was used for denaturation and 2.5 ul 20% SDS was added to 1% SDS final concentration and the sample was incubated 1 min. at 55 °C, then IMMEDIATELY put on ice. This was then diluted with 9 volumes water (450 ul) and 100 μl was used for each IP. Antibodies were bound to protein G beads. 96 μl (12 ul per 3 ug Ab) Protein G magnetic beads (Invitrogen cat # 10004D) were collected on magnetic racks, and the supernatant was discarded. The beads were then resuspended in 20 vol ChIP Buffer 1, collected on the magnetic rack, and the supernatant was discarded. The wash with ChIP Buffer 1 was repeated. The appropriate amount of antibody was diluted in ChIP Buffer 1 to 100 uL (in separate tubes for each antibody). Antibodies for both the DMSO- and pinometostat-treated samples were processed together (12 μl antibody-bound beads per IP).  3 μg of anti-H3K79me2 (Abcam cat # ab3594, lot # GR173874); 3 μg of anti-H3K4me3 (Abcam cat # 12209, lot # GR275790-1); 0.6 μg of anti-H3K27me3 (Cell Signaling cat # 9733, lot # 8) and 3 μg anti-H3K36me3 (RevMab RM155 cat # 31-1051-00, lot # R-05-01575) were used per IP. The diluted antibodies were added to the beads and pipetted up & down to re-suspend the beads and then incubated on a rotator for 15 min. The beads were then collected on a magnetic rack and the supernatant was discarded. The beads were washed with 20 vol of ChIP Buffer 1, collected on the magnetic rack, and the supernatant was discarded. This wash was repeat once more. Different amounts of the native, non-crosslinked, chromatin were used for immunoprecipitation depending on the prevalence of each modification target. 3 μg of chromatin was added to the beads with anti-H3K4me3 antibody 0.8 μg of chromatin was added to the beads with anti-H3K27me3 antibody and 3 μg of chromatin was added to the beads with anti-H3K36me3 antibody. 100 μl crosslinked, denatured chromatin was added to the beads with anti-H3K79me2 antibody. 10% of the amount of chromatin used for each IP was set aside as input. All samples, including the input, were incubated on a rotator at 4 °C for 15 min., then collected on a magnetic rack and the supernatant was discarded. The beads were resuspended in 1 ml of ChIP buffer 2 again, then transferred to a new siliconized tube and incubated for 5 min. at 4°C on a rotator. The beads were then collected on a magnetic rack and the supernatant was discarded. The beads were resuspended in 1 ml of ChIP buffer 2 then transferred to a new siliconized tube and incubated for 5 min. at 4°C on a rotator. The beads were then collected on a magnetic rack and the supernatant was discarded. The beads were then resuspended in 1 ml of ChIP buffer 3 then transferred to a new siliconized tube and incubated for 5 min. at 4°C on a rotator. The beads were then collected on a magnetic rack and the supernatant was discarded. The beads were then resuspended in 1 ml of ChIP buffer 1 then transferred to a new siliconized tube and incubated for 5 min. at 4°C on a rotator. The beads were then collected on a magnetic rack and the supernatant was discarded. The beads were then resuspended in 1 ml TE buffer, collected on a magnetic rack and the supernatant was discarded. Finally, the beads were then resuspended in 50 μl ChIP Elution Buffer, incubated at 65°C for 5 min., then collected on the magnetic rack. The supernatant containing the eluted sample was then transferred to a new tube. ChIP Elution Buffer was added to the 10% input samples to bring to a final volume of 50 μl. To each sample including the inputs, 2 μl of 5M NaCl (to a final concentration of 0.2 M), 1 μl of 500 mM EDTA (to a final concentration of 10 mM), and 1 μl of 20 mg/mL Proteinase K (to a final amount of 20 μg) were added and the samples were incubated 55°C for 1 hour for proteinase K digestion. The crosslinked IP samples were incubated for an additional hour at 65°C to reverse crosslink. The samples were removed from incubation and 3 volumes of SPRI Serapure beads were added, and mixed by pipetting up and down 10 times, then incubated for 5 minutes at room temperature. The samples were placed on a magnetic rack, allowing the beads to collect for 5 min. then, while still on the rack 200 μl EtOH was added and removed without disturbing the beads. This EtOH wash was repeated. The beads were removed from the magnet and resuspended in 50 μl TE then collected on the magnetic rack. The supernatant containing the purified DNA was transferred to a new tube.
Libraries were prepared using the NEBNext Ultra II DNA Library prep kit (NEB cat # E7645). 3 cycles of PCR amplification were used for native inputs and H3K36me3 IPs, 4 cycles for denaturated inputs and H3K27me3 IPs, 7 cycles for H3K4me3 IPs and 10 cycles for H3K79me2 IPs. The following primer indices were used: denatured DMSO-treated input (index 8), denatured pinometostat-treated input (index 12), DMSO-treated H3K79me2 IP (index 9), pinometostat-treated H3K79me2 IP (index 11), native DMSO-treated input (index 8), native pinometostat-treated input (index 12), DMSO-treated H3K36me3 IP (index 9), pinometostat-treated H3K36me3 IP (index 11), DMSO-treated H3K4me3 IP (index 9), pinometostat-treated H3K4me3 IP (index 11), DMSO-treated H3K27me3 IP (index 2), pinometostat-treated H3K27me3 IP (index 7).

treatment_protocol: Per growth protocol and treatment condition.

value: 10 nM pinometostat (4 days)

tag: chip antibody

value: Abcam cat # ab3594, lot # GR290484-1


title: MV4-11_DMSO_ChIP_Input_R2

value: DMSO


title: MV4-11_pino_H3K79me2

value: 10 nM pinometostat (7 days)

value: Abcam cat # ab3594, lot # GR173874


title: MV4-11_short-pino_ChIP_Input


title: MV4-11_pino_denat_ChIP_Input


title: MV4-11_pino_RNA-seq_Rep1

extract_protocol:
After 7 days of treatment, 1 x 107 cells were spun down at 500 x g 5 min. then cells were resuspended in 1 ml Trizol reagent (Life Technologies cat# 15596018), incubated 5 min. at RT, then 200 μl chloroform was added and samples were shaken rigorously for 15 sec. then incubated 3 min. at RT and spun down 12,000 x g 15 min. at 4 °C. The aqueous layer (~ 500 μl) was removed and mixed with 500 μl EtOH and added to a Zymo Research RNA Clean and Concentrator column (cat # 11-353B) and then spun at 12,000 x g for 1 min.. 100 μl DNase I (1:10 in buffered dH20) (Thermo Fisher Scientific cat # en0521) was added to the column and then it was spun at 500 x g 5 min., incubated 15 min. at RT and then spun 12,000 x g for 30 sec. and the flow through was discarded. After each of the following were added to the column, it was spun down 12,000 x g for 30 sec. and the flow through was discarded. Combined 200 μl RNA binding buffer with 300 μl EtOH and then spun 12,000 x g for 30 sec. and the flow through was discarded. After each of the following were added to the column, it was spun down 12,000 x g for 30 sec. and the flow through was discarded: 400 μl RNA prep buffer; 700 μl RNA wash buffer; and 400 μl RNA wash buffer. RNA was eluted from column with 30 μl RNase-free dH2O. Added RNA standards to 2 μg of each RNA sample- Add the equivalent of 10 copies/cell yeast RAD51; 30 copies/cell RNL2; 200 copies/cell E coli MBP; and 2000 copies/cell yeast SUMO to each sample then proceeded with rRNA removal Ribo Zero Gold kit (Illumina cat # MRZ11124C) according to manufacturer’s protocol. Add sample to Zymo RNA clean and concentrator columns and follow manufacturer's protocol. Elute in 7 μl RNase-free dH2O.
Libraries were prepared using the NEBNext Ultra Directional RNA Library prep kit (NEB cat # E7420S) with 5 μl of purified sample. Primer indices 4, 6 and 12 were used for DMSO-treated samples and 2, 7 and 9 for pinometostat-treated samples. Samples were amplified with 15 cycles of PCR. Libraries were then sequenced on the Illumina NextSEQ500 for paired-end sequencing, combining treated samples and untreated samples in separate lanes.


title: MV4-11_DMSO_H3K36me3


title: MV4-11_pino_native_ChIP_Input


title: MV4-11_pino_H3K27me3

value: Cell Signaling cat # 9733, lot # 8


title: MV4-11_pino_H3K36me3


title: MV4-11_DMSO_H3K27me3


title: MV4-11_DMSO_native_ChIP_Input


title: MV4-11_DMSO_H3K79me2_R2


title: MV4-11_DMSO_H3K4me3


title: MV4-11_DMSO_RNA-seq_Rep2


title: MV4-11_DMSO_RNA-seq_Rep3


title: 49F_rep1_RNAseq

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

data_processing:
For RNAseq, Illumina Nextseq500 reads were demultiplexed using bcl2fastq. Alignment of reads to hg19 was performed using STAR aligner with the default setting in Illumina Basespace.
For ChIPseq, reads were aligned to hg38 using BWA (v. 0.7.17). MACS2 was used for peak calling.
Genome_build: hg19 (RNAseq); hg38 (ChIPseq)
Supplementary_files_format_and_content: For RNA-seq, tab-delimited files contain FPKM values for each sample.
For ChIP-seq, bigWig files were generated using deeptools (v. 2.5.4)

source_name: Prostate cancer cell line 49F

growth_protocol: Cells were cultured in RPMI-1640 media containing 5% fetal bovine serum, with the ENZ-resistant cell lines supplemented with 10mM ENZ.

extract_protocol:
RNA was isolated using the PureLink RNA Mini Kit (Thermo, #12183018A).
Libraries were constructed using the NEBnext Ultra ii Stranded RNA Library Prep Kit.

value: Prostate cancer cell line 49F

tag: tumor type

value: ENZ-resistant CRPC-Adeno


title: 49F_rep2_RNAseq


title: 42D_rep1_RNAseq

source_name: Prostate cancer cell line 42D

value: Prostate cancer cell line 42D

value: ENZ-resistant CRPC-NE


title: 42D_rep2_RNAseq


title: 16D_rep2_RNAseq

source_name: Prostate cancer cell line 16D

value: Prostate cancer cell line 16D

value: CRPC


title: MV4-11_DMSO_H3K79me2


title: MV4-11_DMSO_denat_ChIP_Input


title: LNCaP_rep2_RNAseq

source_name: Prostate cancer cell line LNCaP

value: Prostate cancer cell line LNCaP

value: Prostate adeno


title: 42D_SUZ12_ChIPseq

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were constructed using the KAPA HyperPrep Kit (Roche, #KK8504) with Illumina TruSeq indexes.

value: SUZ12 (Cell Signaling, #3737)


title: 42F_rep2_RNAseq

source_name: Prostate cancer cell line 42F

value: Prostate cancer cell line 42F


title: MV4-11_pino_RNA-seq_Rep2


title: MV4-11_DMSO_RNA-seq_Rep1


title: 293T KO RNA-seq #3

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
RNA-seq datasets were aligned to the hg38 annotation of human genome using STAR 2.6.0c (Dobin et al., 2013) with the parameters "--outFilterMultimapNmax 1" for obtaining the uniquely mapped reads, "--quantMode GeneCounts" for counting the numbers of reads per gene while performing the mapping, and "--twopassMode Basic" for using the two-pass mapping mode.
Bioconductor package DESeq2 was used to analyze differential gene expression.
PSI-Sigma was used to identify alternative splicing events.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig files

source_name: HEK293T cells

growth_protocol: HEK293T cells cultured in DMEM+10%FBS+1%Penicilin/Streptomycin under standard conditions (5% CO2 humified chamber).

extract_protocol:
Total RNA from the cells was prepared using the Direct-zol™ RNA MiniPrep Plus (Zymo Research Corporation) according to manufacturer's protocol. Turbo DNase (Thermo Fisher) treatment was performed according to guidelines of the producer. Quality and quantity of the resulting RNA were confirmed by RNA Nano LabChip Bioanalyzer run (Agilent).
Libraries were constructed from 400 ng of total RNA using the TruSeq Stranded Total RNA LT Sample Prep (with double Ribo-Zero Gold treatment and single indexing). Quality of libraries was ensured with Bioanalyzer High Sensitivity DNA kit (Agilent). Sequencing was performed using the NextSeq 500 High Output v2 kit (150 cycles) Illumina platform.

treatment_protocol: Cells were transduced with lentiviral particles, containing a sequence-specific small guide RNA targeting SCARNA15, spCas9 and eGFP. To obtain individual clones, single GFP+ cells were sorted into 96-well plates and expanded.

tag: crispr cas9 ko

value: SCARNA15 KO


title: 293T WT RNA-seq #1

value: WT


title: 293T KO RNA-seq #1


title: 293T KO RNA-seq #2


title: 293T WT RNA-seq #2


title: 16D_ATACseq

data_processing:
For RNA-seq, data was de-multiplexed using bcl2fastq2 Conversion Software (version 2.20) and the resultant read sequences were aligned to the hg19 human reference genome using STAR aligner. Assembly and differential expression was estimated using Cufflinks software (version 2.2.1) available through the Illumina BaseSpace Sequence Hub. Expression levels (FPMK) were estimated by counting all nucleotides mapped to each gene and were normalized by the total number of mapped nucleotides (per million) and the gene length (per kb).
For ChIP-seq, reads were aligned to the hg38 human reference genome using BWA-MEM software (version 0.7.17) with default parameters. Alignments with quality less than 60 were filtered out (leaving only uniquely mapped reads) using Samtools software (version 1.9). Peaks were called using MACS2 (version 2.1.2) with FDR q-value = 0.05 using the narrow peak caller for all datasets except K27Me and K27Ac which used the broad calling option.
For ATAC-seq, reads were aligned to the hg38 human reference genome using BWA-MEM software (version 0.7.17) with default parameters. Reads with alignment quality less than 60 were filtered out using Samtools software (version 1.9). Peaks were called using MACS2 (version 2.1.2) with FDR q-value = 0.05 from reads with template length between 35 and 130 bp.
Genome_build: hg19 (RNA-seq), hg38 (ChIP-seq, ATAC-seq)
Supplementary_files_format_and_content: For RNA-seq, tab-delimited files contain FPKM values for each sample. For ChIP-seq and ATAC-seq, bigWig files were generated using DeepTools bamCoverage command with bin size of 25.

source_name: Human prostate cancer cell line

growth_protocol: LNCaP, CRPC (16D), and enzalutamide (ENZ)-resistant tNEPC (42D, 42F) cell lines were cultured in RPMI-1640 media containing 10% fetal bovine serum, with the ENZ-resistant cell lines supplemented with 10 µmol/L ENZ. LASCPC-1 and NCI-H660 cell lines were cultured in HITES media, formulated as follows: RPMI-1640, 5% FBS, 10 nM hydrocortisone, 10 nM β-estradiol, 1x Insulin-Transferrin-Selenium, 1x GlutaMAX.

extract_protocol:
Samples were processed for ATAC-seq as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015), with some modification. Briefly, cells grown to 60-70% confluency were collected using CellStripper for 15 min at 24°C with orbital shaking and subsequent centrifugation at 2300 rpm for 5 min at 4°C. Cells were washed with pre-chilled 1x PBS, and 5 x 104 cells were lysed using 50 µl ATAC-seq lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 in 1x PBS] for 1 minute at 4°C. Nuclei were subsequently collected by centrifugation at 2300 rpm for 5 min at 4°C.
Tagmentation reaction was performed using 2.5 µl Illumina TDE1 in 50 µl Illumina TD buffer at 37°C for 30 min. The tagmented DNA library was purified using the QIAquick PCR Purification Kit. Library quantification and number of amplification cycles was determined as described (Buenrostro et al., 2015). Sequencing was performed on an Illumina NextSeq 500 to generate 2x75-bp paired-end reads.

treatment_protocol: Cell lines were treated with 10 µM enzalutamide (ENZ) or 10 μM GSK126, as indicated

value: CRPC (16D)

tag: tumour type


title: 42D-GSK126_RNAseq

description: 42D cells treated with GSK126

data_processing:
Data was de-multiplexed using bcl2fastq2 Conversion Software (version 2.20) and the resultant read sequences were aligned to the hg19 human reference genome using STAR aligner. Assembly and differential expression was estimated using Cufflinks software (version 2.2.1) available through the Illumina BaseSpace Sequence Hub. Expression levels (FPMK) were estimated by counting all nucleotides mapped to each gene and were normalized by the total number of mapped nucleotides (per million) and the gene length (per kb).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files contain FPKM values for each sample

growth_protocol: Enzalutamide (ENZ)-resistant tNEPC (42D) cell lines were cultured in RPMI-1640 media containing 10% fetal bovine serum, supplemented with 10 µmol/L ENZ.

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit (Thermo, #12183018A) following manufacturer’s procedure
Library constructions were performed using the NEBnext Ultra ii Stranded RNA Library Prep Kit. Sequencing was performed on an Illumina NextSeq 500 to generate 2x42-bp paired-end reads.

tag: tissue

value: Human prostate cancer cell line

value: Prostate neuroendocrine


title: 42D-crAR_RNAseq

description: 42D cells with CRISPR/Cas9-mediated AR knockout

value: CRISPR/Cas9-mediated AR knockout


title: 42D-DMSO_RNAseq

description: 42D cells treated with DMSO vehicle

value: DMSO


title: 42D_pEZH2_ChIPseq

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP sequencing libraries (100 ng DNA per sample) were constructed using the KAPA HyperPrep Kit (Roche, #KK8504) with Illumina TruSeq indexes. Sequencing was performed on an Illumina NextSeq 500 to generate 75-bp single-end reads.

value: enzalutamide (ENZ)-resistant tNEPC 42D

value: pEZH2-T350 (custom generated)


title: 42D_ATACseq

extract_protocol:
Samples were processed for ATAC-seq as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015), with some modification. Briefly, cells grown to 60-70% confluency were collected using CellStripper for 15 min at 24°C with orbital shaking and subsequent centrifugation at 2300 rpm for 5 min at 4°C. Cells were washed with pre-chilled 1x PBS, and 5 x 104 cells were lysed using 50 µl ATAC-seq lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 in 1x PBS] for 1 minute at 4°C. Nuclei were subsequently collected by centrifugation at 2300 rpm for 5 min at 4°C.
Tagmentation reaction was performed using 2.5 µl Illumina TDE1 in 50 µl Illumina TD buffer at 37°C for 30 min. The tagmented DNA library was purified using the QIAquick PCR Purification Kit. Library quantification and number of amplification cycles was determined as described (Buenrostro et al., 2015).


title: 16D_rep1_RNAseq


title: 42D_H3K27Ac_ChIPseq

value: H3K27Ac (Active Motif, #39685)


title: 42D_H3K27Me3_ChIPseq


title: 42D_EZH2_ChIPseq

value: EZH2 (Active Motif, #39933)


title: 16D_EZH2_ChIPseq


title: 42D_AR_ChIPseq

value: AR (Millipore, #06-680)


title: 16D_AR_ChIPseq


title: 16D_Reporter-mCherry-GFP_RNAseq

tag: genotype/variation

value: FACS isolated 16D reporter cells following 8 day enzalutamide treatment, expressing ASCL1:mCherry and OCT4:GFP


title: LNCaP_rep1_RNAseq

value: Prostate cancer cell line LNCaP


title: 42D_EED_ChIPseq

value: Prostate cancer cell line 42D

value: ENZ-resistant CRPC-NE

value: EED (Millipore, #17-10034)


title: 16D_Reporter-GFP_RNAseq

value: Prostate adeno

value: FACS isolated 16D reporter cells following 8 day enzalutamide treatment, expressing OCT4:GFP


title: 16D_Reporter-Neg_RNAseq

value: CRPC (16D)

value: FACS isolated 16D reporter cells following 8 day enzalutamide treatment, negative for both ASCL1:mCherry and OCT4:GFP


title: 16D_Reporter-mCherry_RNAseq

value: FACS isolated 16D reporter cells following 8 day enzalutamide treatment, expressing ASCL1:mCherry


title: 293T WT RNA-seq #3

value: WT


title: 16D_EZH2-350D_RNAseq

value: 16D cells with CRISPR-mediated EZH2 knockout, stably expressing EZH2-T350D mutant


title: 16D-crEZH2_3_RNAseq

value: 16D cells with CRISPR-mediated EZH2 knockout


title: 42D-siCtrl_RNAseq

value: enzalutamide (ENZ)-resistant tNEPC 42D

value: Prostate neuroendocrine

value: 42D cells with siCtrl


title: NCI-H660_RNAseq


title: 42D-siAR_RNAseq

value: 42D cells with siRNA-mediated AR silencing


title: LASCPC1_RNAseq


title: MV4-11_pino_RNA-seq_Rep3

value: 10 nM pinometostat (7 days)


title: MV4-11_pino_H3K4me3


title: mIMCD3 Pkd2-/- #3

city: Freiburg

first: Sebastian

last: Friedrich

address: Hugstetter Str. 55

country: Germany

institute: University Hosptial Freiburg

data_processing:
Illumina Casava1.7 software used for basecalling.
Data analysis was performed on Galaxy Europe platform. Sequenced reads were trimmed for adaptor sequence (Trim Galore, Galaxy Tool Version 0.4.3.1, default settings) and quality checked (FastQC, Galaxy Tool Version 0.72, default settings). Reads were mapped to mm10 whole genome using HISAT2 (Galaxy Tool Version 2.1.0+galaxy3) with spliced alignment options: Penalty for canonical splice sites 0, Penalty for non-canonical splice sites 3, Penalty function for long introns with canonical splice sites  Constant [f(x) = B], Constant term (B) 0.0, Coefficient (A) 0.0, Penalty function for long introns with non-canonical splice sites Natural logarithm [f(x) = B + A * log(x)], Constant term (B)  -8.0, Coefficient (A) 1.0, Minimum intron length 20, Maximum intron length 500000)
Mapped reads were counted with htseq-count (Galaxy Tool Version 0.9.1, default settings) . Differential gene expression was tested using DESeq2 (Galaxy Tool Version 2.11.40.4, default settings for estimateSizeFactors). False discovery rate of DGE was controlled with a p-value < 0.05 adjusted for multiple testing (Benjamini-Hochberg procedure).
The reads processed in the RNA-seq analysis were also aligned to the reference genome and tailored for StringTie tool with HISAT2 (Galaxy Tool Version 2.1.0+galaxy3). De novo transcript reconstruction was conducted with StringTie (Galaxy Tool Version 1.3.6). The transcriptome was assembled using StringTie-merge (Galaxy Tool Version 1.3.6). Assembled transcripts were compared to the reference annotation (Mus musculus, mm9) with GFFCompare (Galaxy Tool Version 0.11.2). Exon abundancies were then estimated using DEXSeq-Count (Galaxy Tool Version 1.28.1.0). Differential exon usage (DEU) was tested with DEXSeq (Galaxy Tool Version 1.28.1+galaxy1). False discovery rate of DEU was controlled with a p-value < 0.05 adjusted for multiple testing (Benjamini-Hochberg procedure).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table (.csv) containing DESeq2 normalized counts for every transcript and every sample

organism: Mus musculus

source_name: murine inner medullary collecting duct cells

growth_protocol: Cells were cultured in a mix of Dulbecco’s modified eagle’s and F12 medium (DMEM-F12; Lonza), which was supplemented with 10 % fetal bovine serum and 1 % Penicillin-Streptomycin (10,000 U Penicillin and 10 mg / ml Streptomycin; both Sigma Aldrich). Per genotype, six 10 cm cell culture dishes were grown, starting with 5 × 10^6 cells per dish. Cells were grown at 37 °C and 10 % CO2. PCR-based testing for mycoplasma contamination was performed regularly. New ampules were started after ~25 passages.

extract_protocol:
Per genotype, 6 cell culture dishes were grown to full confluency, starting with 5 × 10^6 cells per dish. RNA Isolation was performed 4 days after full confluency according to manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen), harvesting 2 × 10^6 cells per dish. Purification of RNA samples was performed by solvent extraction with 100 % ethanol followed by precipitation with ammonium acetate.10 µl glycogen was added to 100 µl RNA solution. RNA was solved in 10 µl  ammonium acetate (7,5 M) and 250 µl ethanol (100 %). After 30 min at -80 °C RNA was precipitated and separated by centrifugation for 30 min with 13,000 rpm at 4 °C. RNA was then washed twice in 200 µl cold ethanol (80 %) followed by 30 min centrifugation with 13,000 rpm at 4 °C. RNA pellets were dried for 5 min at room temperature and resuspended in 10-15 µl RNAse-free water. Quality of RNA was checked by a Nanodrop photometer (Thermo Fisher). Four of the six samples were chosen for RNA sequencing according to highest ratios for A260/280 (> 2.0) and A260/230 (> 2.0).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested using 0.25 % Trypsin-EDTA (Gibco). Cell counts were performed by Countess II cell counter (Thermo Fisher).

tag: genotype

tag: mutation details


title: mIMCD3 Pkd2-/- #1

value: murine inner medullary collecting duct cells


title: mIMCD3 Pkd2-/- #2


title: mIMCD3 Pkd2-/- #4


title: mIMCD3 Pkd1-/- #4


title: mIMCD3 Pkd1-/- #1


title: mIMCD3 Pkd1-/- #3


title: mIMCD3 Pkd1-/- #2


title: siDNMT1 [RNA-seq]

city: Guangzhou

first: Jianwei

last: Li

address: South Shatai Road

country: China

institute: southern medical university southern hospital

data_processing:
Total RNA quantity and purity were analyzed using a Bioanalyzer 2100 and an RNA 6000 Nano LabChip kit (Agilent), with RNA integrity values of >7.0.
The final cDNA library were created in accordance with the protocol for the TruSeq RNA Sample Preparation v.2
Before assembly, low-quality reads were removed using Trimmomatic software.
Sequencing reads were aligned to the reference genome using the HISAT2 package.
The mapped reads of each sample were assembled and counted using the featureCounts package and a matrix of read counts was generated.
Genome_build: mm10
Supplementary_files_format_and_content: read counts matrix

source_name: C3H10T1/2 MSCs

growth_protocol: C3H10T1/2 cells  were cultured in Modified Eagle’s Medium (MEM) supplemented with 10% FBS, 1% non-essential amino acids, L-glutamine and sodium pyruvate.

extract_protocol:
Total RNA was extracted with Trizol.
Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v.2 (cat. no. RS-122-2001, RS-122-2002) (Illumina)

treatment_protocol: The cells were transfected with control siRNA or siRNA of DNA methyltransferase 1(DNMT1) for 48h, and induced for OB differentiation or left untreated. For OB induction, cells were maintained in complete medium supplemented with 50 μM L-ascorbic acid, 10 mM β-glycerophosphate, 10-3 μM dexamethasone, and 1% penicillin-streptomycin for 3 days.

tag: cell line

value: C3H10T1/2 MSCs

value: mesenchymal stem cells

value: transfeted with DNMT1 siRNA


title: siDNMT1_OB [RNA-seq]

value: transfeted with DNMT1 siRNA, followed by OB induction


title: control [RRBS]

data_processing:
Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.
The library preparations were sequenced on an Illumina Hiseq 2500/4000 or Novaseq platform and 125bp/150bp paired-end reads were generated.
Image analysis and base calling were performed with Illumina CASAVA pipeline, and finally 125bp/150bp paired-end reads were generated.
After filtering the raw reads with Trimmomatic (Version 0.36), bisulfite-treated reads were aligned to the mm10 reference genome with the Bismark software (version 0.16.3).
Differentially methylated regions (DMRs) were then identified using the DSS software.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation level at regions

extract_protocol:
A total amount of 5.2 μg genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions.
DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X).

value: transfeted with control siRNA


title: 16D_EZH2-350A_RNAseq

value: CRPC (16D)

value: Prostate adeno

value: 16D cells with CRISPR-mediated EZH2 knockout, stably expressing EZH2-T350A mutant


title: siDNMT1_OB [RRBS]


title: siDNMT1 [RRBS]


title: Dis3l2 P4 cKO3

city: Bethesda

first: Zhengpin

last: Wang

state: MD

address: National Institutes of Health, 9000 Rockville Pike

department: Laboratory of Cellular and Developmental Biology

institute: NIDDK, NIH

data_processing:
removing adapter sequences with cutadapt
aligning the reads with hisat2 against Mus musculus
using featurecounts to estimate the number of gene reads
using a R script to perform differential expression analysis
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: featurecounts output  and fastq files

molecule: polyA RNA

source_name: P4 Testis

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testes isolated from P4 aged control and knockout mice.

extract_protocol:
Testess were isolated, total RNA was isolated using a RNeasy Micro Kit.
The libraries were constructed by using a Universal RNA-Seq Library Preparation Kit (TECAN) per the manufacturer’s protocol in which double-strand cDNA was generated using a mixture of random and poly(T) priming, followed by fragmentation of double-stranded cDNA, end repair, adaptor ligation, strand selection, targeted transcript depletion with AnyDeplete, and PCR amplification to produce the final library.

tag: strain

value: B6D2F1 inbred

value: Testis

value: Dis3l2 cKO

tag: age

value: postnatal day 4 (P4)


title: OB [RNA-seq]

tag: cell type

value: transfeted with control siRNA, followed by OB induction


title: control [RNA-seq]


title: Dis3l2 P4 cKO2


title: Dis3l2 P4 WT3

value: Dis3l2 WT


title: Dis3l2 P4 cKO1


title: Dis3l2 P4 WT2


title: Dis3l2 P4 WT1


title: mouse-male-young-qNSC-rep1

city: Houston

first: Weiwei

last: Dang

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low quality reads using Trim Galore version 0.4.4 with default parameters.
Reads were aligned to the hg19/mm10  genome assembly using using HISAT2 version 2.1.0 with default parameters.
Transcript-level read count, and subsequent FPKM and TPM measurements, were performed using salmon version 1.0.0
Genome_build: hg19 for human and mm10 for mouse
Supplementary_files_format_and_content: read counts file generated by salmon

source_name: neural stem cells

growth_protocol: Human cord blood mesenchymal stem cells (hMSCs) were purchased from ATCC (PCS-500-010, lot #63216949). Cells were grown in low glucose DMEM (Life Technologies 11885-084) supplemented with 10% FBS (Life Technologies 16000-044, lot #1314735) and 1× penicillin/streptomycin (Life Technologies 15140-122) at 37ºC with 5% CO2 and 3% O2. Medium was replaced every 4 days in the absence of passaging. Cells were grown to ~70% confluence and split 1:4 as needed. Cell density was below the concentration needed for reliable detection with a hemocytometer (105 cells/mL), so the growth curve was estimated as 2 population doublings per passage.

extract_protocol:
Total RNA was extracted from PD12 and PD32 hMSCs using the RNEasy Mini Kit (Qiagen 74104) following the manufacturer’s protocol, including the optional DNase treatment. 100ng of total RNA was depleted of rRNA (NEB, E6310) following the manufacturer’s protocol;NSCs were isolated by FACS using the surface markers prominin-1 (CD133) and the EGF receptor, and GFAP-GFP fluorescence. For sorting, cells were stained with 1:300 EGF-Alexa 647 (Molecular probes, E-35351), and 1:400 Prominin-1-biotin (eBioscience, 13-1331-80). Dead cells were excluded using propidium iodide and cells were sorted on a BD FACS Aria into PBS. aNSCs and qNSCs can be distinguished by the surface expression of EGFR. Using this scheme, aNSC are prominin-1+; GFP+; EGFR+ and qNSC are prominin-1+; GFP+; EGFR-. We performed this experiment in biological triplicate, generating each RNA-seq library from a single animal, using ~400 cells per library.
hMSC rRNA-depleted RNA was used as the template for a stranded RNA-seq library using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760) following the manufacturer’s protocol. mNSC RNA-seq libraries were generated by GENEWIZ LLC. using the SMART-Seq v4 Ultra Low Input RNA Kit for cDNA synthesis and the Nextera XT DNA Library Preparation Kit.

treatment_protocol: human MSC were cultured to PD12 and PD32. Activated and quiescent NSCs (aNSC and qNSC, respectively) were freshly isolated from the subventricular zone of adult (~7 month) and aged (19-21 month) hGFAP-GFP transgenic mice according to established methods (Leeman, D. S. et al. Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging. Science (80-. ). 359, 1277–1283 (2018)).

value: quiescent neural stem cells

tag: cell passage/age

value: 7 month

value: hGFAP-GFP transgenic


title: mouse-male-young-aNSC-rep1

value: activated neural stem cells


title: mouse-male-old-qNSC-rep1

value: 19-21 month


title: mouse-female-young-qNSC-rep2


title: mouse-male-old-aNSC-rep1


title: OB [RRBS]

value: C3H10T1/2 MSCs

value: mesenchymal stem cells


title: mouse-female-old-aNSC-rep1


title: mouse-female-young-aNSC-rep1


title: mouse-female-old-qNSC-rep2


title: mouse-female-young-qNSC-rep1


title: mouse-female-old-qNSC-rep1


title: mouse-female-old-aNSC-rep2


title: B2_16 month old C57BL/6

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with CASAVA (version 1.8.2)
STAR version 2.3.0e_r291 was used to align the reads to the mm10 genome
featureCounts version 1.5.0-p1 was used to quantify reads for genes in mm10 version 84
Genome_build: mm10 gene version 84
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: whole cortical tissue of 16 months old C57BL/6 mouse

growth_protocol: 3 month and 16 month old mice were housed under 12 h  light/dark conditions with ad libitum access to food and water. All animal procedures were performed in strict  compliance with the EU directives 86/609/EWG and  2007/526/EG guidelines for animal experiments and were  approved by the local government (Thueringer Landesamt,  Bad Langensalza, Germany).

extract_protocol:
Mice were deeply anesthetized by intraperitoneal injection of 50% chloral hydrate in PBS (pH 7.4; 2.5 mg chloral hydrate per g body weight). Adult cortical hemispheres were dissected from whole brain and frozen in liquid nitrogen. Samples were subjected to standard RNA isolation procedure using Trizol Reagent (Life Technologies, United States).
The TruSeq RNA Sample Preparation Kit (Illumina, Cat. No RS-122-2002, United States) was used for library preparation (1 mg total RNA), the QuantiFluorTM dsDNA System (Promega, United States) for quantitation and the DNA 1000 chip on the Bioanalyzer 2100 (Agilent Technologies) to determine the size range of final cDNA libraries prior to amplification and sequencing (cBot and HiSeq2000 from Illumina; PE; 2 100 bp; ca. 30 million reads per sample).

value: 16 month

value: brain

tag: region

value: cortex


title: A2_6 month old C57BL/6

source_name: whole cortical tissue of 6 months old C57BL/6 mouse

value: 6 month


title: A1_6 month old C57BL/6


title: B1_16 month old C57BL/6


title: mouse-female-young-aNSC-rep2

tag: treatment


title: In vitro transcribed pri-miR-143/145 (A) digested with RNAseI

city: Brescia

first: Leonardo

last: Elia

state: Brescia

address: v.le Europa 11

department: Dipartimento di Medicina Molecolare e Traslazionale

country: Italy

institute: Università degli Studi di Brescia

data_processing:
Fastq files were generated using bcl2fastq v2.19.0.316 with --no-lane-splitting option
The raw reads were  trimmed with cutadapt  v1.18 with parameters -m 15 -u 3 -a AAAAAAAAAA
The reads of WT sample were aligned to pri-miR-143/145 sequence and the reads of SNP sample to pri-miR-143/145 sequence with rs41291957 polimorphsim using bowtie v1.2.3 with default options
The reference sequence were divided into 50 bp bins and the reads mapped inside the bins have been counted, assigning the reads to the bin on which they overlap for more than 50% of their length using BEDTools v2.29.0 with command bedtools coverage with -f 0.51 option
The count of the mapped reads in each bin has been converted to a relative percentage of the total number of the reads mapped on the sample reference sequence
For the analysis of the distribution of the lengths of the reads, the duplicated reads were removed from bam files, resulting from sequence alignment, using  samtools rmdup command of SAMtools package v1.6
Genome_build: pri-miR-143/145, pri-miR-143/145 sequence with rs41291957 polimorphsim
Supplementary_files_format_and_content: tab-delimited text files with numbers of mapped reads for each bin expressed as raw count and relative percentages
Supplementary_files_format_and_content: tab-delimited text files with the raw count for each length of dereplicated reads present in the samples

molecule: other

source_name: In vitro transcribed pri-miR-143/145

extract_protocol:
Digested RNAs were purifiied with DirectzolT RNA Miniprep (ZymoResearch # ZYR2052)
The libraries were prepared with the SMARTer smRNA-Seq Kit for Illumina (Takara, Ca# 635031) and sequenced on the Illumina Next Seq550 platform

treatment_protocol: In vitro transcribed and folded pri-miRs were digested with RNAseI for 30 minutes

value: in vitro transcribed RNA

value: RNAsel


title: In vitro transcribed pri-miR-143/145 (G) digested with RNAseI

value: wild type


title: A3_6 month old C57BL/6


title: PI_mouse

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie version 2 (Langmead and Salzberg 2012). Only reads that aligned concordantly exactly one time were passed to further analysis.
After alignment, read duplicates were removed using Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). Also, peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version) (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Peak calling was performed using MACS version 2 against preimmune control (Zhang et al. 2008) in paired-end mode (option format=BAMPE).
Peaks with p value less than 1x10-2 were passed to the IDR pipeline to access reproducibility of chip-seq replicates (https://sites.google.com/site/anshulkundaje/projects/idr).
Optimal set of reproduced peaks (IDR p value was set to 0.05 for true replicates and 0.01 for pseudoreplicates) was chosen for each sample and passed to further analysis.
Chip-seq coverage tracks (BedGraph) were obtained using deepTools (Ramírez et al. 2014) bamCoverage function with bin width 100 bp and RPKM normalization.
Genome_build: dm6
Supplementary_files_format_and_content: Processed data was obtained by IDR and deeptools bamCoverage and includes: extended bed (narrowPeak) peak calls regions and coverage (bedGraph)

organism: Drosophila melanogaster

source_name: whole organism

growth_protocol: Wild-type Drosophila melanogaster (Oregon R) flies were grown in population cages at 25 degrees. 2 g of 2-3 day adult flies were frozen in liquid nitrogen.

extract_protocol:
Dynabeads were resuspended in TE with 0.5% SDS, treated with RNase A for 30 min and protease K overnight, incubated at 65 degrees for 6 hours and extracted on columns (ChIP ZymoResearch).
Libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Custom-made indexed adapters were ligated, after which the material was size selected at ~200-600 bp with Ampure XP beads (Beckman Coulter). PCR amplification was performed using PE1.0 and PE2.0 primers (custom-made) for 12 cycles for Input samples and 14 to 15 cycles for IP-ed samples using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). The libraries were sequenced on a HiSeq 2000 (Illumina) in single end mode.

treatment_protocol: Approximately 2g of Drosophila adult flies were resuspended in 15ml ice-cold 0.1% Triton X-100 in PBS with protease inhibitors (PIs) and dounced 20x with loose pestle on ice, followed by centrifugation at 400g for 1min at 4 degrees. The supernatant was transferred to a fresh tube and centrifuged at 1100g for 10min at 4 degrees. The pellet was resuspended in 15ml ice-cold Cell lysis buffer with PIs (5 mM HEPES pH 8.0, 85 mM KCl, 0.5% NP40) and dounced 20x with tight pestle. Two equal aliquots were transferred into 15ml falcon tubes and centrifuged at 2000g for 4min at 4 degrees. The pellets consisting of nuclei were resuspended in 1ml of ice-cold Nuclear Lysis Buffer with PIs (50 mM HEPES pH 8.0, 10 mM EDTA, 0.5% N-laurylsarcosine) and incubated for 20min at RT. 1ml ice-cold Nuclear Lysis Buffer with PIs was added to each tube and sonicated using Covaris. Chromatin was then transferred to 1.5 ml-eppendorf tubes and centrifuged at 14000 rpm for 10 min at 4 degrs. Finally, supernatants were pooled, aliquoted and frozen in liquid nitrogen. Chromatin (50 ug of DNA) was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF) and incubated with anti-HA, anti-dCTCF, anti-CP190 antibodies, rat and mouse  IgG at 4 degrees on a rotary shaker overnight. The antibody/antigen complexes were precipitated with 20 ul protein G Dynabeads at 4 degrees for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with 500 mM NaCl.

tag: antibody source

value: mouse

value: Oregon-R

value: wt


title: CP190_dCTCF_wt, rep2

description:
CP190_dCTCF_wt_100_RPKM.bedGraph
CP190_dCTCF_wt_vs_PI_mouse.narrowPeak

tag: development stage

value: adult

value: dCTCFwt


title: B3_16 month old C57BL/6


title: PI_rat

value: rat


title: CP190_dCTCF_delta, rep2

description:
CP190_dCTCF_delta_100_RPKM.bedGraph
CP190_dCTCF_delta_vs_PI_mouse.narrowPeak


title: dCTCF_dCTCF_wt, rep2

description:
dCTCF_dCTCF_wt_100_RPKM.bedGraph
dCTCF_dCTCF_wt_vs_PI_rat.narrowPeak


title: CP190_dCTCF_delta, rep1


title: dCTCF_dCTCF_delta, rep2

description:
dCTCF_dCTCF_delta_100_RPKM.bedGraph
dCTCF_dCTCF_delta_vs_PI_rat.narrowPeak


title: HA_dCTCF_wt, rep1

description:
HA_dCTCF_wt_100_RPKM.bedGraph
HA_dCTCF_wt_vs_PI_mouse.narrowPeak


title: dCTCF_dCTCF_delta, rep1


title: HA_dCTCF_wt, rep2


title: HA_dCTCF_delta, rep1

description:
HA_dCTCF_delta_100_RPKM.bedGraph
HA_dCTCF_delta_vs_PI_mouse.narrowPeak


title: HA_dCTCF_delta, rep2


title: 42F_rep1_RNAseq

value: Prostate cancer cell line 42F

value: ENZ-resistant CRPC-NE


title: KO_Male_2hr_3

city: Detroit

first: Ekta

middle: J

state: Michigan

address: 275 E.  Hancock

institute: Wayne State University

data_processing:
After de-multiplexing with Illumina’s CASAVA 1.8.2 software, the 50 bp reads were aligned to the Drosophila genome (Build dm3) with STAR_2.4 and tabulated for each gene region.
Differential gene expression analysis was used to compare transcriptome changes between conditions using edgeR v.3.22.3 and transcripts were defined  as significantly differentially expressed at absolute Log2 fold change >1, FDR <0.05
Genome_build: Dm3

source_name: Brain

extract_protocol:
Direct-zol RNA MicroPrep kit
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (low-input protocol and 15 ng RNA input)

value: Tau-KO

tag: Sex

value: Male

value: Brain


title: KO_Male_4hr_2


title: KO_Male_4hr_1


title: KO_Male_2hr_2


title: KO_Male_2hr_1


title: KO_Male_4hr_3


title: KO_Male_Ctrl_3


title: KO_Male_1hr_2


title: KO_Male_1hr_1


title: KO_Male_Ctrl_2


title: KO_Male_Ctrl_1


title: CP190_dCTCF_wt, rep1


title: KO_Female_4hr_2

value: Female


title: dCTCF_dCTCF_wt, rep1

description:
dCTCF_dCTCF_wt_100_RPKM.BedGraph
dCTCF_dCTCF_wt_vs_PI_rat.narrowPeak


title: KO_Male_1hr_3


title: KO_Female_4hr_3


title: KO_Female_4hr_1


title: KO_Female_2hr_1


title: KO_Female_2hr_2


title: KO_Female_2hr_3


title: KO_Female_1hr_3


title: KO_Female_Ctrl_2


title: KO_Female_1hr_1


title: KO_Female_Ctrl_3


title: HPC-5

city: Guilin

first: Xiaoli

last: Yang

state: Guangxi

address: Zhiyuan Road

institute: Guilin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hepatocellular carcinma cells

extract_protocol:
Total RNA was extracted using Trizol Reagent from the cells.Sequencing libraries were generated using NEBNext ® Ultra™ RNA Library Prep Kit for Illumina ® (#E7530L, NEB, USA) according to manufacturer’s instructions. Following analysis of the library, RNA sequencing was completed using the Illumina Hi Seq X Ten sequencing platform, and paired-end sequence reads were obtained.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Huh7 hepatocellular carcinma cells

value: silence


title: HPC-4


title: HPC-3

value: control


title: HPC-2


title: F2-input

city: Shanghai

first: Wangsheng

state: Please Select

address: 845 Lingshan Rd.

institute: Shanghai Jiao Tong University

data_processing:
Raw sequence reads were initially processed by FastQC for quality control, and adapter sequences and poor-quality reads were removed
Quality filtered reads were then mapped to reference genome using Bowtie2, and only mapped reads were kept
Sam files were converted to Bam format using Samtools for peak calling
MACS2  was used to call peaks with the sonicated input as a control and an initial threshold p-value of 0.01 as cut off.
The binding sites were annotated in terms of genomic annotations using the ‘‘annotatePeaks.pl’’ script supplied by Homer2
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig files were generated using deeptools; Scores represent peak values
Supplementary_files_format_and_content: peak text files

source_name: amnion fibroblasts

extract_protocol:
Lysates were clarified from sonicated nuclei and protien-DNA complexes were isolated with CEBPδ antibody.
5 ng of purified ChIP DNA were used to generate the sequencing library using a NEB kit

treatment_protocol: treated with cortisol for 12 hours

value: fibroblasts

value: treated with cortisol for 12 hours

tag: chip antibody

value: amnion


title: F1-input


title: F3-input


title: C2-input

value: untreated


title: C1-input


title: F2

value: CEBPdelta (GeneTex, GTX115047)


title: C3-input


title: F1


title: C3


title: normal snRNA-seq of mouse hippocampus (n=1 PBS and n=1 KA treated mice, pooled)

description:
single nucleus polyA RNA transcriptome;
Mouse hippocampus nuclei from PBS (n=1) and kainic acid (KA; n=1) treated mice. One PBS and one KA were pooled as a single batch (with two total batches) using nucleus-hashing antibodies, loaded on a single 10x channel, and computationally demultiplexed as PBS vs. KA with DemuxEM

data_processing:
Raw bcl files were converted to fastq, and aligned to either hg19_premrna or mm10_premrna genomes using cellranger v4.0.0 running on Cumulus version 1.0
Genome_build: hg19_premrna or mm10_premrna
Supplementary_files_format_and_content: csv files for gene expression, nucleus hashtag HTO counts, protein ADT counts, and pooled batches (if applicable). Load as anndata object.

source_name: normal snRNA-seq of mouse hippocampus

extract_protocol:
nuclei extraction with EZ prep
3' polyA RNA seq; 10X Genomics Chromium Prep V3 3'

treatment_protocol: 8-week-old male mice were acclimated into the procedure room for 1hr, then injected intraperotineally with PBS or 20 mg/kg kainic acid dissolved in PBS. After 2 hrs, mice were euthanized by CO2 and perfused through the left ventricle of the heart with 20mL PBS. The entire brain was removed, and the hippocampus was dissected on ice before freezing on dry ice. Nuclei extracted from one PBS and one KA treated mice were pooled together with nucleus-hashing antibodies.

tag: tissue/cell type

value: Adult mouse hippocampus


title: C2


title: F3


title: KO_Female_1hr_2


title: 68R-EM

city: College Station

first: Michael

last: Golding

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

data_processing:
Galaxy version 21.05.1.dev0, commit 55a261f0dfa2fdac4e78959f70bdbbca471ac679
trimmed Illumina adapters with Trimmomatic
mapped trimmed seq files to genome with RNA STAR
measured gene expression with featureCounts
differential analysis with DESeq2
Genome_build: mm39.fa
Supplementary_files_format_and_content: tabular

source_name: Male Fetal Placenta_ethanol

extract_protocol:
GD 16.5 Male Fetal Placentas were removed from gestational sac and fetus with forceps and surgical scissors, divided in half with surgical razor blades, and snap frozen on dry ice, stored in -80 C, and thawed for RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sexually mature C57BL/6J male sires voluntarily consumed alcohol for 6+ weeks and mated naive CD-1 or B6J females

value: Ethanol

value: C57BL/6J x CD-1

value: Male Fetal Placenta


title: 84R-EM


title: C1


title: 20R-EM


title: HPC-6


title: KO_Female_Ctrl_1


title: 77R-EM


title: 66R-CM

source_name: Male Fetal Placenta_control

value: Control


title: 44R-CM


title: 62R-CM


title: 32R-CM


title: HPC-1


title: TLR4_KO_TGF-ß-2

city: Manhasset

first: Siavash

last: Bolourani

state: NY

address: 350 Community Dr

department: Molecular Medicine

institute: Feinstein Institutes for Medical Research

data_processing:
FastQC was used to insure there was no adapter contamination and reads had acceptable quality scores.
Sequenced reads were aligned using STAR2 with the ENCODE options to the mouse GENCODE NCBIM37 assembly.
The counts per gene were obtained using ht-seq counts in reverse stranded mode to the GENCODE annotation.
The mRNA sequencing raw counts were obtained using ht-seq counts
Genome_build: NCBIM37
Supplementary_files_format_and_content: Raw counts represented

source_name: Pulmonary Fibroblasts

growth_protocol: The lungs of 4-8-week-old WT and TLR4-/- mice were explanted, and each group of pulmonary fibroblasts was isolated from a pool of 3-4 lungs. The isolated fibroblasts were then cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS, MP Biomedicals), 2% penicillin-streptomycin, and L-glutamine (Gibco, ThermoFisher Scientific). At passages 3-6, the cultured medium was replaced with reduced serum media Opti-MEM

extract_protocol:
RNA was isolated using Ambion’s mirVana kit (catalog #AM1561, Thermo Fisher) following the manufacturer’s recommendations, and quantified on a Nanodrop 2000 (catalog # ND-2000, Thermo Fisher). All samples had 260/280 and 260/230 ratios between 1.8 and 2.1. RNA quality was further assessed with an RNA Nano Chip using a Bioanalyzer 2100 (Agilent). All samples had a RIN number of 8 or higher.
Illumina TruSeq Stranded Total RNA Library Prep Kit (catalog # RS-122-2203, Illumina Inc). The mRNA expression was obtained by RNA-Seq libraries run on NextSeq 550 following the manufacturer’s instructions.

treatment_protocol: After incubation overnight in Opti-MEM, the pulmonary fibroblasts were treated with phosphate-buffered saline (PBS), 1 μg/mL recombinant mouse (rm) CIRP, 2 ng/mL rmTGF-β1 (R&D Systems), or rmCIRP plus rmTGF-β1. The rmCIRP was produced in our lab, as previously described (1). The cell lysates collected at 24 hours were used for high throughput mRNA sequencing

value: lung

value: Fibroblasts


title: TLR4_KO_CIRP_TGF-ß-2

value: rmCIRP + rmTGF-Beta1


title: TLR4_KO_TGF-ß-3


title: TLR4_KO_CIRP_TGF-ß-3


title: TLR4_KO_CIRP_TGF-ß-1


title: TLR4_KO_TGF-ß-1


title: TLR4_KO_CIRP-3

value: rmCIRP


title: TLR4_KO_PBS-3

value: PBS


title: TLR4_KO_PBS-1


title: TLR4_KO_CIRP-1


title: WT_CIRP_TGF-ß-3

value: Wild Type


title: WT_CIRP_TGF-ß-1


title: WT_TGF-ß-2


title: TLR4_KO_PBS-2


title: WT_CIRP_TGF-ß-2


title: WT_PBS-3


title: WT_CIRP-1


title: WT_CIRP-2


title: WT_CIRP-3


title: WT_TGF-ß-3


title: WT_PBS-2


title: WT_PBS-1


title: WT_TGF-ß-1


title: RNA-seq_mouse_EBs_del-cIDR_clone72_rep2

city: Charlottesville

first: Bi

address: 1340 JPA Pinn Hall Room 6017

institute: University of Virginia

data_processing:
RNA-seq reads were aligned to the human genome assembly GRCH38/hg38 or mouse genome assembly GRCm38/mm10 using STAR. RNA-seq counts were annotated using RSEM. Differentially expressed genes were calculated using DESeq2.
ChIP-seq and PRO-seq sequence reads were aligned to the human genome assembly GRCH38/hg38 using BWA. Sam files were converted into bam files using Samtools. MACS2 was used to call peaks under the FDR threshold of 0.01.
H3K4me3/H3K27ac HiChIP data were performed with MAPS.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Peak file, loop bedpe or gene count

source_name: Mouse embryoid body cells

extract_protocol:
For Chip-seq, genomic DNA were pulled down by antibodies. For RNA-seq, RNA was extracted with Qiagen miRNA-ease RNA extraction kit. HICHIP DNA was collected with Arima HICHIP kit.
For ChIP-seq and HICHIP, library preparation using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. For RNA-seq, NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina was used for library prepapration.
Library quality was assessed by Tapstation and Qubit concentration measurement.

value: Cultured mouse embryoid body cells


title: RNA-seq_mouse_EBs_del-cIDR_clone3_rep1


title: RNA-seq_mouse_EBs_del-cIDR_clone72_rep1


title: RNA-seq_mouse_EBs_del-cIDR_clone3_rep2


title: RNA-seq_mouse_EBs_UTX-KO_rep2


title: RNA-seq_mouse_EBs_UTX-KO_rep1


title: RNA-seq_mouse_EBs_WT_rep1


title: RNA-seq_mouse_ESCs_del-cIDR_clone72

source_name: Mouse ES cells

value: Cultured mouse ES cells


title: RNA-seq_mouse_ESCs_del-cIDR_clone3


title: RNA-seq_mouse_ESCs_WT


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_219

city: New York

first: Johanne

last: Jacobsen

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Raw FASTQ sequence files generated from Smartseq2 libraries were aligned to the mouse genome (v. mm10) with the annotated transcriptome (v. gencode M22) using STAR (v. 2.6). Subsequently, genome-mapped BAM files were processed using RSEM (v. 1.3.1) for gene quantification. The matrix of gene counts was used as input for analysis using the R package Seurat (v. 3.1.4.). To control unwanted sources of experimental variation, we eliminated any experiment-specific variables by regressing out the batch effect factors as described. Additionally, cells containing more than 10% of sequence reads aligned to mitochondrial genes were excluded before normalization.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contains RSEM results for each cell.

source_name: Germinal Centers

extract_protocol:
Single T cells were index-sorted into 96-well PCR plates containing 5 μl of TCL buffer (Qiagen) with 1% β-mercaptoethanol.
SmartSeq2: Libraries were prepared as previously described (Trombetta et al., 2014). Briefly, nucleic acids were extracted from sorted single cell using RNAClean XP SPRI beads (Beckman Coulter), and RNA was hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) then reverse-transcribed into cDNA using TSO primer (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG) and RT maxima reverse transcriptase (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (AAGCAGTGGTATCAACGCAGAGT) and KAPA HiFi HotStart ReadyMix (Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina). For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A-D (Illumina). Finally, dual-barcoded libraries were pooled and sequenced using the Illumina Nextseq 500.

tag: sequencing plate

value: OT-II CD4-Cre-ERT2 Rosa26Foxp3

tag: experiment

tag: cell annotation


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_217


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_216


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_213


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_214


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_215


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_211


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_209


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_218


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_212


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_208


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_207


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_204


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_203


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_201


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_206


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_202


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_200


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_205


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_198


title: RNA-seq_mouse_EBs_WT_rep2

last: Shi


title: RNA-seq_mouse_ESCs_UTX-KO


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_197


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_196


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_195


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_193


title: TLR4_KO_CIRP-2

tag: tissue

tag: genotype


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_210


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_192


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_188


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_187


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_189


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_190


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_186


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_184


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_185


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_183


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_181


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_182


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_175


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_199


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_191


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_180


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_176


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_178


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_179


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_174


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_177


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_194


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_173


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_169


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_170


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_172


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_171


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_165


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_166


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_164


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_163


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_160


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_159


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_156


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_157


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_161


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_158


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_153


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_152


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_149


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_147


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_168


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_146


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_144


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_150


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_148


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_145


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_167


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_141


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_142


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_140


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_139


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_138


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_137


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_162


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_155


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_135


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_154


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_151


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_134


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_133


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_130


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_131


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_128


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_127


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_126


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_125


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_123


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_121


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_122


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_120


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_119


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_118


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_143


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_115


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_117


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_116


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_124


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_114


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_136


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_113


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_112


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_111


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_110


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_129


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_108


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_107


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_109


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_132


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_106


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_102


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_104


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_103


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_105


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_101


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_99


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_95


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_97


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_96


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_93


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_91


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_92


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_98


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_90


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_88


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_87


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_89


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_86


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_85


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_83


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_84


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_82


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_81


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_79


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_80


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_77


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_100


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_74


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_73


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_72


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_94


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_71


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_68


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_70


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_67


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_66


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_65


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_63


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_64


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_62


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_60


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_56


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_57


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_55


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_76


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_53


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_54


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_51


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_75


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_52


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_58


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_50


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_61


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_59


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_49


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_47


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_45


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_46


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_69


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_43


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_44


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_39


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_41


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_38


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_42


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_40


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_37


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_36


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_35


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_48


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_30


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_28


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_31


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_29


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_23


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_18


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_27


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_26


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_25


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_33


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_20


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_19


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_16


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_32


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_34


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_21


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_24


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_10


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_13


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_11


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_9


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_7


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_17


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_8


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_15


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_14


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_12


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_22


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_78


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_6


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_4


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_3


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_1


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_5


title: OT-II CD4-Cre-ERT2 Rosa26Foxp3_2


title: PA-GFP Foxp3IRES-RFP_1243

value: PA-GFP Foxp3IRES-RFP

value: Filtered cell


title: PA-GFP Foxp3IRES-RFP_1242


title: PA-GFP Foxp3IRES-RFP_1238


title: PA-GFP Foxp3IRES-RFP_1241


title: PA-GFP Foxp3IRES-RFP_1240


title: PA-GFP Foxp3IRES-RFP_1235


title: PA-GFP Foxp3IRES-RFP_1236


title: PA-GFP Foxp3IRES-RFP_1233


title: PA-GFP Foxp3IRES-RFP_1237

value: Tfr


title: PA-GFP Foxp3IRES-RFP_1234


title: PA-GFP Foxp3IRES-RFP_1228

value: CD4+ Resting


title: PA-GFP Foxp3IRES-RFP_1230


title: PA-GFP Foxp3IRES-RFP_1232


title: PA-GFP Foxp3IRES-RFP_1227


title: PA-GFP Foxp3IRES-RFP_1225


title: PA-GFP Foxp3IRES-RFP_1231


title: PA-GFP Foxp3IRES-RFP_1226


title: PA-GFP Foxp3IRES-RFP_1223


title: PA-GFP Foxp3IRES-RFP_1229


title: PA-GFP Foxp3IRES-RFP_1224


title: PA-GFP Foxp3IRES-RFP_1244


title: PA-GFP Foxp3IRES-RFP_1222


title: PA-GFP Foxp3IRES-RFP_1221


title: PA-GFP Foxp3IRES-RFP_1239


title: PA-GFP Foxp3IRES-RFP_1217


title: PA-GFP Foxp3IRES-RFP_1216


title: PA-GFP Foxp3IRES-RFP_1219


title: PA-GFP Foxp3IRES-RFP_1220


title: PA-GFP Foxp3IRES-RFP_1218

value: Cycling


title: PA-GFP Foxp3IRES-RFP_1215


title: PA-GFP Foxp3IRES-RFP_1214


title: PA-GFP Foxp3IRES-RFP_1212


title: PA-GFP Foxp3IRES-RFP_1213


title: PA-GFP Foxp3IRES-RFP_1210


title: PA-GFP Foxp3IRES-RFP_1211


title: PA-GFP Foxp3IRES-RFP_1207


title: PA-GFP Foxp3IRES-RFP_1205


title: PA-GFP Foxp3IRES-RFP_1208


title: PA-GFP Foxp3IRES-RFP_1209


title: PA-GFP Foxp3IRES-RFP_1202


title: PA-GFP Foxp3IRES-RFP_1201


title: PA-GFP Foxp3IRES-RFP_1204


title: PA-GFP Foxp3IRES-RFP_1200


title: PA-GFP Foxp3IRES-RFP_1199


title: PA-GFP Foxp3IRES-RFP_1196


title: PA-GFP Foxp3IRES-RFP_1195


title: PA-GFP Foxp3IRES-RFP_1192


title: PA-GFP Foxp3IRES-RFP_1194


title: PA-GFP Foxp3IRES-RFP_1193


title: PA-GFP Foxp3IRES-RFP_1191


title: PA-GFP Foxp3IRES-RFP_1190


title: PA-GFP Foxp3IRES-RFP_1185


title: PA-GFP Foxp3IRES-RFP_1184


title: PA-GFP Foxp3IRES-RFP_1206


title: PA-GFP Foxp3IRES-RFP_1186


title: PA-GFP Foxp3IRES-RFP_1189


title: PA-GFP Foxp3IRES-RFP_1188


title: PA-GFP Foxp3IRES-RFP_1187


title: PA-GFP Foxp3IRES-RFP_1181


title: PA-GFP Foxp3IRES-RFP_1182


title: PA-GFP Foxp3IRES-RFP_1180


title: PA-GFP Foxp3IRES-RFP_1203


title: PA-GFP Foxp3IRES-RFP_1179


title: PA-GFP Foxp3IRES-RFP_1178


title: PA-GFP Foxp3IRES-RFP_1176


title: PA-GFP Foxp3IRES-RFP_1174


title: PA-GFP Foxp3IRES-RFP_1197


title: PA-GFP Foxp3IRES-RFP_1173


title: PA-GFP Foxp3IRES-RFP_1198


title: PA-GFP Foxp3IRES-RFP_1171


title: PA-GFP Foxp3IRES-RFP_1170


title: PA-GFP Foxp3IRES-RFP_1183


title: PA-GFP Foxp3IRES-RFP_1172


title: PA-GFP Foxp3IRES-RFP_1177


title: PA-GFP Foxp3IRES-RFP_1169


title: PA-GFP Foxp3IRES-RFP_1175


title: PA-GFP Foxp3IRES-RFP_1168


title: PA-GFP Foxp3IRES-RFP_1167


title: PA-GFP Foxp3IRES-RFP_1166


title: PA-GFP Foxp3IRES-RFP_1165


title: PA-GFP Foxp3IRES-RFP_1164


title: PA-GFP Foxp3IRES-RFP_1160


title: PA-GFP Foxp3IRES-RFP_1159


title: PA-GFP Foxp3IRES-RFP_1163


title: PA-GFP Foxp3IRES-RFP_1162


title: PA-GFP Foxp3IRES-RFP_1161


title: PA-GFP Foxp3IRES-RFP_1158


title: PA-GFP Foxp3IRES-RFP_1157


title: PA-GFP Foxp3IRES-RFP_1154


title: PA-GFP Foxp3IRES-RFP_1156


title: PA-GFP Foxp3IRES-RFP_1155


title: PA-GFP Foxp3IRES-RFP_1153


title: PA-GFP Foxp3IRES-RFP_1150


title: PA-GFP Foxp3IRES-RFP_1146


title: PA-GFP Foxp3IRES-RFP_1152


title: PA-GFP Foxp3IRES-RFP_1148


title: PA-GFP Foxp3IRES-RFP_1143


title: PA-GFP Foxp3IRES-RFP_1149


title: PA-GFP Foxp3IRES-RFP_1151


title: PA-GFP Foxp3IRES-RFP_1141


title: PA-GFP Foxp3IRES-RFP_1145


title: PA-GFP Foxp3IRES-RFP_1144


title: PA-GFP Foxp3IRES-RFP_1138


title: PA-GFP Foxp3IRES-RFP_1142


title: PA-GFP Foxp3IRES-RFP_1137


title: PA-GFP Foxp3IRES-RFP_1139


title: PA-GFP Foxp3IRES-RFP_1136


title: PA-GFP Foxp3IRES-RFP_1135


title: PA-GFP Foxp3IRES-RFP_1133


title: PA-GFP Foxp3IRES-RFP_1130


title: PA-GFP Foxp3IRES-RFP_1134


title: PA-GFP Foxp3IRES-RFP_1132


title: PA-GFP Foxp3IRES-RFP_1131


title: PA-GFP Foxp3IRES-RFP_1129


title: PA-GFP Foxp3IRES-RFP_1127


title: PA-GFP Foxp3IRES-RFP_1128


title: PA-GFP Foxp3IRES-RFP_1126


title: PA-GFP Foxp3IRES-RFP_1147


title: PA-GFP Foxp3IRES-RFP_1124


title: PA-GFP Foxp3IRES-RFP_1140


title: PA-GFP Foxp3IRES-RFP_1121


title: PA-GFP Foxp3IRES-RFP_1123


title: PA-GFP Foxp3IRES-RFP_1122


title: PA-GFP Foxp3IRES-RFP_1119


title: PA-GFP Foxp3IRES-RFP_1118


title: PA-GFP Foxp3IRES-RFP_1120


title: PA-GFP Foxp3IRES-RFP_1116


title: PA-GFP Foxp3IRES-RFP_1117


title: PA-GFP Foxp3IRES-RFP_1113


title: PA-GFP Foxp3IRES-RFP_1110


title: PA-GFP Foxp3IRES-RFP_1109


title: PA-GFP Foxp3IRES-RFP_1112


title: PA-GFP Foxp3IRES-RFP_1108


title: PA-GFP Foxp3IRES-RFP_1107


title: PA-GFP Foxp3IRES-RFP_1105


title: PA-GFP Foxp3IRES-RFP_1106


title: PA-GFP Foxp3IRES-RFP_1103


title: PA-GFP Foxp3IRES-RFP_1102


title: PA-GFP Foxp3IRES-RFP_1104


title: PA-GFP Foxp3IRES-RFP_1125


title: PA-GFP Foxp3IRES-RFP_1099


title: PA-GFP Foxp3IRES-RFP_1101


title: PA-GFP Foxp3IRES-RFP_1100


title: PA-GFP Foxp3IRES-RFP_1098


title: PA-GFP Foxp3IRES-RFP_1115


title: PA-GFP Foxp3IRES-RFP_1097


title: PA-GFP Foxp3IRES-RFP_1095


title: PA-GFP Foxp3IRES-RFP_1096


title: PA-GFP Foxp3IRES-RFP_1114


title: PA-GFP Foxp3IRES-RFP_1088


title: PA-GFP Foxp3IRES-RFP_1089


title: PA-GFP Foxp3IRES-RFP_1093


title: PA-GFP Foxp3IRES-RFP_1091


title: PA-GFP Foxp3IRES-RFP_1087


title: PA-GFP Foxp3IRES-RFP_1092


title: PA-GFP Foxp3IRES-RFP_1090


title: PA-GFP Foxp3IRES-RFP_1094


title: PA-GFP Foxp3IRES-RFP_1111


title: PA-GFP Foxp3IRES-RFP_1083


title: PA-GFP Foxp3IRES-RFP_1085


title: PA-GFP Foxp3IRES-RFP_1081


title: PA-GFP Foxp3IRES-RFP_1086


title: PA-GFP Foxp3IRES-RFP_1082


title: PA-GFP Foxp3IRES-RFP_1080


title: PA-GFP Foxp3IRES-RFP_1079


title: PA-GFP Foxp3IRES-RFP_1075


title: PA-GFP Foxp3IRES-RFP_1078


title: PA-GFP Foxp3IRES-RFP_1073


title: PA-GFP Foxp3IRES-RFP_1072


title: PA-GFP Foxp3IRES-RFP_1071


title: PA-GFP Foxp3IRES-RFP_1068


title: PA-GFP Foxp3IRES-RFP_1070


title: PA-GFP Foxp3IRES-RFP_1069


title: PA-GFP Foxp3IRES-RFP_1066


title: PA-GFP Foxp3IRES-RFP_1084


title: PA-GFP Foxp3IRES-RFP_1065


title: PA-GFP Foxp3IRES-RFP_1064


title: PA-GFP Foxp3IRES-RFP_1058


title: PA-GFP Foxp3IRES-RFP_1059


title: PA-GFP Foxp3IRES-RFP_1062


title: PA-GFP Foxp3IRES-RFP_1056


title: PA-GFP Foxp3IRES-RFP_1055


title: PA-GFP Foxp3IRES-RFP_1063


title: PA-GFP Foxp3IRES-RFP_1054


title: PA-GFP Foxp3IRES-RFP_1077


title: PA-GFP Foxp3IRES-RFP_1061


title: PA-GFP Foxp3IRES-RFP_1057


title: PA-GFP Foxp3IRES-RFP_1050


title: PA-GFP Foxp3IRES-RFP_1051


title: PA-GFP Foxp3IRES-RFP_1052


title: PA-GFP Foxp3IRES-RFP_1074


title: PA-GFP Foxp3IRES-RFP_1076


title: PA-GFP Foxp3IRES-RFP_1049


title: PA-GFP Foxp3IRES-RFP_1067


title: PA-GFP Foxp3IRES-RFP_1046


title: PA-GFP Foxp3IRES-RFP_1047


title: PA-GFP Foxp3IRES-RFP_1043


title: PA-GFP Foxp3IRES-RFP_1044


title: PA-GFP Foxp3IRES-RFP_1042


title: PA-GFP Foxp3IRES-RFP_1041


title: PA-GFP Foxp3IRES-RFP_1060


title: PA-GFP Foxp3IRES-RFP_1040


title: PA-GFP Foxp3IRES-RFP_1039


title: PA-GFP Foxp3IRES-RFP_1053


title: PA-GFP Foxp3IRES-RFP_1035


title: PA-GFP Foxp3IRES-RFP_1037


title: PA-GFP Foxp3IRES-RFP_1034


title: PA-GFP Foxp3IRES-RFP_1036


title: PA-GFP Foxp3IRES-RFP_1032


title: PA-GFP Foxp3IRES-RFP_1031


title: PA-GFP Foxp3IRES-RFP_1033


title: PA-GFP Foxp3IRES-RFP_1030


title: PA-GFP Foxp3IRES-RFP_1027


title: PA-GFP Foxp3IRES-RFP_1048


title: PA-GFP Foxp3IRES-RFP_1026


title: PA-GFP Foxp3IRES-RFP_1025


title: PA-GFP Foxp3IRES-RFP_1029


title: PA-GFP Foxp3IRES-RFP_1028


title: PA-GFP Foxp3IRES-RFP_1045


title: dsRed Foxp3IRES-GFP_152

value: dsRed Foxp3IRES-GFP


title: dsRed Foxp3IRES-GFP_151


title: PA-GFP Foxp3IRES-RFP_1023


title: PA-GFP Foxp3IRES-RFP_1024


title: PA-GFP Foxp3IRES-RFP_1022


title: dsRed Foxp3IRES-GFP_150


title: dsRed Foxp3IRES-GFP_149


title: dsRed Foxp3IRES-GFP_147


title: dsRed Foxp3IRES-GFP_148


title: dsRed Foxp3IRES-GFP_146


title: PA-GFP Foxp3IRES-RFP_1038


title: dsRed Foxp3IRES-GFP_144


title: dsRed Foxp3IRES-GFP_145


title: dsRed Foxp3IRES-GFP_142


title: dsRed Foxp3IRES-GFP_141


title: dsRed Foxp3IRES-GFP_139


title: dsRed Foxp3IRES-GFP_140


title: dsRed Foxp3IRES-GFP_136


title: dsRed Foxp3IRES-GFP_137


title: dsRed Foxp3IRES-GFP_135


title: dsRed Foxp3IRES-GFP_134


title: dsRed Foxp3IRES-GFP_132


title: dsRed Foxp3IRES-GFP_128


title: dsRed Foxp3IRES-GFP_130


title: dsRed Foxp3IRES-GFP_129


title: dsRed Foxp3IRES-GFP_127


title: dsRed Foxp3IRES-GFP_125


title: dsRed Foxp3IRES-GFP_126


title: dsRed Foxp3IRES-GFP_124