title: E14_WT_H3K18ub_ChIP_seq_rep

first: Falong

last: Lu

address: 1 West Beichen Road Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Clean reads were aligned to the human reference genome (hg38) and mouse reference genome (mm10), respectively, using Bowtie2 with default parameters.
Unmapped reads, multiple mapped reads and PCR duplicates were removed by samtools and Picard.
HeLa H3K18ub peaks were called using MACS2 with the parameters: --broad -g 2.9e9 -q 0.05 -f BAMPE --nomodel --extsize 147 -B.
E14 H3K18ub peaks were called using SICER with the parameters: --window size 200 --gap size 200.
E14 H3K27me3 peaks were called by SICER with parameters: --window size 200 --gap size 600.
Hela H3K27me3 peaks were called by SICER with parameters: --window size 2000 --gap size 8000.
Genome_build: mm10;hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage(v3.3.1); Scores represent RPKM.
Supplementary_files_format_and_content: peak text files

growth_protocol: WT and SUZ12 KO HeLa-S3 cells were grown in Dulbecco’s Modiﬁed Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. WT, Suz12 KO, Uhrf1 KO and Suz12/Uhrf1 DKO E14Tg2a mESCs were cultured on 0.2% gelatin-coated plates in DMEM supplemented with 15% fetal bovine serum, 1% penicillin/streptomycin, 1% nonessential amino acid, 1% sodium pyruvate, β-mercaptoethanol and 1000 U/mL LIF (ESGRO, Millipore).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 minutes. After quenching with 125 mM glycine, the cells were harvested and digested by MNase (NEB, M0247S, 2 U/μL) at 37 °C for 20 minutes to produce soluble chromatin with DNA fragments in the range of 150-300 bp. The lysates were then sonicated for 5 minutes (30 sec on / 30 sec off) using Bioruptor Sonicator (Diagenode, Inc., Denville, NJ) and centrifuged at 21,130 g for 10 minutes. The supernatants were collected and the chromatin content was incubated with Protein A and Protein G Dynabeads pre-linked with antibodies against H3K27me3 or H3K18ub overnight at 4 °C. Bound chromatin was washed extensively, then eluted and reverse-crosslinked at 65 °C overnight using elution buffer. After being treated by RNase A and proteinase K, the samples were extracted by phenol: chloroform and precipitated with ethanol in the presence of linear acrylamide. After dissolving in nuclease free TE buffer, the samples are ready for sequencing library construction.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: WT

tag: chip antibody

value: H3K18ub (custom-made)


title: AB6603

status: Public on Jun 27 2022

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: MARS

library_source: transcriptomic

data_processing:
bcl2fastq/2.20.0.422
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
paired-end (read2 used to read cell and molecule barcodes only)
Assembly: mm10
Supplementary files format and content: Tab-separated UMI matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: Whole brain

extract_protocol:
Mice were euthanized using an overdose of ketamine-xylazine, followed by transcardial perfusion with cold PBS, and whole brains were excised. Tissues were chopped into small pieces and subjected to 30 minutes of enzymatic digestion using papain (Worthington, LS003127) in 37oC, followed by manual trituration using a 5ml pipette and filtering through a 70μm cell strainer. Cells were pelleted at 800g for 5 min in 4oC and then suspended in ovomucoid protease inhibitor (Worthington, LS003086) solution to stop papain activity. Cells were pelleted again in 600g, 5 min, 4oC, washed, and myelin debris was removed by 30% Percoll gradient (GE healthcare, 17-0891-01). Then, cells were pelleted and washed again and subjected to 20 min Fc block (1:200), following 30 min cell surface staining. Immediately before FACS, cells were washed, filtered through a 70μm cell strainer, suspended in sorting buffer (PBS supplemented with 0.2mM EDTA pH8 and 0.5% BSA), and DAPI was added. Samples were kept on ice at all times except for enzymatic digestion. Cell populations were sorted using FACS-AriaIII or FACSymphony-S6 and FACS DIVA software (BD Biosciences, San Jose, CA). For the sorting of all the non-immune populations, samples were gated for CD45- (APC, clone 30F-11, 17-0451-82, eBioscience or 103115, BioLegend, 1:200), while excluding debris (FSC-A vs. SSC-A), dead cells (DAPI+), and doublets (FSC-A vs. FSC-H). In order to enrich for different cell populations, the following markers were used: GalC (oligodendrocytes, FITC, clone mGalC, FCMAB312F, Milli-Mark, 1:10), Ly6A/E (endothelial, BV605, clone D7, 108133, BioLegend, 1:150). Isolated cells were single-cell sorted into 384-well cell capture plates containing 2μl of lysis solution and barcoded poly(T) reverse-transcription (RT) primers for single-cell RNA-seq15. Four empty wells were kept in each 384-well plate as a no-cell control. Immediately after sorting, each plate was spun down to ensure cell immersion into the lysis solution, snap-frozen on dry ice, and stored at –80oC until processing. To record the marker level of each single cell, the FACS Diva ‘index sorting’ function was activated during single-cell sorting. Following the sequencing and analysis of the single cells, each surface marker was linked to the genome-wide expression profile. This methodology was used to optimize the gating strategy and to eliminate autofluorescent cells.
mRNA from the cells sorted into cell capture plates were barcoded, converted into cDNA, and pooled. The pooled sample was linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality as described in MARS-seq 2.0 protocol
MARS-seq2.0 protocol

tag: cell type

value: CD45- cells

tag: tissue

value: Whole brain

tag: strain

tag: age

value: 6 months


title: AB6442

description: MARS

value: 8 months


title: DNA methylation profile for 201414140130_R04C01

type: genomic

city: Exeter

first: Eilis

last: Hannon

address: RILD building

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
Dasen normalized betas (BDR_processed_signals.csv.gz)
Unmethylated and methylated signal intensities (BDR_raw_Signal.csv.gz)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol:
500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer’s standard protocol.
hapten-labeled dideoxynucleotides

extract_protocol: DNA was extracted using a phenol/chloroform method

tag: developmental stage

value: adult

value: brain

tag: brain region

value: Occipital

tag: gender

value: female

tag: cell proportion double negative

tag: cell proportion neun+

tag: cell proportion sox10+


title: DNA methylation profile for 201508110010_R03C01

value: Prefrontal

value: male


title: DNA methylation profile for 201508110010_R04C01


title: E14_Uhrf1_KO_H3K18ub_ChIP_seq

city: Beijing

country: China

library_source: genomic

tag: genotype


title: MLN

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

country: USA

institute: NYU Langone Health

data_processing:
Reads were processed using 10X’s Cell Ranger version 3.0.2 using the mm10 reference genome, resulting in a filtered HDF5 file
Further processing and analysis of scRNA-Seq data were performed in R version 3.6.3 using the Seurat package version 3.2.1
Cell Ranger output was imported using the Read10X_h5. Seurat objects were created using only genes appearing in at least 3 cells. Cells were further filtered to exclude those with fewer than 1000 genes detected, more than 5000 genes detected, or more than 10 percent mitochondrial reads.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 (.h5) files generated by CellRanger 3.0.2
Supplementary_files_format_and_content: TSV file contains cell (barcode) metadata from final processed Seurat object. Includes cluster identities and UMAP embedding coordinates

molecule: total RNA

source_name: GFP+ TCRb+ cells and GFP+ TCRb- cells sorted from mesenteric lymph nodes

extract_protocol: Standard Illumina/10X protocols


title: E14_Uhrf1_KO_H3K18ub_ChIP_seq_rep


title: DNA methylation profile for 201524770070_R05C01


title: DNA methylation profile for 201525200036_R06C01


title: E14_WT_H3K18ub_ChIP_seq


title: E14_Suz12_KO_2_WGBS

data_processing:
Base-calling were perform with Illumina sequencing system running RTA v1.18.54.
Reads were trimmed to remove the adapter sequences and low quality bases using Trim Galore.
Bismark v0.19.0 was used to align reads to a reference genome (hg38/mm10) and extract the coverage depth and methylation level of each cytosine
Genome_build: mm10;hg38
Supplementary_files_format_and_content: Coverage files (using 1-based genomic genomic coordinates) that feature methylated and unmethylated counts.

extract_protocol:
Genomic DNA (500 ng) with 1% lambda DNA spike-in was sheared by Bioruptor sonicator to an average size of 350 bp in length. DNA was then end-repaired, dA-tailed, and ligated with methylated adaptors according to the manufacturer’s instruction (NEBNext Ultra DNA Library Prep Kit for Illumina #E7645S). Bisulfite conversion was carried out using an EpiTect fast bisulfite conversion kit (Qiagen) according to the manufacturer’s instructions. Twenty minutes were used in both conversion steps.
Bisulfite-converted DNA was then amplified by PCR to obtain the final library. The WGBS libraries were subjected to pair-end (150 bp) sequencing on a Novaseq instrument (Illumina).


title: DNA methylation profile for 201525200036_R05C01


title: E14_Uhrf1_KO_WGBS


title: DNA methylation profile for 201414140130_R03C01


title: E14_WT_input_ChIP_seq

value: none (input)


title: E14_WT_WGBS


title: Rep2_4J_75min_VCPinh_RPB1ChIP

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: ChIP-seq

data_processing:
Reads were aligned to a hybrid genome (hg38 and mm10) using the DNAmapping and ChIPseq modules from snakePipes
Mouse spike-in reads were used to calculate size factors. Normalized bigwig files for human reads were generated using deeptools based on the calculated size factors
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files for ChIP-seq coverage

extract_protocol: Cells were fixed in 1% methanol-free formaldehyde (Thermo Scientific, 28906) in PBS at room temperature for 10 min, followed by 5 min blocking in 0.125 M glycine. Cells were washed twice with ice-cold PBS. The cell pellet was resuspended in Farnham buffer (5 mM PIPES, pH 8; 85 mM KCl; 0.5% Igepal). Cell suspensions were sonicated for 4 min in 1 ml Covaris tubes (Covaris, 520130) using Covaris S220 with the following settings: peak power = 75; duty factor = 2; cycles/burst = 200. Isolated nuclei were washed with Farnham buffer and suspended in shearing buffer (10 mM Tris-HCl, pH 8; 0.1% SDS; 1 mM EDTA). Chromatin was sheared by sonication for 12 min in 1-ml Covaris tubes using the following settings: peak power = 140; duty factor = 5; cycles/burst = 200. Debris was removed by centrifugation. A DNA fragment–size distribution of 200–600 bp was considered as ideal chromatin for ChIP. Chromatin was diluted 1:1 with IP buffer (10 mM Tris-HCl, pH 8; 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxicholate, 0.1% N-lauroylsarcosine) to achieve a final 0.05% SDS concentration. Good quality chromatin (200 μg) was used for immunoprecipitation as described {Montrose, 1985 #102}. Briefly, Protein A magnetic beads (Life Technologies, 10002D) were incubated (rotated) with 10 μg of f Rpb1 NTD (D8L4Y) Rabbit mAb (Cell Signaling #14958) for 6 h at 4 °C. This bead–antibody complex was then incubated overnight at 4 °C with chromatin.

tag: treatment

value: 4J irradiation for 75min in the presence of VCP inhibitor

value: RPB1 NTD (D8L4Y), Cell signaling #14958


title: DNA methylation profile for 201438350162_R06C01


title: DNA methylation profile for 201508110016_R02C01


title: DNA methylation profile for 201438350162_R05C01


title: DNA methylation profile for 201524770070_R06C01


title: Rep2_4J_75min_RPB1ChIP

description: ChIP-seq

value: 4J irradiation for 75min


title: AB6440

description: MARS


title: DNA methylation profile for 201508110016_R01C01


title: DNA methylation profile for 201438350120_R04C01


title: E14_Suz12_Uhrf1_KO_WGBS


title: DNA methylation profile for 201438350096_R08C01


title: DNA methylation profile for 201438350125_R06C01


title: DNA methylation profile for 201438350125_R05C01


title: E14_Suz12_KO_WGBS


title: Rep2_0J_VCPinh_RPB1ChIP

description: ChIP-seq

value: No irradiation in the presence of VCP inhibitor


title: DNA methylation profile for 201438350178_R08C01


title: DNA methylation profile for 201438350178_R07C01


title: H3K27ac_proB_KO_Rep1

city: Badalona

first: Maribel

last: Parra

state: Barcelona

address: Ctra. de Can Ruti, Camí de les Escoles, s/n

department: Lymphocyte Development and Disease

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Reads were aligned to mm10 using Bowtie v2.3.2
Filtering was based on ENCODE standards and removed those mapping to the blacklist and duplicates using samtools (v.1.9) and sambamba (v.0.7.0)
For peak calling MACS2 v2.2.7.1 was used
narrowPeak or broadPeak files were generated using MACS v2 with default settings
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (for H3K27ac) and broadpeak (for H3K27me) and excepting input samples

source_name: pro-B lymphocyte

growth_protocol: Cells were extracted from fresh murine bone marrow and sorted to obtain purified pro-B and pre-B cells.

extract_protocol:
Murine proB and preB lymphocytes were fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer. DNA sequencing libraries were prepared using the TRUESEQ ChIP kit (Illumina). Libraries were sequenced using HiSeqX 150+150PE platform from Magrogene Inc.
Libraries were constructed using TRUSEQ ChIP kit from Illumina

treatment_protocol: HDAC7 knockout cells have a floxed Hdac7 and a CRE

value: pro-B lymphocyte

value: Hdac7 knock-out


title: H3K27ac_proB_KO_Rep2


title: Input_proB_KO_Rep1


title: H3K27me3_proB_KO_Rep2


title: DNA methylation profile for 201438350120_R03C01


title: DNA methylation profile for 201525200030_R07C01


title: Rep2_0J_RPB1ChIP

description: ChIP-seq

value: No irradiation


title: H3K27me3_proB_KO_Rep1


title: Input_proB_KO_Rep2


title: DNA methylation profile for 201438350031_R01C01


title: H3K27me3_proB_WT_Rep2

value: wild-type


title: DNA methylation profile for 201525200030_R08C01


title: H3K27ac_proB_WT_Rep1


title: DNA methylation profile for 201506830044_R01C01


title: DNA methylation profile for 201506830044_R02C01


title: H3K27me3_proB_WT_Rep1


title: ATAC_PreB_KO_Rep2

data_processing:
Reads were aligned to mm10 using Bowtie v2.3.2
Filtering was based on ENCODE standards and removed those mapping to the blacklist and duplicates using samtools (v.1.9) and sambamba (v.0.7.0)
For peak calling MACS2 v2.2.7.1 was used
Peaks were generated using MACS v2 with default settings
Assembly: mm10
Supplementary files format and content: bw files were generated using MACS2

source_name: pre-B lymphocyte

extract_protocol:
Cells were extracted from bone marrow (femur and tibia of both hind legs) of Hdac7+/- and Hdac7fl/- mice. Cells were stained and sorted as pro-B cells (IgM-,CD19+,B220+, CD43+) and pre-B cells (IgM-,CD19+,B220+, CD43-). Fresh whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina). Two duplicates per condition were processed.
DNA libraries were prepared as described in Buenrostro et al., 2015

value: pre-B lymphocyte


title: Input_proB_WT_Rep2


title: Input_proB_WT_Rep1


title: DNA methylation profile for 201525200133_R02C01


title: DNA methylation profile for 201414140202_R05C01


title: DNA methylation profile for 201438350096_R07C01


title: H3K27ac_proB_WT_Rep2


title: ATAC_ProB_WT_Rep2


title: DNA methylation profile for 201508110045_R02C01


title: ATAC_ProB_WT_Rep1


title: Tcf7KO-DN3_BC_96

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
Unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails.
Next, we removed reads with adapter contaminants and low-quality bases (N>10%)
The cleaned reads were aligned to the mm10 mouse transcriptome (Genocode) using Tophat (version 2.1.1)
uniquely mapped reads were counted using htseq-count of the HTSeq package, For each gene, duplicated transcripts with the same UMI sequence were removed. for each cell, the transcript copy number of each gene were counted on the basis of the number of distinct UMIs of that gene.
Genome_build: mm10

source_name: thymus DN2&DN3 cells (CD45+Lin-CD4-CD8-CD25+)

extract_protocol:
Single-cell cDNA amplification was carried out by using the STRT protocol with several modifications to allow for multiplexed single-cell RNA-seq. Libraries were prepared using KAPA Hyper Prep Kits (KK8505). The NEB U-shaped adapter was used for ligation. The libraries were sequenced on an Illumina Hiseq x ten platform to generate 150-bp paired-end reads (sequenced by BGI).
Libraries are constructed according to the standard protocol for Smart-seq2

value: thymus

value: 6~8 wks


title: DNA methylation profile for 201508110016_R05C01

value: adult

value: brain


title: Tcf7KO-DN3_BC_95


title: ATAC_PreB_KO_Rep1


title: Tcf7KO-DN3_BC_9


title: DNA methylation profile for 201438350120_R06C01

value: Occipital


title: DNA methylation profile for 201438350031_R02C01


title: ATAC_ProB_KO_Rep2


title: DNA methylation profile for 201438350120_R05C01

value: Prefrontal


title: DNA methylation profile for 201508110016_R06C01

value: male


title: DNA methylation profile for 201414140202_R06C01


title: DNA methylation profile for 201438350036_R06C01


title: DNA methylation profile for 201508110045_R01C01


title: ATAC_PreB_WT_Rep1


title: DNA methylation profile for 201438350178_R02C01

value: female


title: ATAC_PreB_WT_Rep2


title: Tcf7KO-DN3_BC_92


title: DNA methylation profile for 201438350178_R01C01


title: Tcf7KO-DN3_BC_93


title: Tcf7KO-DN3_BC_94


title: DNA methylation profile for 201438350049_R05C01


title: Tcf7KO-DN3_BC_91


title: ATAC_ProB_KO_Rep1


title: Tcf7KO-DN3_BC_90


title: DNA methylation profile for 201438350036_R05C01


title: DNA methylation profile for 201414140202_R02C01


title: DNA methylation profile for 201525200133_R01C01


title: DNA methylation profile for 201525200028_R02C01


title: Tcf7KO-DN3_BC_88


title: DNA methylation profile for 201438350049_R06C01


title: Tcf7KO-DN3_BC_85


title: Tcf7KO-DN3_BC_84


title: Tcf7KO-DN3_BC_89


title: DNA methylation profile for 201438350096_R06C01


title: DNA methylation profile for 201525200028_R01C01


title: DNA methylation profile for 201414140130_R05C01


title: Tcf7KO-DN3_BC_83


title: DNA methylation profile for 201438350162_R08C01


title: DNA methylation profile for 201438350124_R02C01


title: Tcf7KO-DN3_BC_8


title: DNA methylation profile for 201438350162_R07C01


title: Tcf7KO-DN3_BC_81


title: DNA methylation profile for 201438350124_R01C01


title: Tcf7KO-DN3_BC_80


title: DNA methylation profile for 201508110054_R06C01


title: Tcf7KO-DN3_BC_77


title: DNA methylation profile for 201508110054_R05C01


title: Tcf7KO-DN3_BC_86


title: DNA methylation profile for 201438350096_R05C01


title: Tcf7KO-DN3_BC_82


title: DNA methylation profile for 203205080153_R08C01


title: Tcf7KO-DN3_BC_75


title: Tcf7KO-DN3_BC_74


title: Tcf7KO-DN3_BC_87


title: Tcf7KO-DN3_BC_79


title: DNA methylation profile for 201438350120_R08C01


title: DNA methylation profile for 201525200080_R06C01


title: Tcf7KO-DN3_BC_73


title: DNA methylation profile for 201438350107_R02C01


title: Tcf7KO-DN3_BC_71


title: DNA methylation profile for 201438350116_R07C01


title: Tcf7KO-DN3_BC_70


title: Tcf7KO-DN3_BC_7


title: DNA methylation profile for 201414140130_R06C01


title: DNA methylation profile for 201438350120_R07C01


title: DNA methylation profile for 201525200080_R05C01


title: Tcf7KO-DN3_BC_76


title: Tcf7KO-DN3_BC_6


title: DNA methylation profile for 201438350036_R01C01


title: Tcf7KO-DN3_BC_69


title: Tcf7KO-DN3_BC_68


title: Tcf7KO-DN3_BC_78


title: Tcf7KO-DN3_BC_72


title: Tcf7KO-DN3_BC_66


title: DNA methylation profile for 201438350116_R08C01


title: DNA methylation profile for 203205080153_R07C01


title: DNA methylation profile for 201438350107_R01C01


title: DNA methylation profile for 201525200125_R03C01


title: DNA methylation profile for 201438350036_R02C01


title: Tcf7KO-DN3_BC_62


title: DNA methylation profile for 201525200125_R04C01


title: DNA methylation profile for 201414140176_R02C01


title: DNA methylation profile for 201525200066_R05C01


title: Tcf7KO-DN3_BC_61


title: Tcf7KO-DN3_BC_64


title: DNA methylation profile for 201524770103_R08C01


title: Tcf7KO-DN3_BC_67


title: Tcf7KO-DN3_BC_63


title: DNA methylation profile for 201524770103_R02C01


title: DNA methylation profile for 201525200066_R06C01


title: DNA methylation profile for 201524770103_R07C01


title: Tcf7KO-DN3_BC_56


title: Tcf7KO-DN3_BC_60


title: DNA methylation profile for 201525200133_R06C01


title: Tcf7KO-DN3_BC_5


title: DNA methylation profile for 201438350125_R01C01


title: Tcf7KO-DN3_BC_53


title: Tcf7KO-DN3_BC_65


title: Tcf7KO-DN3_BC_52


title: DNA methylation profile for 201438350154_R02C01


title: DNA methylation profile for 201414140176_R01C01


title: Tcf7KO-DN3_BC_58


title: DNA methylation profile for 201438350125_R02C01


title: DNA methylation profile for 201524770103_R01C01


title: DNA methylation profile for 201438350116_R03C01


title: Tcf7KO-DN3_BC_57


title: Tcf7KO-DN3_BC_55


title: Tcf7KO-DN3_BC_46


title: DNA methylation profile for 201438350103_R04C01


title: Tcf7KO-DN3_BC_51


title: DNA methylation profile for 201525200133_R05C01


title: DNA methylation profile for 201438350154_R01C01


title: DNA methylation profile for 201438350103_R03C01


title: DNA methylation profile for 201525200140_R04C01


title: DNA methylation profile for 201525200102_R01C01


title: Tcf7KO-DN3_BC_59


title: DNA methylation profile for 201525200140_R03C01


title: Tcf7KO-DN3_BC_4


title: Tcf7KO-DN3_BC_49


title: Tcf7KO-DN3_BC_50


title: Tcf7KO-DN3_BC_42


title: Tcf7KO-DN3_BC_43


title: DNA methylation profile for 201438350093_R04C01


title: Tcf7KO-DN3_BC_54


title: DNA methylation profile for 201438350116_R04C01


title: DNA methylation profile for 201438350093_R03C01


title: DNA methylation profile for 201525200102_R02C01


title: Tcf7KO-DN3_BC_47


title: Tcf7KO-DN3_BC_48


title: Tcf7KO-DN3_BC_45


title: DNA methylation profile for 201508110012_R01C01


title: Tcf7KO-DN3_BC_3


title: Tcf7KO-DN3_BC_41


title: Tcf7KO-DN3_BC_40


title: DNA methylation profile for 201508110012_R02C01


title: DNA methylation profile for 201438350095_R05C01


title: DNA methylation profile for 201508110017_R02C01


title: Tcf7KO-DN3_BC_39


title: DNA methylation profile for 201508110017_R01C01


title: Tcf7KO-DN3_BC_35


title: DNA methylation profile for 201524770062_R08C01


title: Tcf7KO-DN3_BC_44


title: DNA methylation profile for 201524770062_R07C01


title: DNA methylation profile for 201508130008_R08C01


title: DNA methylation profile for 201438350095_R06C01


title: Tcf7KO-DN3_BC_38


title: Tcf7KO-DN3_BC_33


title: DNA methylation profile for 201414140130_R02C01


title: Tcf7KO-DN3_BC_34


title: Tcf7KO-DN3_BC_37


title: DNA methylation profile for 201414140130_R01C01


title: Tcf7KO-DN3_BC_36


title: DNA methylation profile for 201525200140_R06C01


title: Tcf7KO-DN3_BC_31


title: DNA methylation profile for 201508130008_R07C01


title: DNA methylation profile for 201525200140_R05C01


title: Tcf7KO-DN3_BC_32


title: DNA methylation profile for 201414140176_R08C01


title: DNA methylation profile for 201506830044_R06C01


title: Tcf7KO-DN3_BC_30


title: Tcf7KO-DN3_BC_29


title: Tcf7KO-DN3_BC_2


title: DNA methylation profile for 201506830044_R05C01


title: Tcf7KO-DN3_BC_28


title: DNA methylation profile for 201414140176_R07C01


title: Tcf7KO-DN3_BC_26


title: Tcf7KO-DN3_BC_27


title: DNA methylation profile for 201525200110_R04C01


title: DNA methylation profile for 201438350166_R03C01


title: DNA methylation profile for 201438350093_R01C01


title: DNA methylation profile for 201438350166_R04C01


title: DNA methylation profile for 201438350091_R04C01


title: Tcf7KO-DN3_BC_23


title: DNA methylation profile for 201525200110_R03C01


title: Tcf7KO-DN3_BC_21


title: DNA methylation profile for 201438350093_R02C01


title: Tcf7KO-DN3_BC_22


title: Tcf7KO-DN3_BC_24


title: Tcf7KO-DN3_BC_1


title: Tcf7KO-DN3_BC_20


title: DNA methylation profile for 201525200133_R08C01


title: DNA methylation profile for 201524770070_R02C01


title: DNA methylation profile for 201525200079_R07C01


title: Tcf7KO-DN3_BC_19


title: Tcf7KO-DN3_BC_18


title: Tcf7KO-DN3_BC_25


title: DNA methylation profile for 201524770070_R01C01


title: DNA methylation profile for 201438350125_R04C01


title: Tcf7KO-DN3_BC_16


title: Tcf7KO-DN3_BC_15


title: Tcf7KO-DN3_BC_17


title: Tcf7KO-DN3_BC_14


title: DNA methylation profile for 201438350125_R03C01


title: DNA methylation profile for 201525200079_R08C01


title: DNA methylation profile for 201414140202_R08C01


title: Tcf7KO-DN3_BC_12


title: DNA methylation profile for 201525200133_R07C01


title: Tcf7KO-DN3_BC_13


title: DNA methylation profile for 201438350107_R06C01


title: Tcf7KO-DN1_BC_9

source_name: thymus DN1 cells (CD45+Lin-CD4-CD8-CD25-CD44+)


title: Tcf7KO-DN3_BC_11


title: DNA methylation profile for 201438350107_R05C01


title: DNA methylation profile for 201438350107_R04C01


title: DNA methylation profile for 201525200080_R04C01


title: Tcf7KO-DN3_BC_10


title: Tcf7KO-DN1_BC_94


title: DNA methylation profile for 201438350114_R02C01


title: Tcf7KO-DN1_BC_96


title: Tcf7KO-DN1_BC_95


title: DNA methylation profile for 201438350114_R01C01


title: Tcf7KO-DN1_BC_91


title: Tcf7KO-DN1_BC_93


title: DNA methylation profile for 201438350107_R03C01


title: DNA methylation profile for 201525200110_R06C01


title: DNA methylation profile for 201525200030_R02C01


title: DNA methylation profile for 201525200030_R01C01


title: Tcf7KO-DN1_BC_89


title: DNA methylation profile for 201525200110_R05C01


title: Tcf7KO-DN1_BC_92


title: Tcf7KO-DN1_BC_8


title: DNA methylation profile for 201414140202_R07C01


title: DNA methylation profile for 201525200080_R03C01


title: DNA methylation profile for 201438350096_R01C01


title: DNA methylation profile for 201438350096_R02C01


title: Tcf7KO-DN1_BC_88


title: Tcf7KO-DN1_BC_87


title: DNA methylation profile for 201508130008_R05C01


title: DNA methylation profile for 201508130008_R06C01


title: Tcf7KO-DN1_BC_84


title: Tcf7KO-DN1_BC_85


title: Tcf7KO-DN1_BC_86


title: DNA methylation profile for 201525200066_R02C01


title: Tcf7KO-DN1_BC_90


title: DNA methylation profile for 201525200066_R01C01


title: DNA methylation profile for 201438350162_R02C01


title: DNA methylation profile for 201438350162_R01C01


title: Tcf7KO-DN1_BC_82


title: Tcf7KO-DN1_BC_81


title: Tcf7KO-DN1_BC_83


title: Tcf7KO-DN1_BC_80


title: DNA methylation profile for 201438350109_R04C01


title: Tcf7KO-DN1_BC_7


title: DNA methylation profile for 201438350109_R03C01


title: DNA methylation profile for 201508110010_R02C01


title: Tcf7KO-DN1_BC_79


title: DNA methylation profile for 201438350093_R08C01


title: Tcf7KO-DN1_BC_77


title: DNA methylation profile for 201508110010_R01C01


title: DNA methylation profile for 201438350093_R07C01


title: DNA methylation profile for 201438350131_R02C01


title: Tcf7KO-DN1_BC_78


title: Tcf7KO-DN1_BC_75


title: Tcf7KO-DN1_BC_76


title: Tcf7KO-DN1_BC_74


title: DNA methylation profile for 201438350131_R01C01


title: DNA methylation profile for 201524770070_R04C01


title: Tcf7KO-DN1_BC_73


title: DNA methylation profile for 201524770070_R03C01


title: DNA methylation profile for 201508110017_R05C01


title: Tcf7KO-DN1_BC_71


title: Tcf7KO-DN1_BC_70


title: DNA methylation profile for 201438350124_R08C01


title: DNA methylation profile for 201438350120_R02C01


title: Tcf7KO-DN1_BC_69


title: Tcf7KO-DN1_BC_68


title: DNA methylation profile for 201438350120_R01C01


title: DNA methylation profile for 201438350124_R07C01


title: DNA methylation profile for 201525200140_R08C01


title: Tcf7KO-DN1_BC_66


title: Tcf7KO-DN1_BC_67


title: DNA methylation profile for 201525200140_R07C01


title: DNA methylation profile for 201525200080_R08C01


title: Tcf7KO-DN1_BC_64


title: Tcf7KO-DN1_BC_63


title: Tcf7KO-DN1_BC_65


title: Tcf7KO-DN1_BC_61


title: Tcf7KO-DN1_BC_72


title: Tcf7KO-DN1_BC_60


title: DNA methylation profile for 201508110017_R06C01


title: DNA methylation profile for 201438350166_R07C01


title: DNA methylation profile for 201508110012_R06C01


title: DNA methylation profile for 201508110012_R05C01


title: Tcf7KO-DN1_BC_6


title: DNA methylation profile for 201524770116_R04C01


title: HaCaT cells, WT, Control treated, 24h

city: Chengdu

first: Jie

last: Tang

state: Sichuan

address: No. 5, Gong Xing Road

institute: West China Hospital of Sichuan University

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity to low-quality sequence, then mapped to mm8
Reads Per Kilobase of exon per Megabase of library size(RPKM) were calculated using a protocol from Chepelev et al.
Assembly: mm9
Supplementary files format and content: Text files include gene counts and FPKM values for each sample
Supplementary files format and content: Raw gene counts for every sample

source_name: epidermal skin

growth_protocol: HaCaT keratinocyte cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin streptomycin (ps) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA of HaCaT cells treated by CB (25 μg/mL) and S1650b (50 μg/mL) for 24 hours were extracted by Trizol.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's protocols.

treatment_protocol: HaCaT cells were cultured overnight, and then treated with various concentrations of CB (25 μg/mL) and S1650b (50μg/mL) dissolved in FBS-free DMEM medium for another 24 hours.

value: epidermal skin

value: HaCaT

value: keratinocyte

value: WT

value: exposed to none


title: Tcf7KO-DN1_BC_59


title: DNA methylation profile for 201524770116_R03C01


title: HaCaT cells, WT, S_50 treated, 24h

value: exposed to S 1650b


title: Tcf7KO-DN1_BC_58


title: DNA methylation profile for 201438350166_R08C01


title: DNA methylation profile for 201525200079_R06C01


title: DNA methylation profile for 201525200080_R07C01


title: Tcf7KO-DN1_BC_62


title: Independent_HMLER, C1, C2

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

institute: The Hebrew University of Jerusalem

data_processing:
3' RNAseq (10x kit V2)
Demultiplexing is run using Cell Ranger mkfastq.
Cell-ranger count is run using cell-ranger v2.1.1 on firecoud.
R package dropletUtils is used to exclude chimeric reads and identify and exclude empty droplets
Assembly: GRCh38
Supplementary files format and content: Batch and cell barcode information
Supplementary files format and content: GeneID and ensemble ID for all gene features used.
Supplementary files format and content: Matrix Market (MM) sparse count matrix post QC filtering and exclusion of additional cells not used for analysis.
Supplementary files format and content: Basic metdata

growth_protocol: Cells were cultured in 2:1:1 MEGM (Lonza Bullet kit), DMEM and F12 media, supplemented with insulin (10 μg/ml), EGF (10 ng/ml), hydrocortisone (1 μg/ml), and 1x Pen/Strep (50 I.U./mL penicillin and 50 μg/mL streptomycin, Sigma-Aldrich #P4333).

extract_protocol: For single cell RNA-seq, libraries for isolated single cells were generated using 10X genomics Chromium Single Cell 3’ Library & Gel bead   Kit V2 according to the manufacturer’s protocol. The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NextSeq using HO-SE75 kit or on HiSeq2 500 platform using PE50 kit.

value: wild type

value: HMLER

tag: clone

value: HMLER, C1 and C2

tag: culture conditions

value: Independent culture

tag: rna barcode


title: Coculture_HMELR, C1, C2

tag: cell line

value: Co-cutulre


title: Tcf7KO-DN1_BC_55

value: thymus

value: 6~8 wks


title: Tcf7KO-DN1_BC_57


title: Tcf7KO-DN1_BC_56


title: DNA methylation profile for 201525200076_R08C01

value: adult

value: brain

value: Occipital


title: Tcf7KO-DN1_BC_54


title: DNA methylation profile for 201525200076_R07C01

value: Prefrontal

value: male


title: DNA methylation profile for 201438350131_R08C01


title: Tcf7KO-DN1_BC_5


title: Tcf7KO-DN1_BC_53


title: DNA methylation profile for 201438350131_R07C01


title: Tcf7KO-DN1_BC_52


title: DNA methylation profile for 201524770103_R06C01


title: DNA methylation profile for 201524770103_R05C01


title: Tcf7KO-DN1_BC_50


title: DNA methylation profile for 201525200030_R06C01

value: female


title: Tcf7KO-DN1_BC_4


title: HaCaT cells, WT, CB_25 treated, 24h

value: epidermal skin

value: HaCaT

value: keratinocyte

value: exposed to carbon black


title: DNA methylation profile for 201525200030_R05C01


title: DNA methylation profile for 201525200079_R05C01


title: Tcf7KO-DN1_BC_48


title: DNA methylation profile for 201508110054_R07C01


title: DNA methylation profile for 201508110054_R08C01


title: Tcf7KO-DN1_BC_47


title: DNA methylation profile for 201525200079_R01C01


title: Tcf7KO-DN1_BC_46


title: DNA methylation profile for 201525200079_R02C01


title: Tcf7KO-DN1_BC_49


title: DNA methylation profile for 201438350049_R08C01


title: Tcf7KO-DN1_BC_43


title: Tcf7KO-DN1_BC_51


title: DNA methylation profile for 201525200110_R02C01


title: Tcf7KO-DN1_BC_45


title: DNA methylation profile for 201525200110_R01C01


title: Tcf7KO-DN1_BC_40


title: DNA methylation profile for 201524770116_R02C01


title: Tcf7KO-DN1_BC_3


title: Tcf7KO-DN1_BC_39


title: DNA methylation profile for 201524770116_R01C01


title: Tcf7KO-DN1_BC_38


title: Tcf7KO-DN1_BC_37


title: DNA methylation profile for 201525200028_R06C01


title: DNA methylation profile for 201508110017_R04C01


title: DNA methylation profile for 201508110017_R03C01


title: Tcf7KO-DN1_BC_34


title: Tcf7KO-DN1_BC_33


title: Tcf7KO-DN1_BC_36


title: DNA methylation profile for 201525200028_R07C01


title: Tcf7KO-DN1_BC_35


title: Tcf7KO-DN1_BC_42


title: DNA methylation profile for 201525200102_R08C01


title: Tcf7KO-DN1_BC_32


title: DNA methylation profile for 201525200102_R07C01


title: Tcf7KO-DN1_BC_44


title: Tcf7KO-DN1_BC_41


title: DNA methylation profile for 201525200028_R05C01


title: DNA methylation profile for 201438350049_R07C01


title: DNA methylation profile for 201525200080_R02C01


title: Tcf7KO-DN1_BC_31


title: DNA methylation profile for 201525200080_R01C01


title: DNA methylation profile for 201524770062_R06C01


title: Tcf7KO-DN1_BC_30


title: Tcf7KO-DN1_BC_2


title: DNA methylation profile for 201524770062_R05C01


title: DNA methylation profile for 201525200036_R08C01


title: Tcf7KO-DN1_BC_29


title: DNA methylation profile for 201525200028_R08C01


title: DNA methylation profile for 201438350031_R08C01


title: DNA methylation profile for 201525200036_R07C01


title: DNA methylation profile for 201438350091_R01C01


title: Tcf7KO-DN1_BC_24


title: Tcf7KO-DN1_BC_26


title: Tcf7KO-DN1_BC_27


title: Tcf7KO-DN1_BC_28


title: DNA methylation profile for 201438350031_R07C01


title: DNA methylation profile for 201508110045_R04C01


title: DNA methylation profile for 201438350154_R08C01


title: DNA methylation profile for 201438350166_R06C01


title: Tcf7KO-DN1_BC_23


title: DNA methylation profile for 201524770062_R02C01


title: Tcf7KO-DN1_BC_22


title: DNA methylation profile for 201438350154_R07C01


title: Tcf7KO-DN1_BC_20


title: DNA methylation profile for 201438350096_R04C01


title: DNA methylation profile for 201438350096_R03C01


title: Tcf7KO-DN1_BC_16


title: Tcf7KO-DN1_BC_19


title: DNA methylation profile for 201438350166_R05C01


title: DNA methylation profile for 201438350131_R06C01


title: DNA methylation profile for 201524770062_R01C01


title: Tcf7KO-DN1_BC_1


title: Tcf7KO-DN1_BC_18


title: Tcf7KO-DN1_BC_15


title: Tcf7KO-DN1_BC_17


title: Tcf7KO-DN1_BC_14


title: DNA methylation profile for 201438350131_R05C01


title: Tcf7KO-DN1_BC_12


title: Tcf7KO-DN1_BC_25


title: DAR53_post_RNA

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 platform using the single end protocol with a read length of 65-bp.
Sequencing data was aligned to the human reference genome hg38 using TopHat and the number of reads per gene was measured with HTSeq count.
Peak calling over paired input controls (per tissue sample and treatment) was performed using MACS2 and Dfilter. Peaks called by both peak callers were used for analysis.
For QC purposes, total readcounts per sample were determined and hierarchical clustering based on the Euclidean distance was applied. Samples with a readcount ≥ 2 standard deviations below the mean of all sample readcounts were removed, as well as samples that clustered in a separate branch.
Normalized and log2-transformed data is provided in the table DARANA_GE_table.txt
Genome_build: hg38
Supplementary_files_format_and_content: Expression table of samples (columns) by transcript (rows) reporting normalized read counts.

source_name: primary prostate cancer

growth_protocol: FFPE material

extract_protocol:
Prior to RNA isolation, FFPE material was pathologically assessed. The expert pathologist scored tumor cell percentage and indicated most tumor-dense regions for isolation on a hematoxylin and eosin (H&E) slide. RNA and DNA from FFPE material were simultaneously isolated from 3-10 sections (depending on tumor size) of 10 µm using the AllPrep DNA/RNA FFPE isolation kit (80234, Qiagen) and the QIAcube according to the manufacturer’s instructions. cDNA was synthesized from 250 ng RNA using SuperScript III Reverse Transcriptase (Invitrogen) with random hexamer primers.
For RNA-seq, strand-specific libraries were generated with the TruSeq RNA Exome kit (Illumina).

treatment_protocol: Neoadjuvant enzalutamide treatment (160 mg/day) followed by Robotic-Assisted Laparoscopic Prostatectomy (RALP).

tag: patient id

tag: enz treatment

value: post


title: DNA methylation profile for 203249020153_R02C01

tag: tissue


title: Tcf7KO-DN1_BC_11

tag: strain


title: Tcf7KO-DN1_BC_10

tag: age


title: DAR53_pre_RNA

value: pre


title: DNA methylation profile for 201438350095_R08C01

tag: developmental stage


title: DNA methylation profile for 201438350095_R07C01

tag: brain region


title: Tcf7KO-DN1_BC_21


title: Ileum LD3

city: Perth

first: Shamshad

middle: Ul

last: Hassan

state: Western Australia

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
The base-calling was done with an integrated software in DNBSeq platform.
The alignment of clean reads was done using STAR (v2.7.3a) aligner with default parameters.
The featureCounts function in the Subread (version 2.0.0) software was used to enumerate the number of reads mapping to each gene using the following parameters; -p --primary -t gene
DESeq2 R package was used to generate normalised abundance of genes in each sample.
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: Tab-delimited text file includes raw gene counts for each gene in each sample
Supplementary_files_format_and_content: A amtrix table with normalised gene counts for every biological replicate/sample and  gene.

organism: Ovis aries

source_name: Small Intestine (third part)

extract_protocol:
Total RNA was extracted using the RNeasy mini plus kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions with on column DNA digestion with DNase-I as an additional step.
RNA libraries were prepared for sequencing using standard DNBSeq protocols

value: Ileum

value: 1 year


title: DAR55_post_RNA


title: DAR56_post_RNA


title: Tcf7KO-DN1_BC_13


title: DNA methylation profile for 203271750069_R02C01

tag: gender


title: DAR52_pre_RNA


title: DNA methylation profile for 203249020153_R01C01

tag: cell proportion double negative


title: DAR51_post_RNA


title: DNA methylation profile for 203249020044_R06C01

tag: cell proportion neun+


title: DAR55_pre_RNA


title: Ileum LD2


title: DNA methylation profile for 203249020044_R05C01

tag: cell proportion sox10+


title: DAR54_pre_RNA


title: Ileum LD4


title: Lck-cre-Tcf7KO2-DN3_BC_9

description:
PolyA RNA
processed data file: barcode_information.xlsx
processed data file: count_matrix.csv
processed data file: expression_matrix_log2(TPM:10+1).csv

data_processing:
Unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails.
Next, we removed reads with adapter contaminants and low-quality bases (N>10%).
The cleaned reads were aligned to the mm10 mouse transcriptome (Genocode) using Tophat (version 2.1.1).
Uniquely mapped reads were counted using htseq-count of the HTSeq package. For each gene, duplicated transcripts with the same UMI sequence were removed. For each cell, the transcript copy number of each gene were counted on the basis of the number of distinct UMIs of that gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcode_information.xlsx
Supplementary_files_format_and_content: count_matrix.csv
Supplementary_files_format_and_content: expression_matrix_log2(TPM:10+1).csv

extract_protocol:
Single-cell cDNA amplification was carried out by using the STRT protocol with several modifications to allow for multiplexed single-cell RNA-seq. Libraries were prepared using KAPA Hyper Prep Kits (KK8505). The NEB U-shaped adapter was used for ligation. The libraries were sequenced on an Illumina Hiseq x ten platform to generate 150-bp paired-end reads (sequenced by BGI).
Libraries are constructed according to the standard protocol for Smart-seq2.

tag: strain/background

tag: genotype/variation

value: Lck-cre; Tcf7fl/fl

tag: cell type

value: DN2 & DN3


title: DNA methylation profile for 203271750069_R01C01


title: DAR52_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_96

value: thymus

value: 6~8 wks


title: DNA methylation profile for 203271750069_R07C01

value: adult

value: brain


title: Lck-cre-Tcf7KO2-DN3_BC_92


title: DAR49_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_95


title: DNA methylation profile for 203239900239_R03C01

value: Occipital


title: Ileum LD1


title: DAR48_post_RNA


title: DAR50_pre_RNA


title: DNA methylation profile for 203249020050_R01C01


title: Lck-cre-Tcf7KO2-DN3_BC_94


title: Lck-cre-Tcf7KO2-DN3_BC_93


title: Ileum HD1


title: Ileum HD4


title: DNA methylation profile for 203271750069_R08C01

value: Prefrontal

value: male


title: DAR47_pre_RNA


title: DAR50_post_RNA


title: DAR47_post_RNA


title: Ileum HD3


title: Lck-cre-Tcf7KO2-DN3_BC_88


title: Lck-cre-Tcf7KO2-DN3_BC_90


title: Ileum HD2


title: DAR46_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_87


title: DNA methylation profile for 203244500078_R01C01


title: Lck-cre-Tcf7KO2-DN3_BC_91


title: root rep2 [root_2]

city: Shanghai

first: Chao

last: Li

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NL6 whole genome using HISAT2 version 2.1.0 (http://ccb.jhu.edu/software/hisat2/index.shtml) with default parameters -q -p 1 -e 70   -f -v 1 -a -m 10 --best --strata
fragments per kilobase per milion fragments sequenced (FPKM) were calculated using a protocol from Trapnell et al., nature biotechnology, 2010.
Assembly: NL-6
Supplementary files format and content: raw counts, FPKM

organism: Chenopodium quinoa

source_name: roots of 2 days old seedlings

growth_protocol: for the NaCl treatment, quinoa seedlings were grown on solid MS medium in the dark at 25 ℃ for 3 days, and other seedlings were grown on soil under long-day (14 h light/10 h dark) condition for 14 days in greenhouse。

extract_protocol:
samples were flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. mRNA was purified and the construction of sequencing libraries was using VAHTS®mRNA-seq v3 Library Prep Kit for Illumina (Cat#NR612-01).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: for the NaCl treatment, 14 days seedlings grown on soli were submerged in 400 mM NaCl for 8 hours and then the leaf part were harvested, the controls were were treated with water.

value: roots

value: 2 days old seedlings

tag: treatment

value: untreated


title: DAR45_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_86


title: pistil rep3 [pistil_3]

source_name: pistill of newly open flowers

value: pistill

value: newly open flowers


title: stamen rep3 [stamen_3]

source_name: stamen of newly open flowers

value: stamen


title: DAR45_pre_RNA

value: pre


title: DNA methylation profile for 203249020044_R03C01


title: DAR48_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_8


title: DNA methylation profile for 203271750067_R04C01

value: female


title: stamen rep2 [stamen_2]


title: DNA methylation profile for 203249020044_R04C01


title: pistil rep2 [pistil_2]


title: Lck-cre-Tcf7KO2-DN3_BC_89

value: Lck-cre; Tcf7fl/fl


title: stamen rep1 [stamen_1]


title: DNA methylation profile for 203271750067_R03C01


title: Lck-cre-Tcf7KO2-DN3_BC_83

value: DN2 & DN3


title: DNA methylation profile for 203239900239_R04C01


title: Lck-cre-Tcf7KO2-DN3_BC_82

value: thymus


title: DAR43_post_RNA

value: post


title: NaCl treated leaf rep3 [leaf_s3]

source_name: 14 days old leaves teated with NaCl

value: leaves

value: 14 days old

value: treated with NaCl for 8 hours


title: DAR46_pre_RNA


title: DNA methylation profile for 203249020050_R02C01

value: adult

value: brain

value: Prefrontal


title: NaCl treated leaf rep2 [leaf_s2]


title: DNA methylation profile for 203239900239_R05C01

value: Occipital

value: male


title: DNA methylation profile for 203244500078_R02C01


title: leaf rep3 [leaf_3]

source_name: 14 days old leaves

value: untreated


title: Lck-cre-Tcf7KO2-DN3_BC_7

value: 6~8 wks


title: DNA methylation profile for 203239900239_R01C01


title: Lck-cre-Tcf7KO2-DN3_BC_85


title: root rep1 [root_1]

value: roots

value: 2 days old seedlings


title: root rep3 [root_3]


title: DNA methylation profile for 203239900239_R02C01

value: female


title: leaf rep2 [leaf_2]


title: Lck-cre-Tcf7KO2-DN3_BC_79

value: Lck-cre; Tcf7fl/fl


title: Lck-cre-Tcf7KO2-DN3_BC_84

value: DN2 & DN3


title: DAR43_pre_RNA

value: pre


title: DNA methylation profile for 203271750069_R03C01


title: leaf rep1 [leaf_1]


title: DAR44_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_81

value: thymus


title: DNA methylation profile for 203271750069_R04C01


title: Lck-cre-Tcf7KO2-DN3_BC_77


title: DAR44_post_RNA

value: post


title: pistil rep1 [pistil_1]

value: pistill

value: newly open flowers


title: Lck-cre-Tcf7KO2-DN3_BC_76


title: Lck-cre-Tcf7KO2-DN3_BC_80


title: DAR42_pre_RNA


title: DNA methylation profile for 203249020042_R01C01

value: adult


title: DAR41_post_RNA


title: DNA methylation profile for 203239900239_R06C01

value: brain


title: DAR39_pre_RNA


title: DAR42_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_78


title: DNA methylation profile for 203249020153_R06C01

value: Prefrontal


title: DAR40_post_RNA


title: DNA methylation profile for 203249020042_R02C01


title: DAR40_pre_RNA


title: DAR36_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_73


title: LsoB_Infection_7d_rep1

city: Hangzhou

first: Xiaotian

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

data_processing:
The high quality reads were analyzed in Discovery Environment web interface and platform at CyVerse (http://www.cyverse.org/) using the Tuxedo suite.
The expression levels were calculated by using the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) method.
Genes with an adjusted p-value (false discovery rate, FDR) less than 0.01 and fold change greater than or equal to 2.0 were considered as significantly differentially expressed genes (DEGs).
Assembly: Bactericera cockerelli transcriptome, transcript sequences are available on the series record.
Supplementary files format and content: tab-delimited text files include FPKM for each gene

organism: Bactericera cockerelli

source_name: Gut

extract_protocol:
Total RNA was extracted from potato psyllid gut after feeding on Candidatus Liberibacter solanacearum non-, LsoA-, or LsoB- infected plants after 2 and 7 days.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gut

value: LsoB_Infection_7 days


title: Lck-cre-Tcf7KO2-DN3_BC_72


title: LsoB_Infection_2d_rep3

value: LsoB_Infection_2 days


title: LsoB_Infection_7d_rep3


title: Lck-cre-Tcf7KO2-DN3_BC_75

value: 6~8 wks


title: LsoB_Infection_7d_rep2


title: DAR39_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_74


title: NaCl treated leaf rep1 [leaf_s1]

value: leaves

value: 14 days old

value: treated with NaCl for 8 hours


title: DNA methylation profile for 203249020153_R05C01

value: Occipital

value: male


title: DAR37_post_RNA


title: DNA methylation profile for 203249020050_R06C01


title: Lck-cre-Tcf7KO2-DN3_BC_70

value: Lck-cre; Tcf7fl/fl

value: DN2 & DN3


title: DAR35_pre_RNA

value: pre


title: LsoA_Infection_7d_rep2

value: LsoA_Infection_7 days


title: DNA methylation profile for 203244500069_R08C01

value: female


title: DAR36_pre_RNA


title: LsoB_Infection_2d_rep2


title: LsoB_Infection_2d_rep1


title: DNA methylation profile for 203249020050_R05C01

value: adult


title: DNA methylation profile for 203244500078_R06C01

value: brain


title: Lck-cre-Tcf7KO2-DN3_BC_71

value: thymus


title: DAR34_post_RNA

value: post


title: DAR33_post_RNA


title: DAR35_post_RNA


title: DNA methylation profile for 203239900238_R02C01

value: Prefrontal


title: DNA methylation profile for 203244500078_R05C01


title: DNA methylation profile for 203244500069_R07C01


title: Lck-cre-Tcf7KO2-DN3_BC_67


title: LsoA_Infection_2d_rep1

value: Gut

value: LsoA_Infection_2 days


title: LsoA_Infection_7d_rep3


title: Lck-cre-Tcf7KO2-DN3_BC_6

value: 6~8 wks


title: Lck-cre-Tcf7KO2-DN3_BC_69


title: DAR32_post_RNA


title: LsoA_Infection_7d_rep1


title: DAR34_pre_RNA


title: LsoA_Infection_2d_rep3


title: DAR32_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_68


title: DNA methylation profile for 203249020042_R05C01


title: DNA methylation profile for 203244500069_R01C01


title: DAR31_post_RNA


title: LsoA_Infection_2d_rep2


title: Lck-cre-Tcf7KO2-DN3_BC_66


title: DNA methylation profile for 203239900238_R01C01


title: DNA methylation profile for 203239900239_R07C01


title: DNA methylation profile for 203249020042_R06C01


title: Lck-cre-Tcf7KO2-DN3_BC_64


title: Control_No infection_7d_rep1

value: Control_No infection_7 days


title: Control_No infection_7d_rep3


title: Control_No infection_2d_rep2

value: Control_No infection_2 days


title: Lck-cre-Tcf7KO2-DN3_BC_65


title: Control_No infection_2d_rep3


title: DAR30_post_RNA


title: DNA methylation profile for 203239900239_R08C01


title: DNA methylation profile for 203244500069_R02C01


title: DAR29_post_RNA


title: Control_No infection_7d_rep2


title: DAR29_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_63


title: Lck-cre-Tcf7KO2-DN3_BC_62


title: DAR30_pre_RNA


title: DNA methylation profile for 203249020044_R01C01

value: Occipital


title: Lck-cre-Tcf7KO2-DN3_BC_60


title: Control_No infection_2d_rep1


title: DNA methylation profile for 203249020044_R02C01


title: Lck-cre-Tcf7KO2-DN3_BC_61


title: FOXP3 ΔE2 Treg Input rep 3

city: Indianapolis

first: Sheng

last: Liu

state: IN

address: 1044 W Walnut Street, Room R4-272

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
The reads were mapped to the mouse genome using Bowtie2  (v2.4.4) ,Duplicated reads were removed using Picard (v.2.18.26)
BigWig files were generated using bedtools (v2.2.9) and bedGraphToBigWig (v2.8) which were normalized by total number of reads per 10 million reads
Assembly: mm10
Supplementary files format and content: BigWig, normalized reads

source_name: FOXP3 ΔE2 Treg

growth_protocol: Naïve CD4 T cells were cultured with coated anti-CD3 (1 µg/ml), anti-CD28 (1 μg/ml), recombinant human TGFβ (5 ng/ml), and  recombinant human IL-2 (20 ng/ml) for 5 days. Over 90% cells were FOXP3+.

extract_protocol:
Cells were crosslinked and chromatin was isolated by using the truChIP Chromatin Shearing Kit with Formaldehyde (Covaris). Nuclei were resuspended in shearing buffer and the chromatin was sheared with an AFA Focus-ultrasonicator. ChIP was performed with Millipore Magna ChIP™ A/G Chromatin Immunoprecipitation kit.
ChIPed DNA and Input DNA were submitted to BGI Americas Corporation and  libraries were constructed by BGI with Q.C.

tag: isoform

value: FOXP3 ΔE2

value: Treg

tag: chip ab


title: DNA methylation profile for 203244500069_R05C01


title: Lck-cre-Tcf7KO2-DN3_BC_5

value: Lck-cre; Tcf7fl/fl

value: DN2 & DN3


title: DAR28_pre_RNA

tag: patient id

value: pre


title: Lck-cre-Tcf7KO2-DN3_BC_59


title: DAR28_post_RNA

tag: enz treatment


title: FOXP3 ΔE2 Treg Input rep 2


title: Lck-cre-Tcf7KO2-DN3_BC_58

tag: tissue


title: DNA methylation profile for 203271750096_R01C01

value: male


title: DAR27_post_RNA


title: DAR27_pre_RNA


title: FOXP3 ΔE2 Treg Input rep 1

tag: strain


title: DAR26_post_RNA


title: FOXP3 FL Treg Input rep 3

source_name: FOXP3 FL Treg

value: FOXP3 FL


title: Lck-cre-Tcf7KO2-DN3_BC_56

tag: age


title: Lck-cre-Tcf7KO2-DN3_BC_57


title: DNA methylation profile for 203271750096_R02C01

tag: developmental stage

value: adult

value: brain


title: DAR26_pre_RNA


title: FOXP3 ΔE2 Treg ChIPed rep 3

value: Rabbit polyclonal anti-FOXP3


title: Lck-cre-Tcf7KO2-DN3_BC_55

value: thymus


title: FOXP3 FL Treg Input rep 1


title: FOXP3 FL Treg Input rep 2


title: DAR24_post_RNA

value: post


title: DNA methylation profile for 203271750067_R01C01

tag: brain region

value: female


title: FOXP3 ΔE2 Treg ChIPed rep 2


title: Lck-cre-Tcf7KO2-DN3_BC_54

value: 6~8 wks


title: Lck-cre-Tcf7KO2-DN3_BC_53


title: DNA methylation profile for 203271750067_R02C01

value: Prefrontal

tag: gender


title: DNA methylation profile for 203244500069_R06C01

tag: cell proportion double negative


title: DAR24_pre_RNA


title: FOXP3 FL Treg ChIPed rep 3


title: DNA methylation profile for 203249020042_R07C01

tag: cell proportion neun+


title: Lck-cre-Tcf7KO2-DN3_BC_52


title: DNA methylation profile for 203239900238_R05C01

tag: cell proportion sox10+


title: DNA methylation profile for 203249020042_R08C01


title: FOXP3 FL Treg ChIPed rep 2


title: DAR25_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_51

tag: strain/background


title: DAR21_post_RNA


title: FOXP3 FL Treg ChIPed rep 1


title: DAR22_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_50

tag: genotype/variation


title: DNA methylation profile for 203249020044_R07C01


title: DNA methylation profile for 203249020044_R08C01


title: DAR19_post_RNA


title: FOXP3 ΔE2 Treg ChIPed rep 1

tag: cell type


title: Lck-cre-Tcf7KO2-DN3_BC_4


title: DNA methylation profile for 203271750067_R05C01


title: DNA methylation profile for 203271750067_R06C01


title: DAR19_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_49


title: Lck-cre-Tcf7KO2-DN3_BC_47


title: DAR18_post_RNA


title: DNA methylation profile for 203249020050_R07C01


title: DNA methylation profile for 203239900238_R06C01


title: Lck-cre-Tcf7KO2-DN3_BC_46


title: DNA methylation profile for 203249020050_R08C01


title: DAR23_post_RNA


title: DAR18_pre_RNA


title: DAR20_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_45


title: Lck-cre-Tcf7KO2-DN3_BC_44


title: DNA methylation profile for 203271750069_R06C01


title: 29_4_ESC4

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MTA1.0 ST (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls.  RMA normalization is performed using TAC4.0 (Affymetrix) with default parameters

label: biotin

source_name: ESC

label_protocol: 10 ng of total RNA is reverse transcribed following the Ovation PicoV2 System (Tecan). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to TECAN protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (TECAN). After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® HumanGene2.0 ST (Affymetrix) at 45°C for 17 hours

growth_protocol: Undifrentiated hESC, hESC-derived cells and freshly isolated EL cell populations were obtained as decribed in methods.

extract_protocol: RNAs were purified using Direct-Zol ™RNA kit (ZymoResearch) according to manufacturer’s protocol.

treatment_protocol: No treatment

value: Undifferentiated hESC


title: 31_14_CB_144plus_45plus_2

value: hESC-derived cells


title: Lck-cre-Tcf7KO2-DN3_BC_48


title: DAR17_pre_RNA


title: 30_13_CB_144plus_45plus_1


title: 27_CB_2_11

source_name: CB


title: Lck-cre-Tcf7KO2-DN3_BC_43


title: DAR16_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_42


title: DAR16_pre_RNA


title: DNA methylation profile for 203244500069_R04C01


title: DNA methylation profile for 203249020050_R03C01

value: Occipital


title: DNA methylation profile for 203271750069_R05C01


title: 26_Foie_Hemato_45Low_2_G

source_name: EL Hemato 144-45low34+

value: Freshly isolated EL cells


title: Lck-cre-Tcf7KO2-DN3_BC_41

value: Lck-cre; Tcf7fl/fl


title: DNA methylation profile for 203249020050_R04C01


title: Lck-cre-Tcf7KO2-DN3_BC_40

value: DN2 & DN3


title: DAR15_pre_RNA

value: pre


title: 24_Foie_Endo_5_Q


title: 25_Foie_Hemato_45Low_4_O


title: 28_Foie_Hemato_45Low_3_K


title: DNA methylation profile for 203271750067_R07C01

value: male


title: DAR17_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_3


title: DAR14_pre_RNA


title: DAR14_post_RNA


title: DNA methylation profile for 203271750067_R08C01


title: Lck-cre-Tcf7KO2-DN3_BC_38


title: DAR13_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_39


title: 22_Foie_Endo_2_E


title: DNA methylation profile for 203244500069_R03C01


title: DNA methylation profile for 203249020153_R07C01


title: DAR15_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_37


title: 21_Foie_Endo_Hemat_3_J

source_name: EL Endo-Hemato 144+45low34+


title: DAR12_pre_RNA


title: DAR13_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_35

source_name: thymus DN2&DN3 cells (CD45+Lin-CD4-CD8-CD25+)


title: 20_iEC_1_9

source_name: iEC


title: DNA methylation profile for 203249020153_R04C01


title: 19_Foie_Endo_4_M


title: Lck-cre-Tcf7KO2-DN3_BC_33


title: DAR11_post_RNA


title: DAR11_pre_RNA


title: DNA methylation profile for 203244500078_R08C01


title: 23_Foie_Endo_3_I


title: DNA methylation profile for 203249020153_R03C01


title: DAR10_post_RNA


title: DNA methylation profile for 203249020153_R08C01


title: DNA methylation profile for 203726680006_R07C01


title: Lck-cre-Tcf7KO2-DN3_BC_32


title: 15_CB_4_16

value: hPSC-derived cells


title: 16_CB_1_10


title: Lck-cre-Tcf7KO2-DN3_BC_31


title: DNA methylation profile for 203244500078_R07C01

value: adult


title: 18_EB_3_7

source_name: EB


title: DAR10_pre_RNA

source_name: primary prostate cancer


title: DAR09_post_RNA


title: DNA methylation profile for 203726680006_R08C01

value: brain


title: 17_ESC_2_2_bis


title: 13_Foie_Hemato_45High_3_L

source_name: EL Hemato 144-45high34-


title: 14_FoieHemato_45Low_5_S


title: Lck-cre-Tcf7KO2-DN3_BC_34


title: Lck-cre-Tcf7KO2-DN3_BC_30


title: DAR09_pre_RNA


title: DNA methylation profile for 203726680006_R05C01


title: Lck-cre-Tcf7KO2-DN3_BC_2


title: 12_ESC_1_1_bis


title: Lck-cre-Tcf7KO2-DN3_BC_36


title: DAR08_post_RNA


title: DNA methylation profile for 203726680006_R06C01


title: 10_Foie_Hemato_45High_4_P


title: DNA methylation profile for 203730640007_R05C01


title: DAR08_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_28


title: Lck-cre-Tcf7KO2-DN3_BC_29


title: DNA methylation profile for 203730640007_R06C01


title: DAR07_post_RNA


title: 11_EB_2_6


title: DNA methylation profile for 203271750124_R05C01


title: Lck-cre-Tcf7KO2-DN3_BC_27


title: DAR07_pre_RNA


title: 09_Foie_Hemato_45High_2_H_bis


title: Lck-cre-Tcf7KO2-DN3_BC_26


title: DAR06_post_RNA


title: DAR06_pre_RNA


title: DNA methylation profile for 203271750124_R06C01


title: DNA methylation profile for 203734290078_R07C01


title: Lck-cre-Tcf7KO2-DN3_BC_24


title: 08_EB_1_5


title: DNA methylation profile for 203734290078_R08C01


title: Lck-cre-Tcf7KO2-DN3_BC_25


title: DAR04_post_RNA


title: DAR05_post_RNA


title: DNA methylation profile for 203730640128_R05C01


title: DAR04_pre_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_22


title: Lck-cre-Tcf7KO2-DN3_BC_23


title: Lck-cre-Tcf7KO2-DN3_BC_21


title: 06_iEC_3_17


title: 07_iEC_2_15


title: DAR03_pre_RNA


title: DAR03_post_RNA


title: 02_Foie_Hemato_45High_5_T


title: Lck-cre-Tcf7KO2-DN3_BC_20


title: 03_Foie_Endo_Hemat_2_F


title: 01_Foie_Endo_Hemat_5_R


title: DNA methylation profile for 203726680040_R04C01


title: DNA methylation profile for 203726680040_R03C01


title: DAR02_post_RNA


title: DAR01_post_RNA


title: Lck-cre-Tcf7KO2-DN3_BC_1


title: DNA methylation profile for 203271750124_R02C01


title: Lck-cre-Tcf7KO2-DN3_BC_19


title: Lck-cre-Tcf7KO2-DN3_BC_18


title: NOD_Idd22_islet_rep2

city: GAINESVILLE

first: Clayton

middle: E

last: Mathews

state: Florida

address: 1275 Center DRive

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

hyb_protocol: Performed at University of Florida ICBR

scan_protocol: Performed at University of Florida ICBR

data_processing: Performed at University of Florida ICBR use RMA

source_name: Islets

label_protocol: Performed at University of Florida ICBR

extract_protocol: Islets were isolated using common bile duct inflation of liberase, digetsion at 37 C for 17 min followed by hand pick up.  RNA was extracted from islets using RNeasy kits from Qiagen. RNA concentration detected using BioRad RNA chip.


title: DNA methylation profile for 203730640134_R01C01

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
Dasen normalized betas (BDR_processed_signals.csv.gz)
Unmethylated and methylated signal intensities (BDR_raw_Signal.csv.gz)

extract_protocol: DNA was extracted using a phenol/chloroform method


title: NOD_Idd22_islet_rep4


title: DNA methylation profile for 203271750124_R01C01


title: DAR01_pre_RNA


title: DAR52_pre_H3K27ac

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA. Reads were filtered based on mapping quality (MAPQ ≥ 20) and duplicate reads were removed.
Peak calling over paired input controls (per tissue sample and treatment) was performed using MACS2 and Dfilter. Peaks called by both peak callers were used for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.narrowPeak.bed

growth_protocol: fresh frozen material

extract_protocol:
Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A (50 mM HEPES-KOH, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) with 2 mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde (Merck) was added for 20 minutes and subsequently quenched with 2.5 M glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30 sec on, 30 sec off using a Diagenode Bioruptor Pico. For each ChIP, 5 µg of antibody was conjugated with 50 µL magnetic protein A or G beads (10008D or 10009D, Thermo Fisher Scientific). Antibodies used were AR (06-680, Merck Millipore), FOXA1 (ab5089, Abcam) and H3K27ac (39133, Active Motif).
Immunoprecipitated DNA was processed for library preparation using a KAPA library preparation kit (KK8234, Roche)

tag: chip antibody

value: H3K27ac (Active Motif, 39133)


title: Lck-cre-Tcf7KO2-DN3_BC_17

value: thymus


title: Lck-cre-Tcf7KO2-DN3_BC_16


title: DNA methylation profile for 203730640128_R06C01


title: DAR52_post_H3K27ac

value: post


title: DIPGXIII-pool_cells_ChIP1_Input_1

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

data_processing:
ChIP-seq datasets were processed using the ChIP-seq module of GenPipes (v3.1.0 for isogenic cell lines, v3.1.2 for parental cell lines). Raw reads were trimmed using Trimmomatic (v0.32) to remove adaptor and sequencing-primer associated reads then aligned to hg19 using bwa-mem (v0.7.12) with default parameters. PCR duplicate reads as defined by reads with identical mapping coordinates were then collapsed by Picard (v2.0.1) to produce uniquely aligned reads. Reads with a mapping quality of 5 or less were then filtered out. For single-end (SE) 50bp datasets, reads were extended by 250bp.
Wiggle tracks are generated using uniquely aligned reads using Homer (v4.9.1). ChIP-seq RPKM values over CGIs and genome-wide 100kb bins for scatterplots were calculated using VisRSeq (v0.9.40).
Rx- and RPKM-normalized BigWig tracks were produced using the “bamCoverage” functionality of deeptools (v3.5.1). Rx ratios were supplied via the ‘--scaleFactor’ option.  Reads flagged as duplicates, mapping to random, mitochondrial or sex chromosomes, as well as low-mappability regions according to ENCODE’s blacklist were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files. Read coverage for each sample over the human genome

source_name: Pons

extract_protocol:
Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP or HyperPrep Illumina library preparation reagents. Ffor HTP kit, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adapter ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, at 20°C for 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. For HyperPrep kit, end-repair and A tailing were performed in one reaction: 15ul of ChIP sample was incubated with 45ul end repair+A-tailing mix at 20°C for 30 min, then 65°C for 30 min. Directly proceeded to adapter ligation by adding 5ul of IDT for Illumina Unique Dual Indexes (IDT) adapters and 45ul ligation buffer enzyme mix, incubating at 20°C for 15 min, followed by Ampure XP bead purification. Library enrichment: 10 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: material

value: Cell line

tag: histone mark/factor

value: CTCF

tag: crispr

value: Parental

tag: clone or passage


title: Lck-cre-Tcf7KO2-DN3_BC_15

tag: tissue

value: 6~8 wks


title: DNA methylation profile for 203730640007_R03C01


title: DNA methylation profile for 203730640007_R04C01

value: Prefrontal


title: Lck-cre-Tcf7KO2-DN3_BC_14


title: NOD-Rag1_islet_rep3

tag: strain


title: DAR47_pre_H3K27ac

tag: patient id

tag: enz treatment


title: NOD_Idd22_islet_rep1


title: NOD_Idd22_islet_rep3


title: NOD-Rag1_islet_rep1


title: NOD-Rag1_islet_rep2


title: DAR47_post_H3K27ac


title: Lck-cre-Tcf7KO2-DN3_BC_13

tag: age


title: DNA methylation profile for 203271750124_R03C01

tag: developmental stage

tag: brain region

value: Occipital

tag: gender


title: DAR45_pre_H3K27ac


title: DNA methylation profile for 203271750124_R04C01

tag: cell proportion double negative

tag: cell proportion neun+

tag: cell proportion sox10+


title: Lck-cre-Tcf7KO2-DN3_BC_12

tag: strain/background

tag: genotype/variation

tag: cell type


title: BT245p11_cells_ChIP1_CTCF_1

source_name: Thalamus

tag: material

tag: histone mark/factor


title: DNA methylation profile for 203730640134_R02C01


title: DNA methylation profile for 203726680004_R01C01


title: HSJ019-C7-Rx_cells_ChIP1_Input_1

value: Input

tag: crispr

tag: clone or passage


title: BT245-pool_cells_ChIP1_Input_1


title: DAR45_post_H3K27ac

tag: chip antibody


title: DAR44_pre_H3K27ac

tag: patient id


title: DNA methylation profile for 203726680004_R02C01

tag: tissue


title: HSJ019_parental_C4_Input


title: Lck-cre-Tcf7KO2-DN3_BC_11

value: Lck-cre; Tcf7fl/fl

tag: age


title: DIPGXIIIp14_cells_ChIP1_CTCF_1


title: BT416-C11-Rx_cells_ChIP1_Input_1


title: DAR44_post_H3K27ac

tag: enz treatment


title: Lck-cre-Tcf7KO2-DN3_BC_10

value: DN2 & DN3


title: DNA methylation profile for 203734290076_R01C01

tag: developmental stage

tag: brain region

value: female


title: DIPGIVp22-Rx_cells_ChIP1_Input_1


title: DNA methylation profile for 203734290076_R02C01

tag: gender

tag: cell proportion double negative


title: DNA methylation profile for 203726680004_R07C01

value: male

tag: cell proportion neun+

tag: cell proportion sox10+


title: HSJ019-C7-Rx_cells_ChIP1_H3K27ac_1


title: Lck-cre-Tcf7KO1-DN3_BC_95

tag: strain/background

tag: genotype/variation


title: Lck-cre-Tcf7KO1-DN3_BC_96

tag: cell type


title: DNA methylation profile for 203726680004_R08C01


title: HSJ019_parental_C4_H3K27ac

tag: material

tag: histone mark/factor


title: BT416-C11-Rx_cells_ChIP1_H3K27me3_1

tag: crispr

tag: clone or passage


title: Lck-cre-Tcf7KO1-DN3_BC_94


title: DAR39_pre_H3K27ac

tag: chip antibody

tag: patient id

value: pre


title: DNA methylation profile for 203726680040_R08C01

value: adult

tag: tissue


title: DAR40_pre_H3K27ac

tag: enz treatment


title: DNA methylation profile for 203726680040_R07C01

tag: developmental stage

value: brain


title: Lck-cre-Tcf7KO1-DN3_BC_93

tag: age


title: DIPGIVp22-Rx_cells_ChIP1_H3K27ac_1


title: Lck-cre-Tcf7KO1-DN3_BC_92


title: DAR35_pre_H3K27ac

value: H3K27ac (Active Motif, 39133)


title: Lck-cre-Tcf7KO1-DN3_BC_91

value: thymus


title: DAR35_post_H3K27ac

value: post


title: DNA methylation profile for 203730640009_R06C01

tag: brain region

tag: gender


title: senescent cells with TRF2 overexpression – Replicate 3

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

institute: IRCAN

data_processing:
Paired-end sequencing (read length: 2x150bp) was performed by NovoGene company using Illumina sequencer.
Raw RNA-seq reads were trimmed using Trimmomatic. Read mapping and genome index building were performed using STAR.
Differential expression analysis was performed using DESeq2 R package
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: Human fibroblast

growth_protocol: Cells were grown in DEME media supplemented with 10% serum in 5% oxygen

extract_protocol:
RNA extraction was performed using the RNeasy mini kit by Qiagen
Libraries were prepared according to standards Illumina's instructions

treatment_protocol: Cells were transduced with an empty vetor or a lentivirus expressing the TRF2 shelterin protein

tag: cell line


title: DIPGIVp22-Rx_cells_ChIP1_H3K27me3_1

value: Cell line


title: Lck-cre-Tcf7KO1-DN3_BC_90


title: senescent cells with TRF2 overexpression – Replicate 2


title: senescent cells with empty vector – Replicate 3

treatment_protocol: Cells were transduced with an empty vector or a lentivirus expressing the TRF2 shelterin protein

value: Human fibroblast

value: empty vector


title: Lck-cre-Tcf7KO1-DN3_BC_9

value: 6~8 wks


title: DAR41_post_H3K27ac


title: DAR27_pre_H3K27ac


title: DNA methylation profile for 203726680002_R01C01

tag: cell proportion double negative

tag: cell proportion neun+

tag: cell proportion sox10+


title: DAR41_pre_H3K27ac


title: Lck-cre-Tcf7KO1-DN3_BC_8

tag: strain/background

tag: genotype/variation

tag: cell type


title: DNA methylation profile for 203726680002_R02C01

value: Prefrontal


title: Lck-cre-Tcf7KO1-DN3_BC_89


title: DAR39_post_H3K27ac


title: senescent cells with TRF2 overexpression – Replicate 1


title: senescent cells with empty vector – Replicate 2


title: DAR25_pre_H3K27ac


title: DNA methylation profile for 203730640009_R05C01

value: Occipital


title: DNA methylation profile for 203271750096_R07C01


title: Lck-cre-Tcf7KO1-DN3_BC_88


title: DAR25_post_H3K27ac


title: senescent cells with empty vector – Replicate 1


title: DNA methylation profile for 203271750096_R08C01


title: DNA methylation profile for 203271750096_R03C01


title: DNA methylation profile for 203271750096_R04C01


title: Lck-cre-Tcf7KO1-DN3_BC_87


title: DAR24_pre_H3K27ac


title: DAR24_post_H3K27ac


title: Lck-cre-Tcf7KO1-DN3_BC_86


title: DNA methylation profile for 203726680040_R01C01


title: DAR27_post_H3K27ac


title: Bulk RNA-seq of TEC of patient 57

city: Innsbruck

first: Georgios

last: Fotakis

state: Tyrol

address: Innrain 80-82

country: Austria

institute: Medical University Innsbruck

data_processing:
scRNA-seq: FASTQ files were processed with cellranger v3.1
Bulk RNA-seq: FASTQ files were pre-processed using Trimmomatic V0.36 to trim long reads to a maximum length of 200 bp
Bulk RNA-seq: The pre-processed reads were then aligned to the reference genome using STAR v2.5.3a
Bulk RNA-seq: Read counts were generated using htseq-count v0.12.3
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNA-seq: TSV files containing  detected cellular barcodes (barcodes.tsv) and  correspondig genes (features.tsv) as returned from cellranger
Supplementary_files_format_and_content: scRNA-seq: MTX sparse matrix containing counts as returned from cellranger
Supplementary_files_format_and_content: Bulk RNA-seq: tab-delimited text files include gene count values for each bulk RNA-seq sample

source_name: TEC

extract_protocol:
Total RNA was isolated using Trizol (Fisher Scientific - Austria GmbH) followed by final purification through the Qiagen RNeasy Minelute protocol (Qiagen GmbH, Hilden, Germany).
Total RNA was submitted to QuantSeq 3’-mRNA library preparation (Lexogen GmbH, Vienna, Austria) and sequenced using Ion Proton Hi-Q chemistry (Ion Torrent, Fisher Scientific - Austria GmbH).

tag: disease state

value: Tumor


title: DAR18_pre_H3K27ac


title: Bulk RNA-seq of TEC of patient 44


title: Bulk RNA-seq of TEC of patient 52


title: Lck-cre-Tcf7KO1-DN3_BC_85

value: Lck-cre; Tcf7fl/fl


title: Bulk RNA-seq of TEC of patient 59


title: DAR18_post_H3K27ac


title: DNA methylation profile for 203726680040_R02C01

city: Exeter

first: Eilis

address: RILD building

institute: University of Exeter


title: Lck-cre-Tcf7KO1-DN3_BC_84

city: Beijing

value: DN2 & DN3


title: DNA methylation profile for 203730640134_R05C01

value: female


title: Lck-cre-Tcf7KO1-DN3_BC_83


title: DAR17_pre_H3K27ac


title: Lck-cre-Tcf7KO1-DN3_BC_81


title: Bulk RNA-seq of TEC of patient 46


title: DAR15_pre_H3K27ac


title: DNA methylation profile for 203726680004_R03C01

value: male


title: DNA methylation profile for 203730640128_R07C01


title: DAR17_post_H3K27ac


title: DNA methylation profile for 203726680004_R04C01


title: Bulk RNA-seq of TEC of patient 47


title: Bulk RNA-seq of TEC of patient 51


title: DAR15_post_H3K27ac


title: Lck-cre-Tcf7KO1-DN3_BC_7


title: Lck-cre-Tcf7KO1-DN3_BC_80


title: Bulk RNA-seq of TEC of patient 24


title: DNA methylation profile for 203730640128_R08C01


title: DAR14_pre_H3K27ac

value: pre


title: Lck-cre-Tcf7KO1-DN3_BC_82


title: DNA methylation profile for 203726680040_R06C01

value: adult


title: DAR13_post_H3K27ac


title: Bulk RNA-seq of NEC of patient 54

source_name: NEC

value: Benign


title: Lck-cre-Tcf7KO1-DN3_BC_79


title: Bulk RNA-seq of TEC of patient 48


title: DNA methylation profile for 203726680040_R05C01

value: brain


title: DAR13_pre_H3K27ac

value: H3K27ac (Active Motif, 39133)


title: Lck-cre-Tcf7KO1-DN3_BC_78

value: thymus


title: DNA methylation profile for 203726680002_R08C01


title: Bulk RNA-seq of NEC of patient 26


title: Lck-cre-Tcf7KO1-DN3_BC_77


title: DNA methylation profile for 203726680002_R07C01


title: Bulk RNA-seq of TEC of patient 26


title: Bulk RNA-seq of TEC of patient 45


title: Lck-cre-Tcf7KO1-DN3_BC_75


title: DAR09_pre_H3K27ac


title: DNA methylation profile for 203730640134_R07C01


title: Lck-cre-Tcf7KO1-DN3_BC_76


title: DAR09_post_H3K27ac

value: post


title: DNA methylation profile for 203730640134_R08C01


title: Bulk RNA-seq of NEC of patient 51


title: DNA methylation profile for 203734290078_R05C01


title: DAR14_post_H3K27ac


title: DAR08_post_H3K27ac


title: Lck-cre-Tcf7KO1-DN3_BC_74


title: DAR08_pre_H3K27ac


title: Bulk RNA-seq of NEC of patient 48


title: Lck-cre-Tcf7KO1-DN3_BC_73


title: DAR07_pre_H3K27ac


title: Lck-cre-Tcf7KO1-DN3_BC_72


title: Bulk RNA-seq of NEC of patient 50


title: Lck-cre-Tcf7KO1-DN3_BC_71


title: DAR07_post_H3K27ac


title: Bulk RNA-seq of NEC of patient 56


title: Lck-cre-Tcf7KO1-DN3_BC_70


title: Bulk RNA-seq of NEC of patient 52


title: DNA methylation profile for 203271750124_R07C01


title: DNA methylation profile for 203734290076_R07C01


title: DAR06_pre_H3K27ac


title: Lck-cre-Tcf7KO1-DN3_BC_69


title: Lck-cre-Tcf7KO1-DN3_BC_6


title: DNA methylation profile for 203734290076_R08C01


title: DAR06_post_H3K27ac


title: Bulk RNA-seq of NEC of patient 45


title: DAR05_pre_H3K27ac


title: DAR05_post_H3K27ac


title: U2

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

data_processing:
Reads were aligned to mm10 genome using bowtie2 v.2.2.4. The reads which had mapping quality less than 20 along with PCR duplicates were discarded.
Peak were called using MACS2 v.2.1.1. Peaks with FDR < 0.01 and found in atleast 2 samples were retained. Peaks with atleast 50% overlap were merged using bedR package in R to arrive at a final peak set. Reads were assigned to peaks using Rsubread package in R.
To get Differential peaks we first normalized the read counts using conditional quantile normalization (CQN) to account for GC bias and length of peaks along with total reads assigned to the peaks in each sample. The CQN normalized counts were further processed using edgeR and LIMMA packages in R to arrive at differentially enriched peak sets for comparisons across the T cell subpopulations. We used a FDR cutoff of 0.05 to filter out significantly enriched peaks in the comparisons
Assembly: mm10
Supplementary files format and content: Peaks

source_name: DbGP33+ CD8+ T cells

extract_protocol: Lysed nuclei were resuspended in the transposase reaction mix (25 l 2 x TD buffer, 1 l Illumina transposase, and 24 l nuclease-free water) and incubated at 37 °C for 30 min. DNA from the transposase reaction was purified using MinElute PCR purification Kit (Qiagen). PCR amplification was performed by using Nextera PCR primers. The final libraries were quantified using a KAPA Library Quantification Kit.

tag: agent

value: untreated

value: DbGP33+ CD8+ T cells


title: Lck-cre-Tcf7KO1-DN3_BC_67

value: 6~8 wks


title: U1


title: DNA methylation profile for 203734290076_R03C01

last: Hannon


title: DNA methylation profile for 203734290078_R06C01

value: Prefrontal


title: P4


title: P3


title: DNA methylation profile for 203730640007_R07C01

value: Occipital


title: DNA methylation profile for 203734290076_R04C01


title: DNA methylation profile for 203271750124_R08C01


title: Lck-cre-Tcf7KO1-DN3_BC_66


title: U3


title: P2


title: DAR04_post_H3K27ac

tag: chip antibody


title: DAR03_pre_H3K27ac

tag: patient id


title: DNA methylation profile for 203734290078_R01C01

tag: tissue


title: Lck-cre-Tcf7KO1-DN3_BC_64


title: Lck-cre-Tcf7KO1-DN3_BC_65


title: DAR03_post_H3K27ac

tag: enz treatment


title: P1


title: DNA methylation profile for 203734290078_R02C01

tag: developmental stage


title: DAR01_pre_H3K27ac


title: I4


title: Lck-cre-Tcf7KO1-DN3_BC_68

tag: age


title: Lck-cre-Tcf7KO1-DN3_BC_62


title: DNA methylation profile for 203726680006_R01C01

tag: brain region


title: Lck-cre-Tcf7KO1-DN3_BC_61


title: I2


title: DAR01_post_H3K27ac


title: DNA methylation profile for 203726680006_R02C01

tag: gender


title: DAR04_pre_H3K27ac


title: DNA methylation profile for 203730640007_R08C01


title: Lck-cre-Tcf7KO1-DN3_BC_60


title: DAR52_pre_FOXA1

value: FOXA1 (Abcam, ab5089)


title: I1


title: DNA methylation profile for 203726680006_R03C01


title: DAR52_post_FOXA1


title: C7


title: DNA methylation profile for 203726680006_R04C01


title: Lck-cre-Tcf7KO1-DN3_BC_5

value: Lck-cre; Tcf7fl/fl


title: Lck-cre-Tcf7KO1-DN3_BC_63

value: DN2 & DN3


title: DAR47_pre_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_58


title: C6


title: Lck-cre-Tcf7KO1-DN3_BC_59


title: DNA methylation profile for 203734290078_R04C01

value: female


title: I3


title: DNA methylation profile for 203734290078_R03C01


title: DNA methylation profile for 203730640134_R03C01

value: male


title: DAR45_pre_FOXA1

value: pre


title: DAR45_post_FOXA1


title: C4


title: Lck-cre-Tcf7KO1-DN3_BC_57


title: DNA methylation profile for 203730640134_R04C01

value: adult


title: Lck-cre-Tcf7KO1-DN3_BC_56


title: C2


title: DNA methylation profile for 203730640128_R03C01


title: DAR44_post_FOXA1


title: C1


title: Lck-cre-Tcf7KO1-DN3_BC_54


title: DNA methylation profile for 203730640128_R04C01


title: DAR47_post_FOXA1


title: DNA methylation profile for 203734290076_R05C01


title: DAR39_post_FOXA1


title: DAR39_pre_FOXA1


title: FOXP3 ΔE2 Treg rep 3 [OtB0944]

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 2500
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 0 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 2 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Assembly: mm10
Supplementary files format and content: count, normalized abundance (logCPM) , edgeR result in geneexpression, and DAVID functional analysis in KOup/KOdown

source_name: FOXP3 ΔE2 Treg

growth_protocol: Naïve CD4 T cells were cultured with coated anti-CD3 (1 µg/ml), anti-CD28 (1 μg/ml), recombinant human TGFβ (5 ng/ml), and  recombinant human IL-2 (20 ng/ml) for 3 days. Over 90% cells were FOXP3+.

extract_protocol:
Cells were frozen in liquid nitrogen and sent to Otogenetics Corporation. polyA mRNA were extracted by the company with Q.C..
Illumina sequencing libraries were prepared by Otogenetics Corporation with Q.C.

tag: strain

value: Foxp3 exon 2 deletion

value: Treg


title: Lck-cre-Tcf7KO1-DN3_BC_53


title: C5


title: DNA methylation profile for 203726680002_R05C01

value: brain

tag: cell proportion double negative


title: DAR35_post_FOXA1


title: FOXP3 ΔE2 Treg rep 1 [OtB0942]


title: Lck-cre-Tcf7KO1-DN3_BC_52

value: thymus


title: FOXP3 ΔE2 Treg rep 2 [OtB0943]


title: DAR35_pre_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_51


title: FOXP3 FL Treg rep 3 [OtB0941]

source_name: FOXP3 FL Treg

value: FOXP3 FL


title: C3


title: Lck-cre-Tcf7KO1-DN3_BC_50


title: Lck-cre-Tcf7KO1-DN3_BC_55


title: DNA methylation profile for 203726680002_R06C01

tag: cell proportion neun+


title: FOXP3 FL Treg rep 2 [OtB0940]


title: DAR27_post_FOXA1

value: post


title: DNA methylation profile for 203271750096_R05C01

tag: cell proportion sox10+


title: DAR27_pre_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_4

tag: strain/background


title: DAR40_pre_FOXA1


title: DAR25_post_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_49

tag: genotype/variation


title: SRM220498_mDnttip1KO1E6_INPUT

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4)
Reads were mapped to mice reference genome (mm10) with bwa aln, followed by bwa samse or sampe (0.7.17-r1188), dependently on single, or pair-end design; with -K flag set to 10000000
Duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87) and Cross-Correlation analysis was conducted with SPP (v1.11)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: mES cells

growth_protocol: All mESCs were cultured under chemically defined naïve culture conditions (2iL) in 0.1% gelatin-coated flasks or plates.

extract_protocol:
After sequential lysis of the crosslinked cells in Lysis Buffer 1 and Lysis Buffer 2, the nuclear pellet was sonicated in Lysis Buffer 3 with a probe sonicator (Fisher Scientific Model 705 Sonic Dismembrator) at output level 55 (27–33 W) for 16 cycles with each cycle constituting of a 30 sec sonication on followed by a 60 sec off. For each ChIP, 100 ?L Protein G Dynabeads (Invitrogen, 10003D) slurry and 10 µg of antibody was used. Chromatin incubation with antibody was carried out at 4°C with end-to-end rotation for 4-6 hours.
DNA was quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Libraries were prepared with the KAPA HyperPrep Library Kit (Roche, 07962363001) and analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067–4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067–5584, 5067–5585, 5067–5587, 5067–5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay.

treatment_protocol: Dual crosslinking was performed at room temperature first for 30 min with 2 mM disuccinimidyl glutarate (DSG) in DPBS and then by addition of paraformaldehyde to a final concentration of 1% for another 15 minutes. Crosslinking was quenched with 150 mM glycine for 5 min at room temperature. Single crosslinking was performed solely with  paraformaldehyde for 20 min.

tag: cell full name

value: Mouse embryonic stem cells

tag: cell type


title: Lck-cre-Tcf7KO1-DN3_BC_47

value: 6~8 wks


title: DAR25_pre_FOXA1


title: DNA methylation profile for 203271750096_R06C01

value: Prefrontal


title: Lck-cre-Tcf7KO1-DN3_BC_48


title: DNA methylation profile for 203730640009_R07C01

value: Occipital


title: DAR24_pre_FOXA1

value: FOXA1 (Abcam, ab5089)


title: FOXP3 FL Treg rep 1 [OtB0939]


title: DNA methylation profile for 203730640009_R08C01


title: DNA methylation profile for 203734290076_R06C01


title: DAR24_post_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_46

value: Lck-cre; Tcf7fl/fl


title: DNA methylation profile for 203730640009_R04C01


title: DNA methylation profile for 203730640009_R03C01


title: DAR18_pre_FOXA1


title: SRM220498_KaiGe_Bruce4_MLL4-AB1

value: rabbit alpha-MLL4/KMT2D (Ge lab, #3)


title: SRM220498_Dnttip1KO1E6_rep2-H3K4me3-AB8

value: rabbit alpha-H3K4me3 (RevMAb, 31-1039-00)


title: DNA methylation profile for 203726680004_R05C01

value: female


title: SRM220498_Dnttip1KO1E6_rep1-H3K4me3-AB8


title: Lck-cre-Tcf7KO1-DN3_BC_44

value: DN2 & DN3


title: SRM220498_KaiGe_Dnttip1KO1E6_MLL4-AB1


title: DAR18_post_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_43


title: DNA methylation profile for 203730640007_R01C01

value: adult

value: male


title: SRM220498_Dnttip1KO1E6_UTX-AB11

value: rabbit alpha-UTX/KDM6A (Cell Signaling Technology, 33510S)


title: SRM220498_Dnttip1KO1E6_H4K20Ac-AB2

value: rabbit alpha-H4K20ac (RevMAb, 31-1084-00)


title: Lck-cre-Tcf7KO1-DN3_BC_45

value: thymus


title: DNA methylation profile for 203726680004_R06C01

value: brain


title: DAR17_post_FOXA1

value: post


title: DAR15_pre_FOXA1

value: pre


title: Lck-cre-Tcf7KO1-DN3_BC_42

value: 6~8 wks


title: Lck-cre-Tcf7KO1-DN3_BC_40


title: SRM220498_Dnttip1KO1E6_H3K4me2-AB5

value: Mouse embryonic stem cells

value: mouse alpha-H3K4me2 (Active Motif, 39679)


title: Lck-cre-Tcf7KO1-DN3_BC_41


title: SRM220498_Dnttip1KO1E6_H3K4me1-AB4

value: Rabbit alpha-H3K4me1 (RevMAb, 31-1046-00)


title: DAR15_post_FOXA1

value: FOXA1 (Abcam, ab5089)


title: DNA methylation profile for 203730640009_R01C01

value: Occipital


title: DNA methylation profile for 203730640007_R02C01

value: Prefrontal


title: DNA methylation profile for 203726680002_R03C01

value: female


title: DAR14_pre_FOXA1


title: SRM220498_Bruce4_rep2-H3K4me3-AB8

value: rabbit alpha-H3K4me3 (RevMAb, 31-1039-00)


title: Lck-cre-Tcf7KO1-DN3_BC_3

value: Lck-cre; Tcf7fl/fl

value: DN2 & DN3


title: Lck-cre-Tcf7KO1-DN3_BC_39


title: SRM220498_Bruce4_rep1-H3K4me3-AB8


title: DNA methylation profile for 203730640009_R02C01

value: adult


title: DAR14_post_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_38


title: DNA methylation profile for 203726680002_R04C01


title: DAR09_post_FOXA1


title: DAR17_pre_FOXA1


title: SRM220498_Bruce4_UTX-AB11

value: rabbit alpha-UTX/KDM6A (Cell Signaling Technology, 33510S)


title: SRM220498_Bruce4_INPUT


title: DAR08_pre_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_37

value: thymus


title: DNA methylation profile for 203730640128_R01C01

value: brain

value: male


title: DNA methylation profile for 203734300115_R01C01


title: Lck-cre-Tcf7KO1-DN3_BC_36


title: SRM220498_Bruce4_H4K20Ac-AB2

value: rabbit alpha-H4K20ac (RevMAb, 31-1084-00)


title: DNA methylation profile for 203734300115_R02C01


title: Lck-cre-Tcf7KO1-DN3_BC_35

value: 6~8 wks


title: DAR07_pre_FOXA1

value: pre


title: Lck-cre-Tcf7KO1-DN3_BC_34


title: SRM220498_Bruce4_H3K4me2-AB5

value: Mouse embryonic stem cells

value: mouse alpha-H3K4me2 (Active Motif, 39679)


title: DNA methylation profile for 203239900238_R07C01


title: DAR06_pre_FOXA1

value: FOXA1 (Abcam, ab5089)


title: DAR08_post_FOXA1

value: post


title: Lck-cre-Tcf7KO1-DN3_BC_33


title: DNA methylation profile for 203239900238_R04C01

value: Prefrontal


title: DNA methylation profile for 203730640134_R06C01

value: Occipital


title: DAR06_post_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_32


title: SRM213355_Dnttip1KO1E6_INPUT


title: DNA methylation profile for 203239900238_R03C01

value: female


title: SRM213355_Dnttip1KO1E6_H4K20Ac-AB2


title: SRM213355_Dnttip1KO1E6_H3K4me1-AB4

value: Rabbit alpha-H3K4me1 (RevMAb, 31-1046-00)


title: Lck-cre-Tcf7KO1-DN3_BC_31

value: Lck-cre; Tcf7fl/fl

value: DN2 & DN3


title: DAR04_post_FOXA1


title: Lck-cre-Tcf7KO1-DN3_BC_30


title: Lck-cre-Tcf7KO1-DN3_BC_29


title: DNA methylation profile for 202410000210_R03C01

value: adult


title: SRM213355_Dnttip1KO1E6_H3K4me2-AB5


title: DAR01_pre_FOXA1


title: DAR47_pre_AR

value: AR (Merck Millipore, 06-680)


title: Lck-cre-Tcf7KO1-DN3_BC_28

value: thymus


title: Lck-cre-Tcf7KO1-DN3_BC_2


title: DNA methylation profile for 203734300117_R02C01

value: brain


title: DAR52_pre_AR


title: SRM220498_Bruce4_H3K4me1-AB4


title: DAR47_post_AR


title: SRM213355_Dnttip1KO1E6_H3K27me3-AB4

value: rabbit alpha-H3K27me3 (Cell Signaling Technology, 9733S)


title: DNA methylation profile for 202410000173_R02C01


title: Lck-cre-Tcf7KO1-DN3_BC_27

value: 6~8 wks


title: DNA methylation profile for 202410000108_R02C01


title: SRM213355_Bruce4_INPUT


title: DAR45_post_AR


title: SRM213355_Dnttip1KO1E6_H3K27Ac-AB6

value: rabbit alpha-H3K27ac (RevMAb, 31-1056-00)


title: DNA methylation profile for 202410000210_R04C01


title: DNA methylation profile for 202410000173_R03C01

value: male


title: Lck-cre-Tcf7KO1-DN3_BC_25


title: DAR45_pre_AR

value: pre


title: Lck-cre-Tcf7KO1-DN3_BC_23


title: SRM213355_Bruce4_H3K4me1-AB4

value: Mouse embryonic stem cells


title: SRM213355_Bruce4_H3K27Ac-AB6


title: SRM213355_Bruce4_H3K27me3-AB4


title: DNA methylation profile for 202410000234_R01C01


title: DNA methylation profile for 202410000234_R02C01


title: DNA methylation profile for 202410000108_R01C01


title: SRM213355_Bruce4_H4K20Ac-AB2

value: rabbit alpha-H4K20ac (RevMAb, 31-1084-00)


title: DNA methylation profile for 202410160029_R05C01


title: DAR39_post_AR

value: post


title: DAR25_pre_AR


title: Lck-cre-Tcf7KO1-DN3_BC_24


title: Lck-cre-Tcf7KO1-DN3_BC_26


title: SRM202772_WT_H3K4me3-AB8

value: rabbit alpha-H3K4me3 (RevMAb, 31-1039-00)


title: DAR40_pre_AR


title: DAR44_pre_AR


title: DNA methylation profile for 202410160029_R06C01

value: Prefrontal


title: DNA methylation profile for 202410000173_R05C01

value: Occipital

value: female


title: SRM202772_WT_INPUT


title: SRM213355_Bruce4_H3K4me2-AB5

value: mouse alpha-H3K4me2 (Active Motif, 39679)


title: Lck-cre-Tcf7KO1-DN3_BC_22

value: Lck-cre; Tcf7fl/fl

value: DN2 & DN3


title: DNA methylation profile for 202410000173_R04C01

value: adult


title: DAR17_post_AR

value: AR (Merck Millipore, 06-680)


title: DAR52_post_AR


title: DAR27_post_AR


title: Lck-cre-Tcf7KO1-DN3_BC_19

value: thymus


title: SRM202772_WT_H3K27Ac-AB6


title: DNA methylation profile for 202410000210_R08C01

value: brain


title: SRM202772_WT_DNTTIP1-AB1

value: rabbit alpha-DNTTIP1 (Bethyl Laboratories, A304-048A)


title: DNA methylation profile for 202410000217_R08C01


title: Lck-cre-Tcf7KO1-DN3_BC_20

value: 6~8 wks


title: Lck-cre-Tcf7KO1-DN3_BC_16


title: Lck-cre-Tcf7KO1-DN3_BC_1


title: Lck-cre-Tcf7KO1-DN3_BC_21


title: SRM202772_WT_H4K20Ac-AB2


title: DAR24_post_AR


title: Lck-cre-Tcf7KO1-DN3_BC_15


title: SRM202772_MLL34DKO_H3K4me3-AB8


title: SRM202772_WT_H3K27me3-AB4

value: rabbit alpha-H3K27me3 (Cell Signaling Technology, 9733S)


title: Lck-cre-Tcf7KO1-DN3_BC_13


title: DNA methylation profile for 202410000234_R08C01


title: DAR15_pre_AR

value: pre


title: DAR14_post_AR


title: DNA methylation profile for 202410000210_R07C01

value: male


title: DAR15_post_AR

value: post


title: Lck-cre-Tcf7KO1-DN3_BC_18


title: SRM202772_WT_H3K4me1-AB4

value: Mouse embryonic stem cells

value: Rabbit alpha-H3K4me1 (RevMAb, 31-1046-00)


title: Lck-cre-Tcf7KO1-DN3_BC_12


title: Lck-cre-Tcf7KO1-DN3_BC_17


title: DAR04_post_AR


title: SRM202772_MLL34DKO_INPUT


title: SRM202772_MLL34DKO_H3K27me3-AB4


title: DNA methylation profile for 202410000157_R04C01

value: Prefrontal


title: DNA methylation profile for 202410000157_R03C01

value: Occipital

value: female


title: DAR08_pre_AR


title: DAR01_pre_AR


title: DNA methylation profile for 202410160041_R02C01


title: DAR06_post_AR


title: DNA methylation profile for 202410000234_R07C01


title: Lck-cre-Tcf7KO1-DN3_BC_14

value: Lck-cre; Tcf7fl/fl


title: Lck-cre-Tcf7KO1-DN3_BC_10

value: DN2 & DN3