title: Grafted Nude Rat 2

city: La Jolla

first: Samuel

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Human ES-derived NPC samples were aligned to hg19 using STAR with default settings. Rat samples with human grafts were aligned to both human (hg19) and rat (rn5) genomes. Aligned reads were assigned as either rat or human sourced based on their alignment scores to the two genomes. Reads that aligned equally well were discarded as ambiguous.
Human aligned reads and rat aligned reads were converted to wig format via Bedtools. The ‘coverage’ function was called using ‘-split -abam’ flags. Wigs were convered to bigWig format with UCSC tools
Genome_build: hg19 and rn5
Supplementary_files_format_and_content: All processed files are bigWig format. Rat samples have two processed files each: one for the estimated human sourced reads and a second for the estimated rat source reads

organism:
Homo sapiens
Rattus norvegicus

source_name: Rat + Human Graft

extract_protocol:
RNA was isolated from in vitro cultured NPCs or NPC-grafted spinal cord specimens using the miRvana miRNA isolation kit (Ambion AM1560). The protocol for total RNA collection was used.
Paired-end 100 bp or single-end 75 bp RNA sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions

value: spinal cord

tag: graft age

value: 4 weeks post graft

value: H9 ES-derived neural progenitor cell

tag: batch


title: N2_gld-1_elution_cXL

status: Public on Aug 08 2019

type: SRA

city: Berlin

first: Kathrin

last: Theil

address: Hannoversche Str. 28

country: Germany

institute: BIMSB/MDC

library_source: transcriptomic

data_processing:
de-multiplexing (bcl2fastq Conversion Software v2.17.1.14, Illumina)
pseudo-alignment with kallisto (version: 0.43.1; parameters: reads = single end, bootstraps = 100)
Genome_build: C. elegans transcriptome (Caenorhabditis_elegans.WBcel235, Release 81), for pulldown elution samples additionally:  human transcriptome (GENCODE Release 24), if applicable (see description): ERCC spike-in mix 1, transgene sequences (determined by Sanger sequencing)
Supplementary_files_format_and_content: tab-separated text file with five columns: target id, length, effective length, estimated counts, and tpm

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Pulldown elution

extract_protocol:
Rnase H-mediated human ribosomal RNA depletion; contains HEK293 RNA
Trizol
TruSeq Stranded Total LT Sample Prep Kit (Illumina)

tag: strain

tag: developmental stage

value: young adult

tag: genotype/variation

value: wild type


title: Grafted Nude Rat 1

middle: L

state: CA

country: USA

molecule: polyA RNA

tag: tissue

value: 1 week post graft

tag: cell type


title: WT H2O2 versus wt SD

type: RNA

city: Tucson

first: Andrew

last: Capaldi

state: AZ

address: 1007 E Lowell St

department: MCB

institute: Univ of Arizona

hyb_protocol: Hybridization was performed using Agilent Hyb buffers and chambers following the manufactures suggested protocols

scan_protocol: Arrays were scanned on a Genepix 300b scanner

data_processing: Arrays were analyzed using GenePix 6.1, and then LOWESS normalized

organism: Saccharomyces cerevisiae

source_name: ACY044 in SD

label_protocol: mRNA was reverse transcribed incooperatigin aa-UTP and then labelled with Cy5 or Cy3

growth_protocol: Cells were grown to log phase in synthetic complete medium

extract_protocol: Cells were lysed in hot phenol and the polyA RNA purified using oligoDT cellulose

treatment_protocol: select cell cultures were treated with 0.4M KCl or 0.4mM H2O2 for 20min

tag: treatment


title: Rescue_a_8h

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

description: Gene expression data from Esrrb rescued ESCs, treated 8hrs and subsequently 2hrs with Mek inhibitor

hyb_protocol: Samples were then hybridized to the G4852A SurePrint G3 Mouse GE 8x60K Microarray slides (60000 probes, Agilent Technologies).

scan_protocol: Images were scanned using the high sensitivity protocol (AgilentG3_HiSen_GX_1color) on a SureScan microarray scanner (Agilent Technologies) and probe intensities were obtained by taking the gProcessedSignal from the output of Agilent feature extraction software using default settings.

data_processing: gProcessed signal

organism: Mus musculus

label_protocol: RNA was amplified into cRNA and 100ng of total RNA was labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies- 5190-2305).

growth_protocol: mESCs were grown in serum containing medium, supplemented with 1x LIF (made in house) and 2uM Chir99021. 24hrs prior to treatment, media was changed to serum containing media supplemented with 1x LIF and 250nM PD173074.

extract_protocol: Total RNA was collected using  the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen).

treatment_protocol: Cells were left untreated (0h), or treated with 250nM 4OHT (2h, 8h), or treated with 4OHT for 8hrs followed by a subsequent 2h Mek inhibitor treatment (8_2h).

value: Esrrb Knockout Expressing Raf-ErT2

value: ESCs

tag: protocol

value: Rescued with an Esrrb Transgene


title: N2_alg-1_elution_cXL


title: Grafted Nude Rat 3

value: 8 weeks post graft


title: Grafted Nude Rat 10

value: 6 months post graft

value: ESI-017 ES-derived neural progenitor cell


title: C_6_3

city: Changchun

first: Tao

last: Zhang

state: Jilin

address: 2888 Xincheng Street

department: College of Chinese Medicinal Material

country: China

institute: Jilin Agriculture University

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC，including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database，Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggNOG databases using DIAMOND with a threshold of Evalue<0.001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR. Next, GO and KEGG enrichment analysis were again performed on the differentially expressed Unigenes by perl scripts in house.
Genome_build: The Trinity transcriptome assembly is available on the series record.
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample

organism: Panax ginseng

source_name: Panax ginseng_control

growth_protocol: we performed transcriptome sequencing to select the Panax ginseng Embryogenic Calli of the number of treatment days—2, 4, and 6 days under 5 °C (Treatment) and 20 °C (Control).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryogenic Calli

tag: days


title: N2_input_cXL

source_name: Pulldown input

extract_protocol:
Rnase H-mediated C. elegans ribosomal RNA depletion
Trizol
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Grafted Nude Rat 9


title: gfp::lin-41_elution_cXL


title: T_2_1

source_name: Panax ginseng_treatment


title: Grafted Nude Rat 8


title: gfp::lin-41_input_cXL


title: C_4_1


title: 4M_rep1

description: Gene expression data from cells treated with MG132 for 30 mins then a subsequent 6 hours with both 4OHT and MG132

hyb_protocol: Samples were then hybridized to the Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (60000 probes, Agilent Technologies).

data_processing: Probe intensities were analysed using the NIA Array Analysis tool (http://lgsun.grc.nia.nih.gov/ANOVA/).

source_name: mouse ESCs

growth_protocol: Cells were grown in standard ESC medium supplemented with LIF and 250nM PD173074

treatment_protocol: See description above, cells left untreated, or treated with 1uM MG132. 30 minutes later they were treated with or without 250nM 4OHT for 6 hours


title: Grafted Nude Rat 7

value: 2 months post graft


title: MG132_rep1

description: Gene expression data from cells treated with MG132 for 30 mins then a subsequent 6 hours


title: gld-1::gfp_elution_cXL


title: 4M_rep3

value: MG132 for 30 mins then a subsequent 6 hours with both 4OHT and MG132


title: C_2_3


title: C_6_2


title: Grafted Nude Rat 6


title: C_2_1


title: C_4_2


title: Grafted Nude Rat 5


title: Rescue_a_0h

description: Gene expression data from Esrrb rescued ESCs, untreated

source_name: Esrrb rescued ESCs, untreated


title: 4OHTh_rep2

description: Gene expression data from cells treated with 4OHT for 6 hours

value: 4OHT for 6 hours


title: Grafted Nude Rat 4

value: 8 months post graft


title: MG132_rep2

value: MG132 for 30 mins then a subsequent 6 hours


title: 4OHTh_rep3


title: 4M_rep2


title: siw14Δ versus wt SD

source_name: BY4741 in SD

source_name: Siw14D in SD


title: SW480-shSETDB1-KRTnega-3

status: Public on Aug 07 2019

city: Daejeon

first: Soobeom

last: Lee

state: Daejeon

address: E16, 709, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Homo sapiens

source_name: colorectal cancer cell line

growth_protocol: Caco2, HCT116, SW480 human colorectal cancer cells were cultured in DMEM supplemented with 10% FBS and antibiotics (100 units/mL of penicillin, 100 μg/ml of streptomycin, and 0.25 μg/ml of Fungizone; Life Technologies Corp.) at 37°C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: For retrovirus transduction, we cultured cells in above condition with 2 μg/ml of puromycin for three days after transduction and then cultured with 1ug/ml for the rest of the period. Three days after transduction, to activate PPARG and VDR, we supplemented Troglitazone (10 uM; T2573, Sigma Aldrich) and 1α,25-Dihydroxyvitamin D3 (25 nM; D1530, Sigma Aldrich). We called this supplemented medium differentiation medium in the study.

tag: cell line

value: colorectal cancer cell line


title: SW480-shSETDB1-KRTplus-2


title: SW480-unsorted-3


title: SW480-unsorted-2


title: SW480-unsorted-1


title: SW480-shSETDB1-KRTplus-1


title: gld-1::gfp_input_cXL


title: 0h_rep3

description: Gene expression data of untreated cells

value: untreated


title: 4OHTh_rep1


title: SW480-shSETDB1-KRTnega-2


title: SW480-shSETDB1-KRTnega-1


title: HCT116-unsorted-3


title: 0h_rep2

description: Gene expression data of untreated cells


title: 0h_rep1

description: Gene expression data of untreated cells


title: HCT116-unsorted-1


title: HCT116-shSETDB1-KRTplus-3


title: MG132_rep3


title: HCT116-shSETDB1-KRTplus-2


title: HCT116-unsorted-2


title: HCT116-shSETDB1-KRTnega-3


title: HCT116-shSETDB1-KRTplus-1


title: HCT116-shSETDB1-KRTnega-2


title: SW480-shSETDB1-KRTplus-3


title: HCT116-shSETDB1-KRTnega-1


title: Caco2-shScramble_Diff3


title: Caco2-shSETDB1-KRT20-posi3


title: Caco2-shScramble_Veh3


title: XPG2-4 GSC6 KRAB-dCas9 PDGFRA 4C P1 rep2

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing:
ChIP-seq: Reads were uniquely aligned to hg19 using BWA and peak calling was performed using HOMER. Called peaks are provided as bed files.
BS-seq: Reads were processed using Bismark v.0.15 by mapping to a bisulfite converted hg19 genome seqeuence, bismark_methylation_extractor was used for extracting methylated CpGs, and generating a percent methylation coverage bedGraph output. file.
4C-seq: Paired-end sequencing reads were analyzed with the 4C-ker pipeline to identify genomic loci with differential chromosome contacts between conditions. Interaction density is provided as bedGraph files.
Genome_build: hg19
Supplementary_files_format_and_content: bed files: detected peaks in ChIP-seq experiments; bedGraph files: average methylation level in BS-seq experiments, interaction density in 4C-seq experiments; tdf files: coverage files in ChIP-seq experiments

molecule: genomic DNA

source_name: GSC6 KRAB-dCas9 PDGFRA 4C P1

growth_protocol: The human embryonic kidney cell line HEK293 (ATCC, CRL-1573) was cultured in DMEM with 10% FBS, 1% Pen/Strep antibiotic mix (Gibco). GSC6 lines were derived from IDH wild-type tumors resected at Massachusetts General Hospital. Neurosphere cultures contain Neurobasal media supplemented with 20 ng/ml recombinant EGF (R and D Systems), 20 ng/ml FGF2 (R and D Systems), 1×B27 supplement (Invitrogen), 0.5×N2 supplement (Invitrogen), 3 mM L-glutamine, and penicillin/streptomycin. Cultures were confirmed to be mycoplasma-free via PCR methods.

extract_protocol:
ChIP-seq: Cells were crosslinked in 1% formaldehyde at 37C for 10min, quenched with glycine, lysed on ice in buffer containing 1% SDS, diluted to a final concentration of 0.3% SDS and sonicated for 5 minutes total time at ~10W power. Sonicated chromatin was incubated with the relevant antibody overnight at 4C with rotation after dilution to 0.1% SDS. BS-seq: 500ng Genomic DNA was bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research). 4C-seq: 4C sample preparation was performed as previously described (Splinter et al. 2012) using NlaIII (NEB) and Csp6I (Thermo).
ChIP-seq: Performed as previously described using 5 ng (CTCF and H3K27ac), or 20 ng (H3K9me3) of ChIP DNA input. The following antibodies were used: CTCF, Cell Signaling Technology, Catalog Number 3418; H3K9me3, Abcam, Catalog Number 8898; H3K27ac, Active Motif, Catalog Number 39133. BS-seq:Bisulfite converted gDNA was PCR amplified with locus specific primers using EpiMark Hot Start Taq DNA (NEB). Bisulfite-conspecific primers were designed using MethPrimer. Primers were selected such that the CpG of interest was within ~10-12bp of the forward primer to enable detection via short read Illumina sequencing. PCR products were purified using a 2x AmpureXP bead cleanup and eluted in 10ul 10mM Tris-HCl. 4C-seq: Viewpoint primers were selected from a previously reported database (van de Werken et al, 2012). Primers sequences were concatenated with Illumina compatible adapter sequences and unique barcodes and synthesized as Ultramer oligos (IDT). Final library amplification was set up on ice using 3.2 µg of purified 4C sample DNA, 2.5 µM primers, and Ultra II Q5 Master Mix (NEB) split into 16 × 50 µl PCR reactions with extension at 65C. Amplification products were purified using 1.5x Ampure XP (Beckman) bead purification. Size distributions were established using a Bioanalyzer DNA 12000 Assay (Agilent).
All protocols: Paired-end 38bp reads were generated on a NextSeq500 sequencer (Illumina).

treatment_protocol: For transfections, 10 cm plates were seeded 48h in advance with 2M cells per plate. To make transfection mix 8 µg of dCas9 effector plasmid DNA and 1 µg of guide RNA expression plasmid were re-suspended in Opti-MEM media (Thermo). For combinations of effectors, total transfected DNA was kept constant at 8 µg. Fugene HD (Promega) was added to transfection mix according to the manufacturer protocol using a 3:1 ratio to DNA. Cells were harvested 72 h after transfection for ChIP, DNA, or RNA extraction.

tag: perturbation/epigenome editor

tag: grna

tag: assay


title: Caco2-shScramble_Diff2


title: Caco2-shSETDB1-KRT20-nega1


title: Caco2-shScramble_Veh2


title: Caco2-shScramble_Diff1


title: Caco2-shSETDB1-KRT20-posi1


title: XPG2-3 GSC6 KRAB-dCas9 PDGFRA 4C P1 rep1


title: Caco2-shScramble_Veh1


title: XPG2-4 GSC6 KRAB-dCas9 GSX2 4C P1 rep2

source_name: GSC6 KRAB-dCas9 GSX2 4C P1


title: Caco2-shSETDB1-KRT20-nega3


title: XPG2-1 GSC6 KRAB-dCas9 PDGFRA 4C control rep1

source_name: GSC6 KRAB-dCas9 PDGFRA 4C control

value: control


title: XPG2-2 GSC6 KRAB-dCas9 GSX2 4C control rep2

source_name: GSC6 KRAB-dCas9 GSX2 4C control


title: XPG2-3 GSC6 KRAB-dCas9 GSX2 4C P1 rep1


title: XPG2-1 GSC6 KRAB-dCas9 GSX2 4C control rep1


title: XPG2-3 GSC6 KRAB-dCas9 H3K9me3 ChIP-seq P1 rep1

source_name: GSC6 KRAB-dCas9 H3K9me3 ChIP-seq P1

value: ChIP-seq

tag: chip epitope


title: XPG2-4 GSC6 KRAB-dCas9 H3K9me3 ChIP-seq P1 rep2


title: XPG2-1 GSC6 KRAB-dCas9 H3K9me3 ChIP-seq control rep1


title: XPG2-2 GSC6 KRAB-dCas9 H3K9me3 ChIP-seq control rep2


title: XPG2-4 GSC6 KRAB-dCas9 H3K27ac ChIP-seq P1 rep2

source_name: GSC6 KRAB-dCas9 H3K27ac ChIP-seq P1


title: Caco2-shSETDB1-KRT20-posi2


title: Caco2-shSETDB1-KRT20-nega2


title: XPG2-1 GSC6 KRAB-dCas9 H3K27ac ChIP-seq control rep1


title: XPG2-2 GSC6 KRAB-dCas9 CTCF ChIP-seq control rep2

source_name: GSC6 KRAB-dCas9 CTCF ChIP-seq control

value: CTCF


title: XPG2-3 GSC6 KRAB-dCas9 H3K27ac ChIP-seq P1 rep1


title: XPG2-2 GSC6 KRAB-dCas9 PDGFRA 4C control rep2


title: XPG2-2 GSC6 KRAB-dCas9 H3K27ac ChIP-seq control rep2


title: XPG2-3 GSC6 KRAB-dCas9 CTCF ChIP-seq P1 rep1

source_name: GSC6 KRAB-dCas9 CTCF ChIP-seq P1


title: Treg_Input_2

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

description: Chromatin Input from CD127- CD25+ CD4+ Human Treg Cells

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the hg19 genome using Bowtie2
Duplicate reads were removed using PicardTools
Resulting SAM files were merged
Peaks were called using Macs2
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated from Macs2 output

source_name: Regulatory T cells

extract_protocol:
Isolated cells were fixed with 1% formaldehyde in PBS for 10 minutes, then quenched with glycine.  After washing, DNA was extracted using the Illumina SimpleChIP Enzymatic ChIP kit (#9003S). Briefly, nuclei were isolated by incubating in 1ml buffer A for 10 min on Ice, followed by centrifugation and resuspension in 1 ml Buffer B.  Chromatin was sheared to roughly 200-1000bp. Samples were centrifuged to clear lysates, and the supernatant containing the DNA was transferred to a fresh tube for overnight antibody complexing.  Next day, protein G dynabeads were added to each tube, incubated, washed, and isolated with magnet.  DNA complexes were then released from the beads, decrosslinked, and phenol:choloroform:isolamyl alcohol extracted for library prep.
DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina.  Briefly, DNA ends were repaired, followed by ligation of adapter sequences.  DNA was cleaned with AMPure XP beads, and then DNA was PCR amplified with 7-8 cycles.  After final cleaup with AMPure XP Beads, libraries were quantified using Agilent Bioanalyzer high sensitivity DNA kit and were subsequently sequenced.

value: Human PBMC

tag: chip antibody

tag: group

value: input


title: Treg_Input_1


title: XPG2-1 GSC6 KRAB-dCas9 CTCF ChIP-seq control rep1


title: Treg_2

description: CD127- CD25+ CD4+ Human Treg Cells

value: 4ug each of Anti-Bcl11b Antibodies:Abcam ab18465,  Bethyl A300-385, and 20ul of CST D6F1

value: treatment


title: Treg_1

description: CD127- CD25+ CD4+ Human Treg Cells


title: XPW60-29 control n/a BS-seq noguide

data_processing:
ChIP-seq: Reads were uniquely aligned to hg19 using BWA and peak calling was performed using HOMER.
BS-seq: Reads were processed using Bismark v.0.15 by mapping to a bisulfite converted hg19 genome seqeuence, bismark_methylation_extractor was used for extracting methylated CpGs,  and generating a percent methylation coverage bedGraph output file.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

extract_protocol:
ChIP-seq: Cells were crosslinked in 1% formaldehyde at 37C for 10min, quenched with glycine, lysed on ice in buffer containing 1% SDS, diluted to a final concentration of 0.3% SDS and sonicated for 5 minutes total time at ~10W power. Sonicated chromatin was incubated with the relevant antibody overnight at 4C with rotation after dilution to 0.1% SDS.
ChIP-seq library prep: Performed as previously described using 5 ng (CTCF and H3K27ac), or 20 ng (H3K9me3) of ChIP DNA input.
ChIP-seq sequencing: Paired-end 38 bp reads were generated on a NextSeq500 (Illumina).

value: noguide

value: BS-seq


title: XPW60-30 control n/a BS-seq noguide


title: hEHCs-14S-WGBS.fq.gz

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bsmap was used to map the CMS-IP sequences to mm10 and the Whole Genome Bisulfite Sequences to mm10; Bowtie2 was used to map RNAseq and ATAC-seq to mm10 with default parameters. HiChIP data was analyzed using HiC-Pro pipeline.
Macs2 was used to call CMS-IP peaks and ATAC peaks; MOABS was used to call methylation ratios for each CpG site; RPKM was calculated to measure the genes expression level.
DESeq2 was used to call differential 5hmC and ATAC peaks and differential expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for CMS-IP samples, WGBS samples, ATAC samples, RNA-seq samples ; tab-delimited text file include the RPKM for each gene in each RNA-seq sample

source_name: human embryonic heart

growth_protocol: mESCs (E14) were cultured on MEFs in Knock-out Dulbecco's Modified Eagle's Medium (Gibco), supplemented with 15% fetal bovine serum (Omega), 0.5% penicillin-streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 0.1mM 2-mercaptoetanol (Sigma), and 103 U/mL of leukemia inhibitory factor (Millipore).

extract_protocol:
Genomic DNA was isolated using Qiagen DNeasy Blood and Tissue kit. RNA was isolated using Qiagen RNeasy mini kit.
CMS-IP library construction: DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 200 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). The extra adapters were removed by AmpurXP (Beckman). The DNA was then denatured for 10 minutes at 95 °C (0.4 M NaOH, 10 mM EDTA), neutralized by the addition of cold 2M ammonium acetate (pH 7.0) for 10 min on ice. Then denatured DNA fragments were incubated with 1 μl anti-CMS antiserum in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h at 4 °C, and then precipitated with protein A/G beads. Precipitated DNA was eluted with proteinase K, purified with phenol chloroform, amplified and enriched by 10-12 cycles PCR using Kapa HiFi uracil polymerase. RNA-seq library construction is followed standard illumina library construction protocols. MethylC-seq: DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 300 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). Libraries were enriched by 4-6 cycles PCR using Kapa HiFi uracil polymerase.

treatment_protocol: Tet1/2/3 triple knock-out mESCs were generated by the CRISPR/Cas9 technology as described previously with slight modifications. Tet1/2/3 sgRNAs were cloned into PX458 (Addgene 48138). Three sgRNAs were transfected simultaneously into mESCs using the iMfectin DNA transfection reagent (Gendepot). GFP positive cells were sorted into 96-well plates by flow cytometry and individual colonies were genotyped after 7-day culture. C57BL/6 genetic background mouse strains were used. Tet2-/-Tet3f/f and Nkx2.5-Cre (The Jackson Laboratory 024637) mouse strains were used. Timed pregnancies were applied and the day on which a plug was found was defined as E0.5. Mice tails were cut and boiled in 50 mM NaOH for 1h and then neutralized in 10 mM Tris-HCL at pH7.4. PCR was carried out using the EmeraldAmp GT PCR Master Mix (TaKaRa) according to the manual.

value: embryonic heart


title: XPW60-27 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1

value: dCas9-Dnmt3a3l + KRAB-dCas9


title: hEHCs-13S-WGBS.fq.gz


title: XPW60-26 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-28 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: XPG2-4 GSC6 KRAB-dCas9 CTCF ChIP-seq P1 rep2


title: XPW60-24 control n/a BS-seq noguide


title: XPW60-23 control n/a BS-seq noguide


title: XPW60-22 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: XPW60-21 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: TH6729_0 min

city: Beijing

first: Yanni

last: Liu

address: Qinghuayuan, Haidian district

department: Medicine of School

institute: Tsinghua University

description: Sample 1

data_processing:
Base calliing: Illumina Casava software version 1.8
Quality control: FastQC v0.11.5
Trimming: Trimmomatic v0.32
S. pneumoniae reads were mapped with Tophat 2.1.1 and Bowtie 2.3.1
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated internally by Cufflink version 2.2.1 after aligning reads.
Genome_build: Streptococcus pneumoniae R6 (accession NC_003098.1, assembly GCA_000007045.1) was used directly in the analysis.
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample.

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae cells 0 min (pre-competence)

growth_protocol: S. pneumoniae cells were grown in acidified THY medium (pH6.8) supplemented with 0.5% glycine to OD620~0.06 in tubes at 37ºC with 5% CO2.

extract_protocol:
Total RNAs were extracted with the TIANGEN RNA extraction kit (TIANGEN, Beijing, China) based on the supplier’s instructions, treated with RNase-free DNase I (New England Biolabs, Beijing, China), and final purified with QIAGEN RNA purification kit (QIAGEN, Beijing, China) according to manufacturer's protocol.
Sample 1-6: The ribosomal RNA was removed from total RNA (~2 µg) using RiboZeroTM Magnetic Kit (EpiCentre, Cleveland, OH).  The processed RNA samples were used to prepare double-stranded complementary DNA (cDNA) libraries with the M-MuLV Reverse Transcriptase and NEBNext® mRNA Second Strand Synthesis Module.  The cDNA molecules were fragmented by sonication, and further processed for end repair, adaptor attachment, and sequence amplification.
Sample 7-18: The ribosomal RNA was removed from total RNA (~1.5 µg) using poly-T oligo-attached magnetic beads. Fragmentation of mRNAs and sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The cDNA molecules were ligated with the NEBNext Adaptor, and further processed for selected, purifed, and sequence amplification.

treatment_protocol: BSA and CaCl2 were added with to final concentration of 0.2% and 1mM. Pre-competence sample was taken at 0 min before the addition of 250 ng/ml CSP, fastly cooled down and kept at 4 oC. Other competence-ON samples were taken at each pre-set time and treated as that with sample at 0 min.

value: rpsL1 (StreptomycinR)

tag: time

value: 0 min (pre-competence)


title: XPW60-20 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-18 control n/a BS-seq noguide


title: XPW60-17 control n/a BS-seq noguide


title: XPW60-15 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: XPW60-16 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: XPW60-13 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-12 control n/a BS-seq noguide


title: XPW60-14 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-25 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-11 control n/a BS-seq noguide


title: XPW60-10 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: XPW60-09 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: XPW60-08 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-05 control n/a BS-seq noguide


title: XPW60-07 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-03 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: XPW60-06 control n/a BS-seq noguide


title: XPW60-19 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-04 dCas9-Dnmt3a3l + KRAB-dCas9 n/a BS-seq P3+P1


title: XPW60-02 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW60-6 control H3K9me3 ChIP-seq noguide


title: XPW60-2 dCas9-Dnmt3a3l H3K9me3 ChIP-seq P3


title: XPW60-5 control H3K9me3 ChIP-seq noguide


title: XPW60-6 control CTCF ChIP-seq noguide


title: XPW60-1 dCas9-Dnmt3a3l H3K9me3 ChIP-seq P3


title: XPW60-4 dCas9-Dnmt3a3l + KRAB-dCas9 H3K9me3 ChIP-seq P3+P1


title: XPW60-5 control CTCF ChIP-seq noguide


title: XPW60-3 dCas9-Dnmt3a3l + KRAB-dCas9 CTCF ChIP-seq P3+P1


title: XPW60-4 dCas9-Dnmt3a3l + KRAB-dCas9 CTCF ChIP-seq P3+P1


title: XPW60-1 dCas9-Dnmt3a3l CTCF ChIP-seq P3


title: XPW55-6 pLV dCas9-KRAB H3K9me3 ChIP-seq P1

value: pLV dCas9-KRAB


title: XPW55-2 pLV dCas9-KRAB H3K9me3 ChIP-seq control


title: XPW55-4 pLV dCas9-KRAB H3K9me3 ChIP-seq P1


title: XPW60-2 dCas9-Dnmt3a3l CTCF ChIP-seq P3


title: XPW55-3 pLV dCas9-KRAB H3K9me3 ChIP-seq control


title: XPW55-5 pLV dCas9-KRAB H3K9me3 ChIP-seq P1


title: XPW60-3 dCas9-Dnmt3a3l + KRAB-dCas9 H3K9me3 ChIP-seq P3+P1


title: XPW55-6 pLV dCas9-KRAB CTCF ChIP-seq P1


title: XPW55-3 pLV dCas9-KRAB CTCF ChIP-seq control


title: XPW55-5 pLV dCas9-KRAB CTCF ChIP-seq P1


title: XPW60-01 dCas9-Dnmt3a3l n/a BS-seq P3


title: XPW55-4 pLV dCas9-KRAB CTCF ChIP-seq P1


title: XPW55-2 pLV dCas9-KRAB CTCF ChIP-seq control


title: shLUC_Res_Kelly_INPUT_BORIS_1

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using STAR (v2.5.1b_modified) and the parameters “--alignIntronMax 1 --alignEndsType EndToEnd--outFilterMultimapNmax 1 --outFilterMismatchMax 5”.
Non-duplicate reads that mapped to the reference chromosomes were retained using Samtools (v1.3.1) and MarkDuplicates (v2.1.1) from Picard tools
For each experimental replicate, antibody enrichment was assessed using the plotFingerprint command from deepTools (v2.2.4).
Peaks were identified with MACS2 (2.1.1) for narrow peaks (BORIS, CTCF, SMC1) with the parameters ”--q 0.01--call-summits” and for broad peaks (H3K27ac) with the parameters ”--broad-cutoff 0.01”.
To create bigwigs we first created input normalized bedgraph tracks with the deepTools command bamCompare and the parameters “--scaleFactorsMethod=readCount --ratio=subtract --binSize=50 --numberOfProcessors=4 --extendReads=200”. Subsequently, negative values were set to zero and counts were scaled to RPM to account for differences in library size. Bigwig files were then created with bedGraphToBigWig
ChIP-seq replicates were merged at the BAM level if they showed strong correlation assessed with the deepTools command “multiBigwigSummary BED-file” using all bigwigs and identified peaks as input. Identification of peaks and generation of tracks were then repeated for these merged files and used for further analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files to visualize ChIPseq reads deposition and bed files to show identified peaks. See data processings steps for a more detailed explanation.

source_name: TAE resistant Kelly cells

growth_protocol: Resistant Kelly cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, in the presence of TAE684 at a concentration of 1µM.

extract_protocol:
Cells were crosslinked with formaldehyde and lysed to obtain purified nuclei that were sonicated to shear chromatin. Protein-DNA complexes were then isolated using Dynabeads with corresponding antibodies, and DNA was isolated through reverse crosslinking and purified by phenol chloroform extraction in order to be used for library construction.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit from NEB (E7645), according to the manufacturer’s protocol.

treatment_protocol: Cells were infected for 24 h with viral particles containing either the shBORIS or the shLUC (control) construct in the presence of polybrene (8 µg/ml), and then selected with puromycin for 48h before performing chromatin immunoprecipitation (ChIP).

tag: antibody

value: INPUT

tag: tae response

value: resistant

value: shLUC

value: Neuroblastoma Kelly cells


title: shLUC_Res_Kelly_INPUT_BORIS_2


title: XPW55-1 pLV dCas9-KRAB CTCF ChIP-seq control

value: control

value: ChIP-seq


title: WT KCl versus wt SD

source_name: ACY044 in SD

tag: strain

value: 0.4 M KCl, 20min


title: David_TC71_BORIS_2

description:
Ewings_TC71_BORIS_vs_David_Ewings_TC71_INPUT_peaks.narrowPeak
Ewings_TC71_BORIS.noNeg.sorted.bw

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using STAR (v2.5.1b_modified) and the parameters “--alignIntronMax 1 --alignEndsType EndToEnd--outFilterMultimapNmax 1 --outFilterMismatchMax 5”.
Non-duplicate reads that mapped to the reference chromosomes were retained using Samtools (v1.3.1) and MarkDuplicates (v2.1.1) from Picard tools
For each experimental replicate, antibody enrichment was assessed using the plotFingerprint command from deepTools (v2.2.4).
Peaks were identified with MACS2 (2.1.1) for narrow peaks (BORIS, SMC1) with the parameters ”--q 0.01--call-summits” and for broad peaks (H3K27ac) with the parameters ”--broad-cutoff 0.01”.
To create bigwigs we first created input normalized bedgraph tracks with the deepTools command bamCompare and the parameters “--scaleFactorsMethod=readCount --ratio=subtract --binSize=50 --numberOfProcessors=4 --extendReads=200”. Subsequently, negative values were set to zero and counts were scaled to RPM to account for differences in library size. Bigwig files were then created with bedGraphToBigWig
ChIP-seq replicates were merged at the BAM level if they showed strong correlation assessed with the deepTools command “multiBigwigSummary BED-file” using all bigwigs and identified peaks as input. Identification of peaks and generation of tracks were then repeated for these merged files and used for further analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files to visualize ChIPseq reads deposition and bed files to show identified peaks. See data processings steps for a more detailed explanation.

source_name: TC-71 cells

growth_protocol: TC-32 and TC-71 cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, in order to obtain 10 million cells to be prepared for each sample before performing chromatin immunoprecipitation (ChIP).

value: BORIS

value: TC-71 cells

value: post-chemotherapy

value: Ewing sarcoma cells


title: XPW55-1 pLV dCas9-KRAB H3K9me3 ChIP-seq control


title: David_TC71_SMC1_2

description:
Ewings_TC71_SMC1_vs_David_Ewings_TC71_INPUT_peaks.narrowPeak
Ewings_TC71_SMC1.noNeg.sorted.bw


title: David_TC71_input_1

value: input


title: David_TC71_SMC1_1


title: David_TC71_input_2


title: David_TC71_H3K27ac_2

description:
Ewings_TC71_H3K27ac_vs_David_Ewings_TC71_INPUT_peaks.broadPeak
Ewings_TC71_H3K27ac.noNeg.sorted.bw


title: David_TC71_H3K27ac_1


title: David_TC32_SMC1_2

description:
Ewings_TC32_SMC1_vs_David_Ewings_TC32_INPUT_peaks.narrowPeak
Ewings_TC32_SMC1.noNeg.sorted.bw

source_name: TC-32 cells

value: TC-32 cells

value: diagnosis


title: David_TC32_SMC1_1


title: David_TC32_input_1


title: Res_Kelly_MYCN_CS_2

description:
Res_Kelly_MYCN_vs_Res_Kelly_MYCN_INPUT_peaks.narrowPeak
Res_Kelly_MYCN.noNeg.sorted.bw

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using STAR (v2.5.1b_modified) and the parameters “--alignIntronMax 1 --alignEndsType EndToEnd--outFilterMultimapNmax 1 --outFilterMismatchMax 5”.
Non-duplicate reads that mapped to the reference chromosomes were retained using Samtools (v1.3.1) and MarkDuplicates (v2.1.1) from Picard tools
For each experimental replicate, antibody enrichment was assessed using the plotFingerprint command from deepTools (v2.2.4).
Peaks were identified with MACS2 (2.1.1) for narrow peaks (MYCN) with the parameters ”--q 0.01--call-summits”.
To create bigwigs we first created input normalized bedgraph tracks with the deepTools command bamCompare and the parameters “--scaleFactorsMethod=readCount --ratio=subtract --binSize=50 --numberOfProcessors=4 --extendReads=200”. Subsequently, negative values were set to zero and counts were scaled to RPM to account for differences in library size. Bigwig files were then created with bedGraphToBigWig
ChIP-seq replicates were merged at the BAM level if they showed strong correlation assessed with the deepTools command “multiBigwigSummary BED-file” using all bigwigs and identified peaks as input. Identification of peaks and generation of tracks were then repeated for these merged files and used for further analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files to visualize ChIPseq reads deposition and bed files to show identified peaks. See data processings steps for a more detailed explanation.

growth_protocol: Sensitive and resistant Kelly cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, in order to obtain 10 million cells to be prepared for each sample.

treatment_protocol: Cells were incubated for 48 h in the presence of DMSO (sensitive) or the ALK inhibitor TAE684 at 1µM(resistant) before performing chromatin immunoprecipitation (ChIP).

value: MYCN


title: David_TC32_BORIS_2

description:
Ewings_TC32_BORIS_vs_David_Ewings_TC32_INPUT_peaks.narrowPeak
Ewings_TC32_BORIS.noNeg.sorted.bw


title: Res_Kelly_MYCN_CS_1


title: Res_Kelly_input_MYCN_CS_2


title: David_TC32_H3K27ac_1

description:
Ewings_TC32_H3K27ac_vs_David_Ewings_TC32_INPUT_peaks.broadPeak
Ewings_TC32_H3K27ac.noNeg.sorted.bw


title: David_TC32_input_2


title: David_TC32_BORIS_1


title: Res_Kelly_input_MYCN_CS_1


title: Kelly_MYCN_CS_2

description:
Par_Kelly_MYCN_vs_Par_Kelly_MYCN_INPUT_peaks.narrowPeak
Par_Kelly_MYCN.noNeg.sorted.bw

source_name: Kelly cells

value: sensitive

value: DMSO


title: shLUC_Res_Kelly_SMC1_1

description:
shLUC_Res_Kelly_SMC1_vs_shLUC_Res_Kelly_INPUT_peaks.narrowPeak
shLUC_Res_Kelly_SMC1.noNeg.sorted.bw


title: shLUC_Res_Kelly_INPUT_2

value: INPUT


title: shLUC_Res_Kelly_SMC1_2

value: resistant


title: shLUC_Res_Kelly_INPUT_1

value: shLUC


title: Kelly_input_MYCN_1

value: Neuroblastoma Kelly cells


title: David_TC32_H3K27ac_2


title: shLUC_Res_Kelly_H3K27ac_1

description:
shLUC_Res_Kelly_H3K27ac_vs_shLUC_Res_Kelly_INPUT_peaks.broadPeak
shLUC_Res_Kelly_H3K27ac.noNeg.sorted.bw


title: shLUC_Res_Kelly_CTCF_2

description:
shLUC_Res_Kelly_CTCF_vs_shLUC_Res_Kelly_INPUT_peaks.narrowPeak
shLUC_Res_Kelly_CTCF.noNeg.sorted.bw

value: CTCF


title: shLUC_Res_Kelly_BORIS_1

description:
shLUC_Res_Kelly_BORIS_vs_shLUC_Res_Kelly_INPUT_peaks.narrowPeak
shLUC_Res_Kelly_BORIS.noNeg.sorted.bw


title: shLUC_Res_Kelly_BORIS_2


title: shLUC_Res_Kelly_H3K27ac_2


title: shLUC_Res_Kelly_CTCF_1


title: Kelly_MYCN_CS_1


title: shB4_Res_Kelly_INPUT_1

value: shBORIS


title: shB4_Res_Kelly_H3K27ac_2

description:
shB4_Res_Kelly_H3K27ac_vs_shB4_Res_Kelly_INPUT_peaks.broadPeak
shB4_Res_Kelly_H3K27ac.noNeg.sorted.bw


title: shB4_Res_Kelly_INPUT_BORIS_2


title: shB4_Res_Kelly_SMC1_1

description:
shB4_Res_Kelly_SMC1_vs_shB4_Res_Kelly_INPUT_peaks.narrowPeak
shB4_Res_Kelly_SMC1.noNeg.sorted.bw


title: shB4_Res_Kelly_INPUT_2


title: shB4_Res_Kelly_CTCF_2

description:
shB4_Res_Kelly_CTCF_vs_shB4_Res_Kelly_INPUT_peaks.narrowPeak
shB4_Res_Kelly_CTCF.noNeg.sorted.bw


title: shB4_Res_Kelly_H3K27ac_1


title: shB4_Res_Kelly_CTCF_1


title: shB4_Res_Kelly_BORIS_1

description:
shB4_Res_Kelly_BORIS_vs_shB4_Res_Kelly_INPUT_peaks.narrowPeak
shB4_Res_Kelly_BORIS.noNeg.sorted.bw


title: shB4_Res_Kelly_INPUT_BORIS_1


title: Res_JQ1_CTCF_2

description:
Res_JQ1_CTCF_vs_Res_JQ1_input_peaks.narrowPeak
norm_Res_JQ1_CTCF_merged.noNeg.sorted.bw

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using STAR (v2.5.1b_modified) and the parameters “--alignIntronMax 1 --alignEndsType EndToEnd--outFilterMultimapNmax 1 --outFilterMismatchMax 5”.
Non-duplicate reads that mapped to the reference chromosomes were retained using Samtools (v1.3.1) and MarkDuplicates (v2.1.1) from Picard tools
For each experimental replicate, antibody enrichment was assessed using the plotFingerprint command from deepTools (v2.2.4).
Peaks were identified with MACS2 (2.1.1) for narrow peaks (BORIS, CTCF, Pol2) with the parameters ”--q 0.01--call-summits” and for broad peaks (H3K27ac, BRD4, H3K27me3) with the parameters ”--broad-cutoff 0.01”.
To create bigwigs we first created input normalized bedgraph tracks with the deepTools command bamCompare and the parameters “--scaleFactorsMethod=readCount --ratio=subtract --binSize=50 --numberOfProcessors=4 --extendReads=200”. Subsequently, negative values were set to zero and counts were scaled to RPM to account for differences in library size. Bigwig files were then created with bedGraphToBigWig
ChIP-seq replicates were merged at the BAM level if they showed strong correlation assessed with the deepTools command “multiBigwigSummary BED-file” using all bigwigs and identified peaks as input. Identification of peaks and generation of tracks were then repeated for these merged files and used for further analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files to visualize ChIPseq reads deposition and bed files to show identified peaks.

source_name: JQ1 treated TAE resistant Kelly cells

treatment_protocol: Cells were incubated for 48 h in the presence of DMSO (sensitive), the ALK inhibitor TAE684 at 1µM, or the BET inhibitor JQ1 at 2.5µM (resistant) before performing chromatin immunoprecipitation (ChIP).

value: Kelly cells

tag: cell origin

value: CTCF (#07-729, Millipore)


title: Res_JQ1_H3K27me3_1

description:
Res_JQ1_H3K27me3_vs_Res_JQ1_input_peaks.broadPeak
norm_Res_JQ1_H3K27me3_merged.noNeg.sorted.bw


title: Res_Pol2_1

description:
Res_narrow_Pol2_vs_Res_input_peaks.narrowPeak
norm_Res_Pol2_2.noNeg.sorted.bw

value: RNA Pol II (sc-899X, Santa Cruz Biotechnology)


title: shB4_Res_Kelly_BORIS_2

value: BORIS


title: Res_JQ1_input_2


title: Res_JQ1_H3K27ac_1

description:
Res_JQ1_H3K27ac_vs_Res_JQ1_input_peaks.broadPeak
norm_Res_JQ1_H3K27ac_merged.noNeg.sorted.bw

value: H3K27ac (ab2729, Abcam)


title: Res_JQ1_BRD4_1

description:
Res_JQ1_BRD4_vs_Res_JQ1_input_peaks.narrowPeak
norm_Res_JQ1_BRD4_merged.noNeg.sorted.bw

value: BRD4 (A301-985A, Bethyl Laboratories)


title: Res_JQ1_input_1


title: Res_JQ1_CTCF_1


title: shB4_Res_Kelly_SMC1_2


title: Res_JQ1_H3K27me3_2


title: Res_Pol2_2


title: Res_JQ1_BORIS_1

description:
Res_JQ1_BORIS_vs_Res_JQ1_input_peaks.narrowPeak
norm_Res_JQ1_BORIS_merged.noNeg.sorted.bw

value: BORIS ( #39851, Active Motif)


title: Res_JQ1_BORIS_2


title: Res_JQ1_BRD4_2


title: Res_input_2


title: Res_input_1


title: Res_H3K27me3_2

description:
Res_H3K27me3_vs_Res_input_peaks.broadPeak
norm_Res_H3K27me3_merged.noNeg.sorted.bw


title: Res_H3K27me3_1


title: Res_CTCF_2

description:
Res_CTCF_vs_Res_input_peaks.narrowPeak
norm_Res_CTCF_merged.noNeg.sorted.bw


title: Res_H3K27ac_2

description:
Res_H3K27ac_vs_Res_input_peaks.broadPeak
norm_Res_H3K27ac_merged.noNeg.sorted.bw


title: Res_H3K27ac_1


title: Res_CTCF_1


title: Res_JQ1_H3K27ac_2


title: Res_BRD4_1

description:
Res_BRD4_vs_Par_input_peaks.narrowPeak
norm_Res_BRD4_merged.noNeg.sorted.bw


title: Res_BORIS_2

description:
Res_BORIS_vs_Res_input_peaks.narrowPeak
norm_Res_BORIS_merged.noNeg.sorted.bw


title: Res_BRD4_2


title: Par_Pol2_1

description:
Par_narrow_Pol2_vs_Par_input_peaks.narrowPeak
norm_Par_Pol2_2.noNeg.sorted.bw


title: Par_Pol2_2


title: Res_BORIS_1


title: Par_input_2


title: Par_BORIS_1

description:
Par_BORIS_vs_Par_input_peaks.narrowPeak
norm_Par_BORIS_merged.noNeg.sorted.bw


title: Par_BORIS_2


title: Treg_KO_EAE_2

description: Bcl11b KO at EAE

data_processing:
Fastq files were trimmed using Seqtk
Trimmed fastq files were aligned to the mm10 genome via Hisat2
Raw counts were extracted from bam files using htseq
Differential analysis was performed on raw counts with DESeq2
Normalized counts were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: deSeq2_counts.txt file contains pre-normalized count values for each sample generated by htseq.

extract_protocol:
WT and Bcl11b KO Regulatory T-cells were sorted from spleen and peripheral lymphnode..  Cells were lysed and RNA was isolated using Qiagen Rneasy Plus Micro Kit (Qiagen #74034). RNA quality was determined on a bioanalyzer (Agilent RNA 6000 Nano #5067-1511)
Libraries were prepared using New England Biolabs NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (cat# E7770S) according to the manufacturer's instructions. Library quality and concentration was checked on a bioanalyzer (Agilent High Sensitivity DNA Kit #5067-4626) and by Qubit (Qubit™ dsDNA HS Assay Kit #Q32854). Libraries were sequenced on a NextSeq500.

value: Bcl11bF/WT Foxp3YFP-Cre +/-

tag: tissue

value: Secondary Lymphoid Organs

tag: genotype


title: Par_H3K27ac_2

description:
Par_H3K27ac_vs_Par_input_peaks.broadPeak
norm_Par_H3K27ac_merged.noNeg.sorted.bw

value: sensitive

tag: treatment


title: Par_CTCF_1

description:
Par_CTCF_vs_Par_input_peaks.narrowPeak
norm_Par_CTCF_merged.noNeg.sorted.bw

value: DMSO


title: Par_BRD4_2

description:
Par_BRD4_vs_Par_input_peaks.narrowPeak
norm_Par_BRD4_merged.noNeg.sorted.bw


title: Par_H3K27me3_2

description:
Par_H3K27me3_vs_Par_input_peaks.broadPeak
norm_Par_H3K27me3_merged.noNeg.sorted.bw


title: Par_H3K27me3_1


title: Par_H3K27ac_1


title: Par_input_1


title: Par_CTCF_2


title: Treg_KO_2

description: Bcl11b KO at steady state

value: KO


title: Treg_WT_1

description: Bcl11b WT at steady state

value: WT


title: Treg_KO_1

description: Bcl11b KO at steady state


title: T2: Riboseq (single-end sequencing

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

data_processing:
Library strategy: Riboseq
Fastq quality was determined by FASTQC in Galaxy server
Adapter removal was done for Riboseq data using Clip (FastX-tool kit) in galaxy server
Riboseq reads were further trimmed using Trim in galaxy server
Riboseq data was aligned to ribosomal mouse RNA sequences (custom genome file) using bowtie 2 in galaxy server and only the reads that dd not align were used for further analysis.
Reads not aligned to mouse genome (mm10) using tophat in galaxy server.
htseq-count in galaxy server was used to count the reads per gene. GTF file from ensembl modified to match the ucsd genome was used for counting.
Genome_build: mm10 (mus musculus)
Supplementary_files_format_and_content: Tabular format with read counts per gene (created using htseq-count.

source_name: resting state T cells

growth_protocol: Cells were isolated using Miltenyi magnetic sorting kit and cultured for 2 hours in complete RPMI medium at 37ºC, 5% CO2

extract_protocol:
Total cell lysate was treated with a mixture of ribonuclease (RNaseA, Rnase T1, S7 nuclease) and monosomes were isolated. RNA from monosomes were used for library preparation.
Ribosome profiling protocol as described in "Ingolia, N.T., Brar, G.A., Rouskin, S., Mcgeachy, A.M., and Weissman, J.S. (2012). The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550."

treatment_protocol: Treated with 100µg/ml cycloheximide for 15 minutes before harvesting

tag: origin

value: Spleen

tag: cell type

value: resting state T cells


title: T1: Riboseq (single-end sequencing


title: B1: Riboseq (single-end sequencing)

source_name: resting state B cells

value: resting state B cells


title: DKO-E12Heart-scRNAseq

source_name: mouse embryo heart E12.5 day

tag: age

value: embryonic heart


title: B3: Riboseq (single-end sequencing


title: Par_BRD4_1

tag: cell line

value: Kelly cells

value: Neuroblastoma Kelly cells


title: Treg_WT_2

description: Bcl11b WT at steady state


title: Treg_KO_EAE_1

description: Bcl11b KO at EAE


title: WT-mESCs-YY1-2

source_name: mESC

value: mESC

value: anti-YY1 (Santa Cruz sc-7341, 1:100)


title: TKO-mESCs-YY1-1


title: DKO.HiCHIP

data_processing:
Library strategy: HiCHIP
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bsmap was used to map the CMS-IP sequences to mm10 and the Whole Genome Bisulfite Sequences to mm10; Bowtie2 was used to map RNAseq and ATAC-seq to mm10 with default parameters. HiChIP data was analyzed using HiC-Pro pipeline.
Macs2 was used to call CMS-IP peaks and ATAC peaks; MOABS was used to call methylation ratios for each CpG site; RPKM was calculated to measure the genes expression level.
DESeq2 was used to call differential 5hmC and ATAC peaks and differential expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for CMS-IP samples, WGBS samples, ATAC samples, RNA-seq samples ; tab-delimited text file include the RPKM for each gene in each RNA-seq sample

tag: developmental stage

value: embryo


title: WT-mESCs-YY1-1


title: WT.HiCHIP


title: TKO-mESCs-YY1-2


title: DKO1.RNAseq

description: GeneExpressionNormalized.txt


title: DKO1.CMS

data_processing:
Library strategy: CMS-IP
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bsmap was used to map the CMS-IP sequences to mm10 and the Whole Genome Bisulfite Sequences to mm10; Bowtie2 was used to map RNAseq and ATAC-seq to mm10 with default parameters. HiChIP data was analyzed using HiC-Pro pipeline.
Macs2 was used to call CMS-IP peaks and ATAC peaks; MOABS was used to call methylation ratios for each CpG site; RPKM was calculated to measure the genes expression level.
DESeq2 was used to call differential 5hmC and ATAC peaks and differential expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for CMS-IP samples, WGBS samples, ATAC samples, RNA-seq samples ; tab-delimited text file include the RPKM for each gene in each RNA-seq sample

value: Home made anti-CMS antibody


title: WT1.RNAseq

description: GeneExpressionNormalized.txt


title: DKO2.ATAC


title: WT2.RNAseq

description: GeneExpressionNormalized.txt


title: DKO.WGBS


title: WT1.ATAC


title: DKO1.ATAC


title: WT2.ATAC


title: WT2.CMS


title: Treg_Bcl11b_ChIP_2

description: WT

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the mm10 genome using Bowtie2
Duplicate reads were removed using PicardTools
Resulting SAM files were merged
Peaks were called using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files were generated from Macs2 output

value: Secondary lymphoid organs

value: 4ug each of Anti-Bcl11b Antibodies:Abcam ab18465,  Bethyl A300-385, and 20ul of CST D6F1

value: treatment


title: DKO2.CMS


title: WT1.CMS


title: Ctrl-E12Heart-scRNAseq

value: Ctrl


title: David_TC71_BORIS_1

description:
Ewings_TC71_BORIS_vs_David_Ewings_TC71_INPUT_peaks.narrowPeak
Ewings_TC71_BORIS.noNeg.sorted.bw

value: BORIS

value: TC-71 cells

value: post-chemotherapy

value: Ewing sarcoma cells


title: CD4_Naive_KO

description: Bcl11b KO

source_name: CD4+ T cells

value: Bcl11b KO

value: Control


title: DKO2.RNAseq

description: GeneExpressionNormalized.txt

value: embryonic heart


title: WT_Treg_1

description: Bcl11b WT

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the mm10 genome using Bowtie2
Duplicate reads were removed using PicardTools
The resulting bam files of the two biological replicates were merged
Peaks were called using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files

extract_protocol:
DNA from 50,000 CD4+ T-cells was prepared as previously described by others (Buenrostro, J.D., Wu, B., Chang, H.Y., and Greenleaf, W.J. (2015). ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21.29.21-29.) Briefly, cells were lysed and the nuclei underwent the transposition reaction at 37oC for 30 minutes.
DNA was purified after transposition reaction using Qiagen MinElute PCR Purification Kit and libraries were generated by amplifying DNA with 12-15 cycles. Necessary cycles determined by qPCR. DNA was purified using AMPure XP beads, quality and quantity was determined by Agilent bioanalyzer (high sensitivity DNA kit), and the libraries were subsequently sequenced.

value: Peripheral Lymphoid Organs

value: Bcl11bF/WT Foxp3YFP-Cre +/-


title: KO_Treg_2

description: Bcl11b deficient

value: Bcl11bF/F Foxp3YFP-Cre +/-


title: WT_Treg_2

description: Bcl11b WT


title: KO_Treg_1

description: Bcl11b deficient


title: Treg_Bcl11b_ChIP_1

description: WT

value: WT


title: Het_KO_Treg_rep2

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

data_processing:
The quality of sequenced reads (50 bp; paired-end) was measured using FastQC , and low quality portions of the sequenced reads were trimmed using Trim Galore (version 0.4.2; with Cutadapt (version 1.12).
The trimmed reads were mapped to the mouse genome (reference assembly mm10) using STAR (version 2.5.1)
The abundances of reference genes were estimated using Cuffnorm (version 2.2.1)
Differentially expressed genes (DEGs) between conditions were identified using Cuffdiff (version 2.2.1) with a false discovery rate (FDR)-adjusted p-value cutoff of 0.05
The fragments per kilobase of transcript per million mapped reads (FPKM) values were used to compare gene’s expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: Text file (normalized expression level by means of FPKM)

source_name: Bcl11b deficient Treg cells

growth_protocol: Single cell supension were prepared from drainig lymphnodes and spleen. Respective cell population were sorted using BD Moflo-XDP cell sorter at >97% purity .

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Qiagen -74004). Integrity and concentration of purified RNA was checked using Agilent RNA 6000 Nano Kit (5067-1511) in Agilent Bioanalyzer and Nanodrop respectively.
Library was prepared from total RNA using TruSeq Stranded Total RNA kit (Illumina- RS-122-2001) following manufacturer's protocols. Briefly, cDNA was made from Total RNA followed by Adenylation, barcoded adaptor-ligation and PCR amplification (15 cycles). Libraries were size selected for 200-300-bp fragments using Agencourt AMPure XP beads (A63880) and size distribution was confirmed using Agilent High Sensitivity DNA Kit (5067-4626)  in Agilent Bioanalyzer. Equivalent amounts of barcoded libraries were pooled and sequenced using HiSeq 2500 or MiSeq (Illumina) instruments.

value: Sorted CD4+YFP+ cells

value: Bcl11b f/f Foxp3-YFP-Cre/+


title: Het_WT_Treg_rep1

source_name: Bcl11b sufficient Treg cells

value: Bcl11b f/+ Foxp3-YFP-Cre/+


title: Het_KO_Treg_rep1


title: Het_WT_Treg_rep2


title: Norm C P3 FIBROBLAST

city: Philadelphia

first: Michael

last: Beers

state: PA

address: 3450 Hamilton Walk

institute: University of Pennsylvania

hyb_protocol: Hybridization of Reference with all samples were carried out by the Duke Institute for Genomic Sciences and Policy.

scan_protocol: Scans were carried out by the Duke Institute for Genomic Sciences and Policy using an Axon Genepix Scanner (Genepix 4000B) according to protocols for that scanner.

data_processing: Raw genepix data files (.GPR) derived from the HO36K human chip (Operon Human Oligo set V4) were downloaded from the Duke Website. All further analysis was carried out LIMMA, a BioConductor package that applies linear model on gene expression microarray data analysis with good statistic performance on experiments with small numbers of arrays.  Normalization and analysis were done using LIMMA in R.  A matrix of spot weights was computed for each comparison, spot with a Flags-value less than -50 was giving zero weight.  Samples with distinct overall density were removed (Total density picture).  Expression data was then normalized by robust spline for within array normalization, and quantile for between arrays normalization to ensure that intensities have the same empirical distribution across arrays and across channels. Fold changes and standard errors were estimated by fitting a linear model, and empirical Bayes smoothing was applied to the standard errors.  Lists of significant were generated by setting the threshold of Benjamini–Hochberg false discovery rate (FDR) to 0.01, and log fold change to 1.3.

source_name: Normal Lung Differential Binding

label_protocol: Starting with about 1 micro gram total RNA at a concentration of about 100 ng/microliter, RNA was reverse transcriebed using the MessageAmp II™ aRNA Kit (Ambion Catalog # 1751).  Second strand cDNA synthesis and cDNA purification were also carried out using the same kit.  Using the same kit, in vitro transcription step was used to amino-allylate RNA with a reacion mixture that included: 3 uL (50 mM) aaUTP, 4 uL (75 mM) T7 ATP solution, 4 uL (75 mM) T7 CTP solution, 4 uL (75 mM) T7 GTP, 2 uL (75 mM) T7 UTP solution, 4 uL T7 10X Reaction Buffer, 4 uL T7 Enzyme mix (total 25 uL per sample). Samples were incubated at 37 C for 14 hours and then maintained at 4 C prior to purification of amino-allylated amplified RNA using the same Message Amp II Kit in 100 uL of nuclease free water. Yield was verified by Nano-drop.  10 micrograms of amino-allylated amplified RNA were then coupled with Cy5 for experiemental and control samples, and Cy3 for Stratagene Human reference aaaRNA by incubation in dark for 1 hour after addition of 1 ul of 1M sodium bicarbonate pH9.0  according to the TIGR protocol used by Duke Institute for Genomic Science and Policy. MEGAclear Kit (Cat#1908) was used to remove unincorporated Cy Dye

extract_protocol: Lung obtained in the operating room within 1 minute of explantation.  Lung tissue was kept in ice cold (4 C) PBS for transportation to the lab.  In the lab, tissue was briefly and rapidly dissected into 1 mm cubed pieces and placed in 4% collagenase P (Roche) in DMEM media with 20% FBS, 2X Penicillin, Streptomycin, Amphotericin B in 37 C humidified incubator with a magnetic stir bar oscillating at a medium rate to dissociate the tissues for 2 hours.  Tissue was strained through sterile strainer and centrifuged for 5 minutes at 1,000 RPM.  The supernatant was removed, and the cell pellet was plated on standard cell culture dish for 45 minutes with DMEM, 20% FBS, 1%P/S/F.  After 45 minutes the plates were vigorously washed with 1X PBS to remove unattached cells.  The attached cells (fibroblasts) were allowed to grow for three passages and then flash frozen, and the RNA extracted using Qiagen RNeasy Kit and QIAShredder columns to remove DNA contaminants.  Fibroblast identity confirmed using immunocytochemistry on cells isolated onto microscope slides.  Cells stained for alpha smooth muscle actin (ACTA2) and the absence of von willebrand's factor (endothelial cell marker), cytokeratin 18 (epithelial cell marker) and cd11b (macrophage/monocyte cell marker).

tag: disease state

value: control

tag: individual

value: Norm C

value: P3 Fibroblast

source_name: Stratagene Human Reference RNA

extract_protocol: RNA QA/QC done on Agilent bio-analyzer to confirm purity and integrity.  RNA quantitated on Thermo-Fisher Nano drop.

tag: reference

value: Stratagene Human Reference RNA


title: Norm B Explant FIB

source_name: Normal Lung Explant Outgroth

value: Norm B

value: Explant FIB


title: Norm B P3 FIBROBLAST


title: SW480

description: Gene expression data

scan_protocol: Arrays were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Signal values were computed using the Affymetrix® GeneChip™ Command Console software. Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

label: Biotin

source_name: Colorectal cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Caco2, HCT116, SW480, SW620 human colorectal cancer cells were cultured in DMEM supplemented with 10% FBS and antibiotics (100 units/mL of penicillin, 100 μg/ml of streptomycin, and 0.25 μg/ml of Fungizone; Life Technologies Corp.) at 37°C in 5% CO2.

extract_protocol: The Affymetrix 3’IVT Expression array process was executed according to the manufacturer's protocol  (GeneChip 3’IVT Plus Reagent Kit).Biotin-labeled, amplified RNA (aRNA) was synthesized from 100 ng total RNA using the 3′IVT Plus reagent Kit. A 12μg labeled cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 min.The fragmented cRNA was hybridized was hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Gene Expression Array at 45°C for 16hour.Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

value: colorectal cancer cell line


title: Bcl11b overexpression (mutant)

city: Yokohama

first: Junji

last: Hirota

state: Kanagawa

address: 4259-B63, Nagatsuta-cho

department: Center for Biological Resources and Informatics

country: Japan

institute: Tokyo Institute of Technology

data_processing:
Illumina MiSeq Reporter (version, 2.5.1) was used for basecalling.
The adaptor sequences and low-quality regions in the raw reads were trimmed using Platanus_trim (version, 1.0.7).
To map the trimmed reads against the mouse reference genome (build, GRCm38.p3), TopHat2 (version, 2.0.13) was applied with the following options: the mouse genome annotation was input as a guide (-G annotation_file.gtf), and the maximum intron length was set to 100,000 (-I 100000).
Based on the mapping results, FPKM (fragments per kilobase of exon per million reads mapped) of all mouse genes were calculated for the control and mutant samples as an indicator of expression, using Cuffdiff in the Cufflinks package (version, 2.2.1)54 with the following options: the minimum number of alignments in a locus was set to 5 (-c 5), and the multi-read correction was applied (-u).
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Olfactory epithelium

growth_protocol: All mice were housed in standard conditions in accordance with institutional and governmental guidelines.

extract_protocol:
Whole MOE tissues from Control and Bcl11b-overexpressing Tg mice were dissected, flesh frozen in liquid nitrogen and stored at -80℃. Total RNA was isolated using an RNeasy Mini Kit (Qiagen) with the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA LT Sample Prep Kit.

value: Mixed-strain of BALB/c and C57BL/6

value: Main olfactory epithelium

value: Postnatal day 0

tag: Sex

value: Female

tag: genotype of transgene

value: Goofy-Cre-IRES-gapVenus; CAGp-LSL-Bcl11b-IRES-lynmRFP double Tg


title: IPF Patient B P3 Fibroblast

source_name: IPF Lung Differential Binding

extract_protocol: Lung obtained in the operating room within 1 minute of explantation.  Lung tissue was kept in ice cold (4 C) PBS for transportation to the lab.  In the lab, tissue was briefly and rapidly dissected into 1 mm cubed pieces and placed in 4% collagenase P (Roche) in DMEM media with 20% FBS, 2X Penicillin, Streptomycin, Amphotericin B in 37 C humidified incubator with a magnetic stir bar oscillating at a medium rate to dissociate the tissues for 2 hours.  Tissue was strained through sterile strainer and centrifuged for 5 minutes at 1,000 RPM.  The supernatant was removed, and the cell pellet was plated on standard cell culture dish for 45 minutes with DMEM, 20% FBS, 1%P/S/F.  After 45 minutes the plates were vigorously washed with 1X PBS to remove unattached cells.  The attached cells (fibroblasts) were flash frozen, and the RNA extracted using Qiagen RNeasy Kit and QIAShredder columns to remove DNA contaminants.  Fibroblast identity confirmed using immunocytochemistry on cells isolated onto microscope slides.  Cells stained for alpha smooth muscle actin (ACTA2) and the absence of von willebrand's factor (endothelial cell marker), cytokeratin 18 (epithelial cell marker) and cd11b (macrophage/monocyte cell marker).

value: IPF

value: IPF Patient B


title: Norm D P3 FIBROBLAST

value: Norm D


title: IPF Patient B Explant Fib

source_name: IPF Lung Explant Outgrowth

value: Explant Fib


title: Venus expression-1

city: Aoba-ku Seiryo

first: Tetsuya

last: Akiyama

state: Sendai Miyagi

department: Neurology

institute: Tohoku university

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA were hybridized for 17 hr at 45C on GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with Robust Multiarray Average (RMA) using Affymetrix default analysis settings.
RMA expression value derived from Expression Console software; gene-level analysis
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: hiPSCs-derived MNs_Venus expression

label_protocol: Biotinylated ssDNA were prepared using Affymetrix GeneChip WT PLUS Reagent Kit according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: hiPSCs-derived MNs were chemically differentiated and lentivirus were infected at MOI = 1.0

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: subject status

value: healthy

tag: gender

value: female

value: human induced pluripotent stem cells (hiPSCs)-derived motor neurons (MNs)

tag: infected with

value: Venus expressing lentivirus


title: SW620

description: Gene expression data

hyb_protocol: The fragmented cRNA was hybridized was hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Gene Expression Array at 45°C for 16hour.Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).


title: IPF Patient D P3 Fibroblast

value: IPF Patient D

value: P3 Fibroblast

value: Stratagene Human Reference RNA


title: IPF Patient C Explant Fib

value: IPF Patient C


title: IPF Patient D Explant Fib


title: Norm D Explant FIB

value: control

value: Explant FIB


title: Fos-B+Venus expression-3

value: Fos-B + Venus expressing lentivirus


title: Fos-B+Venus expression-1


title: Control

tag: strain

value: Mixed-strain of BALB/c and C57BL/6

value: Main olfactory epithelium

value: Postnatal day 0

value: Female

value: Goofy-Cre-IRES-gapVenus Tg


title: Venus expression-2


title: Fos-B+Venus expression-2


title: IPF Patient A P3 Fibroblast

value: IPF

value: IPF Patient A


title: Caco2

description: Gene expression data

value: colorectal cancer cell line


title: IPF Patient C P3 Fibroblast


title: Venus expression-3

value: healthy

value: female

value: human induced pluripotent stem cells (hiPSCs)-derived motor neurons (MNs)


title: IPF Patient A Explant Fib

value: Explant Fib


title: Norm C Explant FIB

value: Norm C

value: Stratagene Human Reference RNA


title: E16VcKO1

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
processed data file:
E16VcKO1_E16WT4.anno

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA extracted from E16.5 embryonic cortex of H2A.Z.2 cKO and WT mice was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain background

tag: development stage

tag: genotype/variation

value: H2A.Z.2 knockout

tag: tissue

value: Brain


title: E16VcKO2

description:
processed data file:
E16VcKO2_E16WT4.anno


title: WT-GS_INPUT_SE_rep2

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

description: Input for SIRT7 ChIPs

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw read quality was first assessed with fastqc (version 0.11.3, Babraham Bioinformatics), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm9) or human (UCSC hg19) reference genome with Bowtie with options –n 2 –k 10 (version 1.1.1), and converted to BAM format with Samtools (version 0.1.19).
SIRT7 peak calling was performed using MACS (version 1.4.2).
chromatin state maps were generated with chromHMM
Genome_build: mm9
Supplementary_files_format_and_content: For chromatin modification ChIP, Log2(ChIP/INPUT) RPKM-normalized signal files (bigWig) were generated from BAM data using DeepTools (version 2.4.2), and bed files contain chromHMM state calls. For SIRT7 ChIP, signal files generated by MACS peakcalling step were converted to bigWig using the UCSC utility wigToBigWig, and bed files contain IDR-passing peaks.

source_name: Mouse Embryonic Fibroblasts (MEFs)

extract_protocol:
Samples were crosslinked in 1% formaldehyde for 10 minutes at 37°C, washed twice with PBS, and then collected from dishes. For SIRT7, ChIP was carried out with nuclear extracts. First, cells were resuspended in Lysis Buffer 1 (5 mM HEPES, 85 mM KCl, 0.5% NP-40) and incubated for 5 minutes on ice to disrupt cellular membranes. After centrifugation, nuclei were resuspended in Lysis Buffer 2 (1% SDS, 10mM EDTA, 50mM Tris, and protease inhibitors) and incubated on ice for 40 minutes. For macroH2A1.1 or H3K27me3 ChIP, whole cell extracts were obtained by directly lysing cells in Lysis Buffer 2 for 40 min on ice. Chromatin was then sonicated to an average fragment size of 150-300bp as analyzed by agarose gel electrophoresis, and subjected to immunoprecipitation with anti-SIRT7 (Cell Signalling, #5360), macroH2A1.1 (Abcam, #ab37264), or anti-H3K27me3 (Cell Signaling C36B11-#9733). ChIPs were washed 5 times with ice cold RIPA buffer (1% NP-40, 0.7% Na deoxycholate, 50mM Tris, 1mM EDTA, 500mM LiCl2, pH 8.0) and crosslinks reversed (1% SDS, 0.1M NaHCO3; 6 hr at 65°C), DNA purified (minElute PCR Purification Kit, Qiagen), and finally the concentration of ChIP and INPUT DNA was measured using PicoGreen (Life Technologies).
ChIP libraries were prepared using a ThruPlex DNA-seq library preparation Kit (Rubicon Genomics) following the manufacturer’s protocol. ChIP libraries were then size selected with PippinPrep (Sage Science) for a final library fragment size of 350-400bp, and quantified with KAPPA qPCR.

tag: cell type

value: Mouse Embryonic Fibroblasts (MEFs)

tag: passages

value: 3 to 4

tag: chip antibody


title: WT-NT_INPUT_SE_rep2

description: Input for SIRT7 ChIPs


title: E16WT4

description:
processed data file:
E16VcKO2_E16WT1.anno

value: wild type


title: E16WT1


title: WT-GS_INPUT_SE_rep1

description: Input for SIRT7 ChIPs


title: SIA_5

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

country: Switzerland

institute: University of Bern

data_processing:
Illumina RTA 1.18.66.3 was used for base calling
Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v2.1.0 (10x Genomics) mkfastq with standard parameters.
Cell Ranger v2.1.0 mkref was used to generate a reference genome from the mouse genome (mm10, Ensembl annotation version 91) and the tdTomato mRNA sequence from the Ai9 Rosa26 targeting vector plasmid (Addgene number 22799).
Cell Ranger v2.1.0 quant was used to map the demultiplexed reads to the reference genome, process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts and estimate the number of cells using standard parameters.
Seurat v2.3 was used under R v3.5.2 to filter cells by the number of genes expressed, cluster and visualize cells by similarity in gene expression and identify cluster markers. Construction of single cell pseudotime trajectories and identification of genes changing as a function of pseudotime was performed using Monocle v2.12.0.
Supplementary_files_format_and_content: tab delimited text files with UMI counts per gene per cell after initial filtering in Seurat (min.cells = 5, min.genes = 400)

source_name: Synovial mononuclear cells

growth_protocol: Cx3cr1creER:tdTomato mice were treated systemically with 4mg/ml Tamoxifen twice within 48h. Four weeks after Tamoxifen pulse mice were injected with arthritogenic K/BxN serum. CD45+CD11b+Ly6G- cells were sorted from hind paws at steady state (day 0), day 1, day 2 and day 5 post K/BxN serum transfer.

extract_protocol:
For each sample 17400 cells were loaded onto a Chromium Single Cell A Chip (10x Genomics) to generate single cell bead emulsions for reverse transcription and cell bar coding according to the manufacturers instructions
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v2 and i7 Mutiplex kit (10X Genomics) according to the manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommended read lengths for Chromium Single Cell 3' v2 chemistry.

value: Hind paw synovial tissue

tag: cell subtype

value: Synovial mononuclear cells

value: Synovial CD45+CD11b+Ly6G- mononuclear cells

tag: days post k/bxn serum tansfer

value: Day 5


title: SIA_2

value: Day 2


title: WT-GS_SIRT7_ChIP-seq_rep2

description:
GS_peaks.gIDR_1.3.bed
ChIP-SIRT7-WT-GS.pooled.log2_CONTROL.bw

value: Cell signaling, #5360


title: WT-GS_SIRT7_ChIP-seq_rep1


title: WT-NT_INPUT_SE_rep1

description: Input for SIRT7 ChIPs


title: WT-NT_SIRT7_ChIP-seq_rep2

description:
NT_peaks.gIDR_1.3.bed
ChIP-SIRT7-WT-NT.pooled.log2_CONTROL.bw


title: SIA_0

value: Day 0


title: BMDM_G

data_processing:
Illumina RTA 1.18.66.3 was used for base calling
Base call files were converted to FASTQ files and libraries demultiplexed using bcl2fastq v2.17.1.14
TruSeq Adapter sequences and low quality bases were trimmed from reads in cutadapt v1.15 (-a AGATCGGAAGAGC -q 20,20 --minimum-length 50 --trim-n  --max-n=0.1). Trimmed reads were mapped to the mouse reference genome GRCm38, Ensembl annotation version 91 (STAR aligner v2.5.4a). Reads mapping to annotated exonic regions were counted and summarized as counts per gene in Subread featureCounts v1.6.1. (-s 2)
The counts per gene were analyzed using the negative binomial model implemented in DESeq2 v1.20.0 under R v3.5.0 to determine differentially expressed genes
Supplementary_files_format_and_content: tab-delimited text file with counts per gene per sample obtained from Subread featureCount

source_name: bone marrow-derived macrophages (BMDM)

growth_protocol: Macrophage precursors were isolated from bone marrow of C57BL/6 mice, cultured and diferentiated to macrophages in MCSF-conditioned medium for 5 days. CD45+CD11b+F4/80+GFP+ or GFP- macrophages were isolated from hind paws of Cx3cr1-GFP hind paws by FACS.

extract_protocol:
RNA isolation was performed using the RNeasy Mini kit (QIAGEN,Cat No./ID: 74104)
Libraries were prepared from 500 ng RNA using the Illumina TruSeq stranded mRNA kit according to the manufacturers instructions and sequenced on an Illumina HiSeq 2500 platform (single end 101 bp)

value: Bone marrow

value: in vitro cultured BMDM

value: bone marrow-derived macrophages (BMDM)


title: interstitial_GFPneg_F

source_name: GFP- synovial interstitial macrophages

value: GFP- synovial interstitial macrophages


title: BMDM_H


title: interstitial_GFPneg_E


title: WT-NT_SIRT7_ChIP-seq_rep1


title: KO-GS_INPUT_PE_rep1

description: Input for H3K27me3 and mH2A1 ChIPs


title: KO-NT_INPUT_PE_rep1

description: Input for H3K27me3 and mH2A1 ChIPs


title: WT-GS_INPUT_PE_rep1

description: Input for H3K27me3 and mH2A1 ChIPs


title: lining_GFPpos_B

source_name: GFP+ synovial lining macrophages

value: GFP+ synovial lining macrophages


title: WT-NT_INPUT_PE_rep1

description: Input for H3K27me3 and mH2A1 ChIPs


title: KO-NT_mH2A1_ChIP-seq_rep2

description:
KO-NT_4_segments.bed
pooled_ChIP_mH2A1_KO-NT.rpkm_norm.log2_INPUT.bw

value: Abcam, #ab37264


title: lining_GFPpos_C


title: WT-GS_mH2A1_ChIP-seq_rep2

description:
WT-GS_4_segments.bed
pooled_ChIP_mH2A1_WT-GS.rpkm_norm.log2_INPUT.bw


title: KO-GS_mH2A1_ChIP-seq_rep2

description:
KO-GS_4_segments.bed
pooled_ChIP_mH2A1_KO-GS.rpkm_norm.log2_INPUT.bw


title: KO-GS_mH2A1_ChIP-seq_rep1


title: SIA_1

value: Day 1


title: alveolar phase (S4)

city: Nanjing

first: mengjie

last: zhang

address: No. 72, Guang Zhou Road

institute: Children's Hospital Affiliated to Nanjing Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with htseq
The circRNA reads were aligned to reference genome using BWA detecting backesplicec junction reads with CIRI
Genome_build: mm10
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: lung

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer
Total RNA was extracted from lung tissues of neonatal and embryonic mice using the TRIzol reagent (Invitrogen, Carlsbad CA, USA), according to the manufacturer’s instructions. Total RNA of each sample was used to prepare the RNA sequencing library

value: lung

tag: developmental stage

value: newborn day 7.5


title: lining_GFPpos_A


title: BMDM_I


title: canalicular phase (S2)

value: embryonic day 16.5


title: HCT116

description: Gene expression data

tag: cell line

value: colorectal cancer cell line


title: pseudo glandular phase (S1)

value: embryonic day 14.5


title: KO-NT_mH2A1_ChIP-seq_rep1

value: Mouse Embryonic Fibroblasts (MEFs)

value: 3 to 4


title: terminal sac phase (S3)

value: embryonic day 18.5


title: WT-NT_mH2A1_ChIP-seq_rep1

description:
WT-NT_4_segments.bed
pooled_ChIP_mH2A1_WT-NT.rpkm_norm.log2_INPUT.bw


title: KO-GS_H3K27me3_ChIP-seq_rep2

description:
KO-GS_4_segments.bed
pooled_ChIP_H3K27me3_KO-GS.rpkm_norm.log2_INPUT.bw

value: Cell Signaling C36B11-#9733


title: interstitial_GFPneg_D

value: Hind paw synovial tissue


title: ATAC-seq_KO_Bcl11b_rep3

description:
processed data file:
KO-Bcl11b_merged_final.ucsc.bigWig
KO-Bcl11b.peaks.bl.bed

data_processing:
The quality of sequenced reads (100 bp; paired-end) was measured using FastQC , and low quality portions of the sequenced reads were trimmed using Trim Galore (version 0.4.2; with Cutadapt (version 1.12).
The trimmed reads were mapped to the mouse genome (reference assembly mm10) using HISAT2 (version 2.1.0).
The mapped reads were sorted by genomic positions using Samtools (version 1.3) , and duplicated mapped reads were removed using Sambamba (version 0.6.5).
Biological replicates for each conditions were merged and the genomic binding sites (peaks) of a given protein were identified using HOMER (version 4.10.1) with a FDR-adjusted p-value cutoff of 0.001
The peaks overlapped with the blacklisted regions that show anomalous, unstructured, and high signal/read counts were discarded.
To identify reliable target genes of a given protein, peaks located 20 kb outside of the gene’s transcription start sites were removed.
To identify common (or specific) peaks between given conditions, the identified peaks in each condition were merged.
Merged peaks were used to define common or specific peaks using HOMER (getDifferentialPeaks) with default parameters.
Deeptools (version 2.5.3-2-503c71b) was used to draw heatmaps
Genome_build: mm10
Supplementary_files_format_and_content: BED (peak positions) and bigWig format

growth_protocol: Single cell supensions were prepared from drainig lymphnodes and spleen. Respective cell population were sorted using BD Moflo-XDP cell sorter.

extract_protocol:
100,000 cells from each sample were lysed in hypotonic lysis buffer followed by tagmentaion (enzymatic fragmenting and tagging simultaneously) of DNA.
Library from Tagmented DNA were prepared according to manufacturer (Nextera DNA Sample Prep Kit -Illumina) protocol.

treatment_protocol: WT vs. KO

tag: strain background

value: Bcl11b f/f  Foxp3-IRES-YFP-Cre

value: Sorted CD4+YFP+ cells

tag: molecule subtype

value: Tagmented DNA


title: KO-NT_H3K27me3_ChIP-seq_rep2

description:
KO-NT_4_segments.bed
pooled_ChIP_H3K27me3_KO-NT.rpkm_norm.log2_INPUT.bw


title: WT-GS_H3K27me3_ChIP-seq_rep2

description:
WT-GS_4_segments.bed
pooled_ChIP_H3K27me3_WT-GS.rpkm_norm.log2_INPUT.bw


title: WT-NT_mH2A1_ChIP-seq_rep2


title: ATAC-seq_WT_Bcl11b_rep3

description:
processed data file:
WT-Bcl11b_merged_final.ucsc.bigWig
WT-Bcl11b.peaks.bl.bed

value: Bcl11b w/w  Foxp3-IRES-YFP-Cre


title: S7KO_GS_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw read quality was first assessed with fastqc (version 0.11.3, Babraham Bioinformatics), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were aligned to the UCSC mm9 reference genome with HISAT2 (version 2.1.0; options: --dta), and converted to sorted and indexed BAM format with samtools
StringTie (version  1.3.3; options –eB) was used to estimate transcript abundance using the UCSC mm9 reference GTF file (Illumina iGenomes).
Transcript abundances were converted to matrix format sutable for DESeq2 using the prepDE.py script provided by the StringTie authors.
Differential expression was analyzed with DESeq2 (version 1.18.1)
Genome_build: mm9
Supplementary_files_format_and_content: Output of prepDE.py

extract_protocol:
Total RNA was extracted using an RNEasy miniprep kit (Qiagen) according to the manufacturer instructions
Illumina TruSeq RNA Sample Preparation Kit v2.

treatment_protocol: WT and SirT7-/- MEFS were cultured in either normal or non-glucose media for 18h and harvested for RNA-seq

tag: treatment

value: Glucose Starvation


title: ATAC-seq_WT_Bcl11b_rep1


title: WT-NT_H3K27me3_ChIP-seq_rep2

description:
WT-NT_4_segments.bed
pooled_ChIP_H3K27me3_WT-NT.rpkm_norm.log2_INPUT.bw


title: KO-NT_H3K27me3_ChIP-seq_rep1


title: S7KO_GS_2


title: WT-GS_H3K27me3_ChIP-seq_rep1


title: ATAC_Seq_Rep_3

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
ChIP-Seq and ATAC-Seq were aligned to hg19 using bwa with default parameters
MACS2 was used to call peaks, with default parameters (--broad was used to call peaks in H3K27me3 and for ATAC a local background correction was applied as no input was used)
RNA-Seq was aligned using the TopHat and Cufflinks pipeline using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq data presented as bed files, RNA-Seq data as a comma separated values, cufflinks output for gene expression differences

growth_protocol: Cells were grown as spheroids in suspension, using cancer stem cell enriching media. Cultures were routinely passaged every 3-4 days.

extract_protocol:
For H3K27me3, cells were fixed with PBS/Formaldehyde 1%, lysed with lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and sonicated for 60 cycles, 30 sec ON, 30 sec OFF using the Bioruptor Plus Sonicator. For ATAC-seq, 30,000 live  cells were washed with PBS and lysed for 5 minutes on ice using a lysis buffer containing 10mM  Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630. After isolating crude nuclei,  samples were treated for 30 minutes at 37ºC with Tn5 transposase, and then the DNA was purified  by MinElute PCR Purification Kit. Transposed DNA fragments were amplified using specific  adapters followed by purification with MinElute PCR Purification Kit.
Library construction was performed using the ThruPLEX DNA-Seq 12S Kit from Rubicon Genomics, following the manufacturer's recommendations. For ATAC-seq, Fragments from 240-360pb  were selected in the PippinHT system. The quality of the library and its DNA concentration were  assessed by Bioanalyzer instruments and sequenced using Illumina HiSeq 2500 sequencer, V4  chemistry.

treatment_protocol: For RNA-seq, cells were treated with DMSO or UNC1999 at 3uM for 7 days prior to RNA extraction

value: patient-derived colorectal cancer initiating cells

tag: culture type

value: suspension culture


title: S7KO_GS_3


title: WT-GS_mH2A1_ChIP-seq_rep1

value: Abcam, #ab37264


title: ATAC-seq_KO_Bcl11b_rep1


title: ATAC_Seq_Rep_1


title: S7KO_NT_2

value: No Treatment


title: DMSO_Rep3_RNA_Seq

extract_protocol:
Cells were peleted and processed for RNA extraction using Rneasy (Qiagen)
For H3K27me3, cells were fixed with PBS/Formaldehyde 1%, lysed with lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and sonicated for 60 cycles, 30 sec ON, 30 sec OFF using the Bioruptor Plus Sonicator. For ATAC-seq, 30,000 live  cells were washed with PBS and lysed for 5 minutes on ice using a lysis buffer containing 10mM  Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630. After isolating crude nuclei,  samples were treated for 30 minutes at 37ºC with Tn5 transposase, and then the DNA was purified  by MinElute PCR Purification Kit. Transposed DNA fragments were amplified using specific  adapters followed by purification with MinElute PCR Purification Kit.
Library construction was performed using the ThruPLEX DNA-Seq 12S Kit from Rubicon Genomics, following the manufacturer's recommendations. For ATAC-seq, Fragments from 240-360pb  were selected in the PippinHT system. The quality of the library and its DNA concentration were  assessed by Bioanalyzer instruments and sequenced using Illumina HiSeq 2500 sequencer, V4  chemistry.

value: DMSO (7 days)


title: S7KO_NT_3


title: DMSO_Rep2_RNA_Seq


title: ATAC-seq_KO_Bcl11b_rep2


title: S7KO_NT_4


title: WT-NT_H3K27me3_ChIP-seq_rep1


title: UNC1999_Rep3_RNA_Seq

value: UNC1999 (7 days)


title: S7WT_GS_2

value: Wild type


title: S7WT_GS_1

value: Mouse Embryonic Fibroblasts (MEFs)


title: ATAC-seq_WT_Bcl11b_rep2


title: S7WT_GS_3

value: 3 to 4


title: UNC1999_Rep1_RNA_Seq


title: UNC1999_Rep2_RNA_Seq


title: KO-GS_H3K27me3_ChIP-seq_rep1


title: ATAC_Seq_Rep_2


title: S7WT_NT_1


title: S7KO_NT_1


title: H3K4me3_Rep2_ChIP-seq

extract_protocol:
cells were fixed with 1% formaldehyde, washed with PBS/BSA and then with PBS. Fixed cells were lysed in lysis buffer  and sonicated using a 4°C waterbath sonicator Bioruptor (Diagenode). Lysates were clarified by centrifugation at 16,000g, 4°C for 15 minutes and the supernatants were transferred to new tubes and processed for ChIP using the indicated antibodies.
For H3K27me3, cells were fixed with PBS/Formaldehyde 1%, lysed with lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and sonicated for 60 cycles, 30 sec ON, 30 sec OFF using the Bioruptor Plus Sonicator. For ATAC-seq, 30,000 live  cells were washed with PBS and lysed for 5 minutes on ice using a lysis buffer containing 10mM  Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630. After isolating crude nuclei,  samples were treated for 30 minutes at 37ºC with Tn5 transposase, and then the DNA was purified  by MinElute PCR Purification Kit. Transposed DNA fragments were amplified using specific  adapters followed by purification with MinElute PCR Purification Kit.
Library construction was performed using the ThruPLEX DNA-Seq 12S Kit from Rubicon Genomics, following the manufacturer's recommendations. For ATAC-seq, Fragments from 240-360pb  were selected in the PippinHT system. The quality of the library and its DNA concentration were  assessed by Bioanalyzer instruments and sequenced using Illumina HiSeq 2500 sequencer, V4  chemistry.

value: H3K4me3 (Abcam ab8580)


title: H3K4me3_Rep1_ChIP-seq


title: S7WT_NT_2


title: S7WT_NT_3


title: H3K27me3_Rep2_ChIP-seq

value: H3K27me3 (Abcam ab6002)


title: S7WT_NT_4


title: H3K27me3_Rep1_ChIP-seq


title: Tcell_FvFcM_rep1

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

description:
FvFcM_1
processed data file:
de-ctrlxFvFvM.csv

data_processing:
Quality check was performed by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Alignments to the Human reference genome hg19 form the UCSC Genome Browser database using open source segemehl (v0.1.9) (Hoffmann S. et al., 2009)
HTSeq-count v0.5.0 (Anders and Huber, 2014) was used to count and compare aligned reads to annotated human genes.
The relative gene expression was calculated using DESeq2 (Anders S, 2010) from the R/Bioconductor package (v2.14).
Genome_build: Homo sapiens hg19 downloaded from the UCSC Genome Browser database.
Supplementary_files_format_and_content: CSV files include normalized gene expression for each treatment

source_name: T cell treated with FvFcM

growth_protocol: Fresh PBMCs were isolated using Ficoll-Paque density gradient centrifugation (GE Healthcare, Sweden). PBMCs were cultured in RPMI media (Invitrogen, Carlsbad, CA, USA) supplemented with 4 mM L-glutamine and 10% FBS in the presence or absence of soluble anti-CD3 antibodies.

extract_protocol:
Total RNA was extracted with the RNeasy kit (Qiagen) according to the manufacturer's instructions. Extracted RNA was quantified in a fluorometer (Qubit) and submitted to Bioanalyzer 2100 (Agilent) to determine its integrity.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A total of 250 ng of antibody was applied to 1x10^6 cells per mL/PBMC. T cells were isolated after 72 hours PBMC treatment, using magnetic beads by negative selection (according to the manufacturer´s instructions). Briefly, PBMC were selectively depleted of CD16+, CD19+, CD20+ cells and were discarded (Dynabeads® Untouched™ Human T Cells Kit, Invitrogen). Purity of T cell preparation was checked using flow cytometry.

tag: subject status

value: Healthy donors

value: peripheral blood

value: T cells

tag: stimuli

value: Antibody FvFc M  (OKT3 murine scFv fused to human IG1 CH1 and CH2 domains)

tag: incubation period

value: 72 hours


title: Tcell_FvFcM_rep2

description:
FvFcM_2
processed data file:
de-ctrlxFvFvM.csv


title: DMSO_Rep1_RNA_Seq


title: WT_Treg_Input_rep3

description: Input DNA

data_processing:
The quality of sequenced reads (50 bp; paired-end) was measured using FastQC , and low quality portions of the sequenced reads were trimmed using Trim Galore (version 0.4.2; with Cutadapt (version 1.12).
The trimmed reads were mapped to the mouse genome (reference assembly mm10) using HISAT2 (version 2.1.0).
The mapped reads were sorted by genomic positions using Samtools (version 1.3) , and duplicated mapped reads were removed using Sambamba (version 0.6.5).
Biological replicates for each conditions were merged and the genomic binding sites (peaks) of a given protein were identified using HOMER (version 4.10.1) with a FDR-adjusted p-value cutoff of 0.001
The peaks overlapped with the blacklisted regions that show anomalous, unstructured, and high signal/read counts were discarded.
To identify reliable target genes of a given protein, peaks located 20 kb outside of the gene’s transcription start sites were removed.
To identify common (or specific) peaks between given conditions, the identified peaks in each condition were merged.
Merged peaks were used to define common or specific peaks using HOMER (getDifferentialPeaks) with default parameters.
Deeptools (version 2.5.3-2-503c71b) was used to draw heatmaps
Genome_build: mm10
Supplementary_files_format_and_content: BED format (peak positions)

growth_protocol: Single cell supensions were prepared from drainig lymphnodes and spleen. Respective cell population were sorted using BD Moflo-XDP cell sorter and fixed.

extract_protocol:
Sheared Chromatin were cleared  and protein-DNA complexes were isolated with antibody-magnetic bead complex.
ChIP-seq library for each sample were prepared according to manufacturer (NEXTFLEX® ChIP-Seq Kit 5143-01) protocols. Briefly,purified immunoprecipitated DNA were end-repaired and size selected for 200–400-bp fragments with Agencourt AMPure XP beads (A63880) followed by Adenylation, barcoded adaptor-ligation and PCR amplification (15 cycles). Size distribution and concentration of each library was checked using Agilent Bioanalyzer. Equivalent amounts of barcoded libraries were pooled and sequenced using HiSeq 2500 (Illumina) instruments.

tag: strain

value: Sorted CD4+YFP+ cells

tag: genotype

tag: antibody

value: Input DNA


title: Tcell_FvFcR_rep2

description:
FvFcR_2
processed data file:
de-ctrlxFvFvR.csv

source_name: T cell treated with FvFcR

tag: tissue

tag: cell type

value: Antibody FvFcR, humanized version of  FvFc M


title: WT_Treg_Input_rep1

description: Input DNA

source_name: Bcl11b sufficient Treg cells


title: Tcell_FvFcR_rep1

description:
FvFcR_1
processed data file:
de-ctrlxFvFvR.csv


title: WT_Treg_Foxp3_rep1

description:
Foxp3 ChIP DNA
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_Bcl11b-KO-Treg-Foxp3-specific.bed
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_common.bed
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_WT-Treg-Foxp3-specific.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_common.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_WT-Treg-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_WT-Treg-Foxp3-specific_.bed


title: Tcell_OKT3_rep2

description:
OKT3_2
processed data file:
de-ctrlxOKT3.csv

source_name: T cell treated with OKT3

value: Antibody Muromonab-CD3 (OKT3) was purchased from eBioscience (San Diego, CA, USA)


title: WT_Treg_Foxp3_rep2

description:
Foxp3 ChIP DNA
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_Bcl11b-KO-Treg-Foxp3-specific.bed
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_common.bed
WT-Treg-Foxp3_vs_Bcl11b-KO-Treg-Foxp3_WT-Treg-Foxp3-specific.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_WT-Treg-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_WT-Treg-Foxp3-specific_.bed


title: Tcell_OKT3_rep1

description:
OKT3_1
processed data file:
de-ctrlxOKT3.csv


title: WT_Treg_Bcl11b_rep3

description: Bcl11b ChIP DNA


title: Tcell_UT_rep2

description:
UT_2
Control

source_name: T cell Control


title: Tcell_UT_rep1

description:
UT_1
Control


title: WT_Treg_Bcl11b_rep1

description:
Bcl11b ChIP DNA
WT-Treg-Bcl11b_vs_KIKO-Bcl11b_KIKO-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_KIKO-Bcl11b_WT-Treg-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_KIKO-Bcl11b_common.bed
WT-Treg-Bcl11b_vs_WT-Tn-Bcl11b_common.bed
WT-Treg-Bcl11b_vs_WT-Tn-Bcl11b_WT-Tn-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_WT-Tn-Bcl11b_WT-Treg-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_common.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_WT-Treg-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_WT-Treg-Foxp3_WT-Treg-Foxp3-specific_.bed


title: WT_Tn_Input_rep2

description: Input DNA

source_name: Bcl11b sufficient Tn cells


title: WT_Treg_Input_rep2

description: Input DNA


title: WT_Tn_Bcl11b_rep2

description:
Bcl11b ChIP DNA
WT-Treg-Bcl11b_vs_WT-Tn-Bcl11b_common.bed
WT-Treg-Bcl11b_vs_WT-Tn-Bcl11b_WT-Tn-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_WT-Tn-Bcl11b_WT-Treg-Bcl11b-specific.bed


title: WT_Tn_Bcl11b_rep3


title: WT_Tn_Bcl11b_rep1


title: WT_Tn_Input_rep1

description: Input DNA


title: KIKO_Input

description: Input DNA

source_name: Treg cells devoid of Foxp3 (Tfn)

value: Sorted CD4+GFP+ cells


title: WT_Treg_Bcl11b_rep2


title: KIKO_Bcl11b_rep1

description:
Bcl11b ChIP DNA
WT-Treg-Bcl11b_vs_KIKO-Bcl11b_common.bed
WT-Treg-Bcl11b_vs_KIKO-Bcl11b_KIKO-Bcl11b-specific.bed
WT-Treg-Bcl11b_vs_KIKO-Bcl11b_WT-Treg-Bcl11b-specific.bed


title: KIKO_Bcl11b_rep2