title: Input data of ChIP-Seq in MDA-MB-231

city: Beijing

first: Chao

last: Yang

address: Youanmenwai rd

institute: Capital Medical University

data_processing:
Alignment through Bowtie version2.
Peak-calling through MACS version2.
ChIPseeker for the annotation of peaks.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig (bw) files contain signal intensity of binding.

source_name: Breast cancer cells

growth_protocol: MDA-MB-231 cells were cultured in L-15 medium supplemented with 10% FBS without CO2.

extract_protocol: Approximately 5 x 10e7 cells were used for each ChIP-seq assay. Chromatin DNAs precipitated by polyclonal antibodies against ZNF704 or SIN3A were purified with the Qiagen PCR purification kit.

treatment_protocol: Treated with specific antibody against ZNF704 and SIN3A.

tag: cell line

tag: passages


title: ChIP-seq data of ZNF704 in MDA-MB-231

status: Public on Jun 24 2020

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: chip antibody


title: ChIP-seq data of SIN3A in MDA-MB-231


title: ChIP-seq_PfArp4_input_rep1

city: Shanghai

first: Xinyu

last: Cui

address: Siping road

institute: Tongji University

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format. Next, the duplicated reads were removed by markdup from sambamba (v0.6.8).
Then, the bam files were converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 25. The bigwig files from ChIP sample were normalized to input sample by bigwigCompare from the deeptools suite (v3.1.3) with parameters: –operation log2 --pseudocount 1. The Integrative Genomics Viewer (IGV) was used to show the signal of histone modification in certain genomic region in a track view.
The peaks were called by MACS2 with parameters:-g 2.33e7 -f BAMPE.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: Arp4 and Arp6 enrichment along the whole genome file  for different samples

organism: Plasmodium falciparum

extract_protocol:
In this experiment, highly synchronized infected red blood cells (iRBC) were collected and centrifuged to remove a portion of the supernatant. Parasites were extracted with 0.15% saponin and washed with pre-chilled PBS until the supernatant was clear. 2ml Lysis Buffer (containing 100× protease inhibitor and 100× DTT) was added to the sample, mixed well, and leave it on ice for 30min to lyse the body. The lysate was placed in a grinding tube and 50ul of 10% NP-40 was added. The cell debris was subjected to liquid phase ultrasound, after centrifuging the ultrasound product, took the supernatant and took 20ul of the supernatant as input (input was stored at -80°C). 100µl of salmon sperm DNA Agrose magnetic beads (50µl/ml) and protease inhibitor were added to the remaining supernatant, samples were incubated overnight. After overnight incubation, 4ug of anti-Ty1 antibody and IgG antibody were added and incubated at 4°C for 2h. The buffers were added in the following order to wash the magnetic beads: the first step is to use 1ml of low-salt wash buffer, followed by the high-salt wash buffer, and finally add the LiCl wash buffer to the EP tube, incubate at 4°C for 5min, and let stand on ice for 2min. Samples were centrifuged at 1000rpm and 4°C for 1min, discard the supernatant after centrifugation. In the second step, 1ml of TE buffer was added to the EP tube and the sample was incubated at 37°C for 5min. Samples were centrifuged at 1000rpm and 37°C for 1min. Discard the supernatant and wash twice. The beads and Input (stored at -80°C) were eluted with 250µl of Elution Buffer, 10µl of 5M NaCl was added to the eluate, and samples were incubated at 65°C overnight. The DNA was extracted by phenol/chloroform and phenol/chloroform/isoamyl alcohol (25:24:1, pH7.8). DsDNA was then extracted by immunoprecipitation and decrosslinking. Take 14µl of RNase-free water to dissolve the extraction product.
The dsDNA was extracted by immunoprecipitation and de-crosslinking, and the dsDNA stored at -80°C was taken out. The END-IT kit was used to repair the sticky ends to blunt ends. The reaction procedure is as follows: ChIP DNA 8ng, 10x NEB Next end repair buffer 1.5µl, dNTP mix 1.5µl, ATP 1.5µl, NEB NEXT end repair enzyme mix 0.5µl, dH2O up to 15µl. Incubate the reaction tube in a thermal cycler at 25°C for 45 minutes. Then add A-tailing to the blunt end of DNA. The reaction procedure is as follows: End repaired DNA 10µl, NEB Next A-tailing buffer 1.5µl, Klenow (3-5’ exo-) 0.5µl, 2.5mM dATP 2µl, dH2O 1µl. Incubate the reaction tube in a thermal cycler at 37°C for 30 minutes. The third step is to connect the adapter to the DNA. The reaction procedure is as follows: End-Repaired A-tailed DNA 7µl, Indexed adaptor (diluted 1/10 in buffer EB) 1µl, NEB quick ligase 1µl, 10xT4 DNA ligase buffer 1µl. Incubate the reaction tube in a thermal cycler at 20°C for 10 minutes. The size of the DNA fragments was selected using Ampure beads. The required fragment size for the experiment is 300-600 bp. Finally, 10µl RNase-free water was used to dissolve the DNA fragment of the target size. The procedure for adaptor-ligated DNA amplification is as follows: DNA from previous step 10µl, 5x HF buffer 6µl, 10Mm dNTP 0.9µl, primer mix 0.5µl, KAPA HiFi enzyme 0.6µl, dH2O 12µl. Run program: 95°C 3min 1cycle, 98°C 20sec 14cycles, 65°C 30sec 14cycles, 65°C 30sec 14cycles, 65°C 3min 1cycle, 10°C 1cycle. The PCR products were cleaned up and eluted with 14µl EB, and the eluted products were sent for sequencing. The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.

tag: development stage

value: Ring

tag: genotype

value: wild type

tag: host

value: Homo sapiens

tag: chip target


title: ChIP_Input_KP3

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

organism: Mus musculus

growth_protocol: Cell medium was composed as follow: RPMI-1640, DMEM-F12, DMEM (Thermo Fisher), 10% serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE. ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter).

treatment_protocol: Cells were treated with dBET6, JQ1 or I-BET-151 for 2, 4 and 8 hours. DMSO was used as control

tag: tissue

value: small cell lung cancer

value: Low passages (6-10)

tag: treatment

value: Parental cells


title: SB-LDN_Exp2

city: Aarhus

first: Mark

last: Denham

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

description: Differentiated human embryonic stem cells

library_source: transcriptomic

data_processing:
Primary sequencing data, called as raw reads, was subjected to quality control.
Raw reads were filtered into clean reads which were aligned to the reference sequences.
clean reads are mapped to reference using  HISAT and Bowtie2 tool.
Genes expression level is quantified by a software package RSEM.
Genome_build: UCSC build HG19
Supplementary_files_format_and_content: TXT file is comma-delimited file that contain FPKM values for each Sample.

molecule: total RNA

source_name: SB-LDN NGN2-derived Neurons Day 21

extract_protocol:
Total RNA was extract using the Qiagen Rneasy kit. RNA was treated with DNase
mRNA was enriched by oligo dT selection using magnetic beads. RNA was fragment and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primers. The dscDNA was end repaired with phosphate at 5' end and adenylated at the 3' end. Adapters were then ligated with 'T' overhangs at the 3' end to the dscDNA. Two specific primers were used to amplify the ligation product. The PCR products were denatured and single strand DNA was cyclized by splint oligo and DNA ligase. Sequencing was performed on a BGISEQ-500 platform.

tag: differentiation days

value: day 21

tag: pre-patterning molecules

tag: cell type

value: Human ES-derived Neurons


title: SB-LDN_Exp3


title: ChIP-seq_PfArp6_input


title: ChIP-seq_PfArp4_rep3


title: 4T1 Allograft orthotopic injection lung met RNA (4T1-ortho_LuMet2_mouse10_KS28)

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: RNA-seq data from snap frozen tissue or cultured cells

data_processing:
RNA-seq reads were aligned to the mouse mm9 genome assembly using TopHat Software
differentially expressed genes were determined using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: lung metastasis

growth_protocol: cells were grown in tissue culture or isolated from mice and snap frozen

extract_protocol:
RNA was isolated from flash-frozen tissue. First the tissue was mechanically dissociated using a tissue grinder while submerged in 1 ml of TriPure (Roche). 200 µl of chloroform (Sigma-Aldrich) was then added and the soluble fraction was isolated by centrifugation at 12,000 rpm for 15 minutes at 4°C. RNA was then precipitated with the addition of 500 µl isopropanol and incubation of the sample at -20°C for 2 hours. Pure RNA was then extracted using the RNA: DNA mini-prep kit (Zymogen) and finally samples were eluted in 100 µl (PT) or 50 µl (metastases) of DEPC water (Quality Biological). RNA was isolated from cell lines using TriPure as described above but following isopropanol precipitated RNA was washed with 75% ethanol (Sigma-Aldrich), and then again with 95% ethanol before being resuspended in 100 µl DEPC water.
Preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.

treatment_protocol: all samples are untreated

tag: mouse strain

value: BALB

tag: oncogenic driver

value: unknown

tag: cell line name

tag: model

value: Allograft orthotopic injection


title: ChIP-seq_PfArp4_rep2


title: SB-LDN_Exp1


title: ChIP_ASXL3_Ab2_KP3

tag: antibody

value: anti-ASXL3-2 (homemade)


title: SB-CHIR_Exp3

source_name: SB-CHIR NGN2-derived Neurons Day 21


title: ChIP_ASXL3_Ab1_KP3

tag: cell line

value: anti-ASXL3-1 (homemade)


title: ChIP-seq_PfArp4_rep1


title: SB-CHIR_Exp2


title: SB-CHIR_Exp1


title: C2C12_Input_Myog

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
For p300, sequencing reads were mapped to the mouse genome build mm9 using Bowtie, allowing for 3 mismatches and reporting the single best alignment per 50bp read. For myogenin, sequence reads were aligned to the mouse mm9 reference genome build using BWA-Mem with default parameters. Picard was used to filter out replicated reads and BAM files were converted into BED files after which aligned reads were extended by 125 bp at their 3’ end, and converted to bedgraph format using the bedtools2 package. The bedgraphtobigwig package was used for visualization of experiment results.
Peak calling was performed with Hypergeometric Optimization of Motif EnRichment (Homer) v4.10 with -style factor and FDR of 1.0 x 10-4.
Genome_build: mm9
Supplementary_files_format_and_content: Myogenin and p300 peaks were called by HOMER and represent significant enrichment of aligned reads compared to input control.

source_name: C2C12 myoblasts

growth_protocol: Cells of the murine myoblasts cell line C2C12 (ATCC) were maintained in growth medium (GM), Dulbecco’s Modified Eagle Medium (D-MEM) supplemented with 10% Fetal Bovine Serum, at 37ºC with 5% CO2. To induce differentiation, the medium of 80% confluent cell cultures was changed to differentiation medium (DM), D-MEM supplemented with 2% horse serum, and 50 nM of bexarotene was added for treatment conditions.

extract_protocol:
Cells were crosslinked in formaldehyde and sonicated with a Bioruptor (Diagenode). DNA was precipitated with the appropriate antibody and sent for sequencing to the McGill University Genome Quebec Innovation Centre.
Genomic DNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.

treatment_protocol: For treatment conditions, 50 nM of bexarotene was added at the induction of differentiation.

tag: strain

value: C2C12 myoblasts


title: Normal_Exp3

source_name: NGN2-derived Neruons Day 21


title: WT-3

city: Fuzhou

first: Yonghe

last: Hong

state: --- Select a state ---

address: 15 shangxiadian road

department: College of Life Sciences

institute: Fujian Agriculture and Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Magnaporthe oryzae (MG8, http://fungi.ensembl.org/Magnaporthe_oryzae/Info/Index)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Pyricularia oryzae

source_name: Mycelia

growth_protocol: Mycelia of both wild type strain Ku80 and MoCreA deletion mutant ΔMocreA-2 cultured in liquid CM medium for 5 days at 26℃

extract_protocol:
Total RNAs were extracted using EastepTM Super Total RNA extraction Kit (Promega) according to manufactory's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type


title: WT-2


title: Normal_Exp2


title: Adult_uninjured_mSSC_2

type: RNA

city: Palo Alto

first: Gunsagar

middle: Singh

last: Gulati

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

hyb_protocol: RNA was fragmented and hybridized to an Affymetrix Mouse 430 2.0 array (Applied Biosystems™, Cat#900495).

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running the GCOS 1.1.1 software.

data_processing:
For mSSCs profiled from P3, Ad, and Ad/MF joints, the corresponding CEL files were normalized by MAS5 using the affy v1.66.0 R package, mapped to NCBI Entrez gene identifiers using a custom chip definition file for Mouse Genome 430 2.0 microarrays (‘mouse4302mmentrezgcdf’), and converted to Mouse Genome Informatics (MGI) gene symbols using the org.Mm.eg.db v3.11.1 R package. Gene expression values were log2-normalized prior to downstream analysis.
For bulk tissues and mSSCs from Ad/MF joints treated with control (PBS), BMP2, and VEGFR1, the corresponding CEL files were normalized using the Gene Expression Commons platform (https://gexc.riken.jp) and. Briefly, gene expression profiles were normalized against a common reference of >11,939 Affymetrix Mouse Genome 430 2.0 microarrays. Each gene’s expression was then transformed to percentile ranks (range: –100% to +100%) based on its relative value to the reference.
Two matrices consisting of (1) percentile ranks or relative gene expression activity from GEXC for bulk tissues and mSSCs from Ad/MF joints treated with control (PBS), BMP2, and VEGFR1 and (2) custom-cdf- and MAS5-normalized expression for mSSCs profiled from P3, Ad, and Ad/MF joints.

label: streptavidin

label_protocol: RNA was streptavidin-labeled as recommended by Affymetrix protocol.

extract_protocol: For RNA extraction of mSSCs, 500 to 1,000 cells were FAC-sorted directly into 1 mL TRIzol LS (Invitrogen, Cat#10296028). For bulk tissues, bones were flash frozen in liquid nitrogen, crushed into powder, and added directly into 1 mL TRIzol. RNA was isolated with the RNeasy Micro Kit (Qiagen, Cat#74004) and twice amplified with an Arcturus™ RiboAmp™ PLUS Kit (Applied Biosystems™, Cat#KIT0521).

value: Distal Femur

tag: cell

value: mSSC

tag: age

tag: gating strategy


title: ChIP_H3K27Ac_KP3

tag: passages

value: anti-H3K27Ac (CST)


title: WT-1

tag: genotype


title: ATAC-seq_shCtrl-1

first: Luzhang

last: Ji

address: 1239 Siping Rd.

data_processing:
Paired-end reads were aligned to the mouse genome (mm9) using Bowtie2 (Langmead and Salzberg, 2012) with parameters “-X 2000”.
Mitochondrial and PCR duplicate reads were removed after alignment.
Peaks were identified using MACS2 (Zhang et al., 2008) with a q value threshold of 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ATAC-seq signal for each replicate.

source_name: shCtrl

growth_protocol: AML12 cells were cultured in  DMEM/F12 supplemented with 10% fetal bovine serum,  ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.

extract_protocol:
The ATAC-seq was performed as described (Buenrostro et al., 2015) with minor modifications: starting with 30,000 AML12 cells and transposition reaction at 37°C for 45 min.
Illumina sequencing library were prepared according to the standard Illumina protocol.

value: AML12 cells

tag: genotype/variation

value: shCtrl


title: Normal_Exp1


title: Adult_MF_mSSC_3

tag: tissue


title: Adult_uninjured_mSSC_1


title: C3

city: Suzhou

first: Yanfei

last: Bi

state: Jiangsu

address: Yulu NO.2

institute: Jiangsu Changshu National Agricultural Science and Technology Park Management Committee

description: growth in  normal temperature enviroment at day / night temperature of 20°C / 15°C

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl  scripts
Index of the reference genome was built using HISAT2 v2.0.4 and  paired-end clean reads were aligned to the reference genome using  HISAT2(Langmead, B.et al) v2.0.4.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/007/265/GCA_002007265.1_ASM200726v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Spinacia oleracea

growth_protocol: illumination incubator

extract_protocol:
RNA  was isolated using TRIZOL.RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA).RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0  Flurometer.RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: spinach in response to day / night temperature of 35°C / 25°C compared to 20°C / 15°C for 4 days

tag: treatment

value: Control


title: Adult_uninjured_mSSC_3


title: H9_Exp3

description: human embryonic stem cells

source_name: Undifferentiated hESCs

tag: differentiation days

value: day 0

tag: pre-patterning molecules

value: human embryonic stem cell


title: MoCreA_M-3


title: Adult_MF_mSSC_2


title: MoCreA_M-2


title: Adult_MF_mSSC_1


title: H9_Exp2

description: human embryonic stem cells

tag: cell type


title: P3_uninjured_mSSC_4


title: RNA-seq_retina_atoh7_44hpf

first: Lei

last: Du

address: No. 320, Yueyang Road

institute: Institute of Neuroscience, Chinese Academy of Sciences

data_processing:
Raw datasets of single-cell RNA-seq were aligned (zebrafish genome, GRCz10), filtered, and counted using the Cell Ranger software (v2.1.0, 10x Genomics) to generate the processed matrix data.
Raw data of single-cell ATAC-seq were aligned (zebrafish genome, GRCz10), filtered, and counted using the Cell Ranger ATAC software (v1.1, 10x Genomics) to generated the processed matrix data.
Genome_build: GRCz10
Supplementary_files_format_and_content: Processed data files are in tar.gz format, containing matrix files for further analysis.

organism: Danio rerio

source_name: retina

extract_protocol:
Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single-cell RNA-seq. The single nuclei were further extracted by digitonin for single-cell ATAC-seq.
The libraries were constructed using the Chromium Single Cell 3' Library &Gel Bead kit v2 Chip kit (10x genomics, PN-120237) or the Chromium Single Cell ATAC Library & Gel Bead Kit (10x genomics) following the manufacturer’s protocol

value: retina

tag: developmental stage

value: 44 hpf


title: EGF-stimulated A431 cells under treatment of Gefitinib, biological rep2

city: Koto-ku

first: Harumi

last: Kagiwada

state: Tokyo

department: Cellular and Molecular Biotechnology Research Institute (CMB)

country: Japan

institute: National Istitute of Advanced Industrial Science And Technology (AIST)

description:
A431_Gefitinib-2
Gene expression data from A431 cells stimulated with EGF under treatment of Gefitinib.

hyb_protocol: The biotinylated DNA was hybridized to Clariom S (Affymetrix) according to the manufacturer's instruction.

scan_protocol: Microarrays were scanned using laser confocal scanner.

data_processing: The data were analyzed with Transcriptome Analysis Console (Applied Biosystems).

label: biotin

label_protocol: RNA samples were labeled using the WT PLUS Reagent Kit (Affymetrix), according to the manufacturer's instruction.

growth_protocol: A431 cells were grown in E-MEM media supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA from EGF-treated cells were extracted using QIAGEN RNeasy kit.

treatment_protocol: After 24-hr starvation, cells were treated with 100ng/ml EGF and/or 10uM Gefitinib. Cells were harvested after 30 min.

value: EGF and Gefitinib


title: P3_uninjured_mSSC_3


title: H9_Exp1

description: human embryonic stem cells


title: P3_uninjured_mSSC_2


title: EGF-stimulated A431 cells, biological rep2

description:
A431_EGF2
Gene expression data from A431 cells stimulated with EGF.

source_name: A431 cells stimulated with EGF

value: EGF


title: EGF-stimulated A431 cells under treatment of Gefitinib, biological rep1

description:
A431_Gefitinib-1
Gene expression data from A431 cells stimulated with EGF under treatment of Gefitinib.


title: EGF-stimulated A431 cells, biological rep1

description:
A431_EGF-1
Gene expression data from A431 cells stimulated with EGF.


title: A431 cells, biological rep2

description:
A431_Control-2
Gene expression data from A431 cells with no treatment.

source_name: A431 cells with no treatment


title: A431 cells, biological rep1

description:
A431_Control-1
Gene expression data from A431 cells with no treatment.


title: ATAC-seq_retina_48hpf

value: wild type

value: 48 hpf


title: P3_uninjured_mSSC_1


title: Kidney 7 IRI anti-G-CSFR mAb

status: Public on Jun 23 2020

city: Parkville

first: Katherine

middle: R.

last: Martin

state: VIC

address: 1G Royal Parade!

department: John T. Reid Trusts Laboratory

country: Australia

institute: WEHI

data_processing:
Sequenced reads were mapped to reference genome GRCm38.p4 using bowtie2 (v2.2.5) and TopHat2 (v2.1.0) with default parameters except for the –b2-very-sensitive option, and –library-type fr-firststrand setting.
Reads were summarized at the gene level using featureCounts function (v1.4.6) from Rsubread package in a strand-specific manner
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: CSV, raw counts

source_name: Perfused kidney, Treated with anti-G-CSFR mAb 24h pre-IRI

extract_protocol:
Kidneys were perfused with saline and cut longitudinally upon harvest, then immediately submerged in RNAlater (QIAGEN). Samples were stored at 4°C for 24 hrs and then at −80°C. Before RNA preparation, kidneys were dissociated in RLT Plus (QIAGEN) with 1% β-mercaptoethanol in ceramic bead vials (Geneworks Pty Ltd) using a Cryolys cooling device and a Precellys 24 homogeniser (Bertin Technologies). RNA was then prepared using an RNeasy Plus Mini kit (QIAGEN). RNA integrity was confirmed on the 2100 Bioanalyser (Agilent Technologies).
cDNA libraries were prepared for sequencing using standard strand specific kits. 100 bp single-end reads were generated using Illumina HiSeq 3000 using standard protocols at the Australian Genome Research Facility.
Single-end

tag: Sex

value: Male

value: Perfused kidney, all cells

tag: stress

value: ischemia-reperfusion injury (IRI)

tag: time of analysis

value: 24h post-IRI


title: Kidney 9 IRI anti-G-CSFR mAb


title: Kidney 5 IRI Isotype control mAb

source_name: Perfused kidney, Treated with Isotype control mAb 24h pre-IRI

value: Iso


title: Kidney 10 IRI anti-C5 mAb

source_name: Perfused kidney, Treated with anti-C5 mAb 24h pre-IRI


title: Kidney 8 IRI anti-G-CSFR mAb


title: Kidney 2 Sham

source_name: Perfused kidney, Untreated

value: control

value: Sham

value: 24h post sham operation


title: Kidney 11 IRI anti-C5 mAb


title: Kidney 12 IRI anti-C5 mAb


title: Kidney 4 IRI Isotype control mAb


title: Kidney 1 Sham


title: Kidney 3 Sham


title: MoCreA_M-1


title: PfArp4_S_GlcN+_rep2_RNAseq

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0) with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1) with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.

extract_protocol:
The experiment began to collect the highly synchronized Plasmodium, centrifuge and remove the supernatant, then the cells was lysed by adding 1:5 triazole. Next to depolymerize the proteins and nucleic acids in the cells to release them, and extract RNA according to reagent specification of Direct-zol RNA MiniPrep (R2052). The resullts of RNA extraction were verified on a 2% agarose gel.
The mRNA was enriched with magnetic beads with Oligo (dT). It has been optimized to isolate mature mRNA from total RNA by capturing twice using the KAPA mRNA Capture Beads. This experiment was performed using the KAPA Stranded mRNA-seq Kit. Here, the required fragment size for the experiment is 300-400 bp. It carried out the fragmentation and priming program as follows: 85°C 6min. In particular, some changes to the library amplification procedure have been made as follows: initial 98°C 45sec 1cycle; denaturation 98°C 15sec 14cycles; annealing 65°C 30sec 14cycles; extension 65°C 30sec 14cycles; final extension 65°C 5min 1cycle; hold 10°C 1cycle. Resuspend the dried beads in 22µl of RNase-free water to obtain the final library building results. The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.

value: Schizont

tag: host

value: Homo sapiens


title: Kidney 6 IRI Isotype control mAb

tag: strain


title: E2

city: Chengdu

first: Ling

last: xu

state: Sichuan

address: No. 211 Huimin road

department: College of animal science and technology

institute: Sichuan Agricultural University

data_processing:
Clean Reads was sequenced to the reference genome using TopHat2
The Mapped notes were pieced together using Cufflinks software and compared with the original genome annotation information to search for previously unannotated transcriptional areas and to excavate new transcripts and new genes of the species to complement and refine the original genome annotation information.
Cuffquant and Cuffnorm used FPKM (Fragments Per Kilobase of transcript Per Million Fragments mapped) as an indicator to measure transcription or gene expression level.
The set of genes obtained by differential expression analysis is called differential expression gene set and is named "A_vs_B".Differentially expressed genes can be classified into up-regulated and down-regulated genes, depending on the relative level of expression between the two samples.
Genome_build: OryCun2.0_NCBI.Oryctolagus_cuniculus
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Oryctolagus cuniculus

source_name: rabbit endometrium

extract_protocol:
RNA was harvested using Trizol reagent
A sequencing library was generated using the Illumina kit. The eukaryotic mRNA was enriched with magnetic beads with Oligo (dT); the mRNA was randomly interrupted by the addition of Fragmentation Buffer; the first cDNA strand was synthesized using random hexamers using mRNA as a template, and then The second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I, and the cDNA was purified by AMPure XP beads; the purified double-stranded cDNA was subjected to end repair, A tail was added and the sequencing linker was ligated, and then AMPure XP beads were used. Fragment size selection; finally, a cDNA library was obtained by PCR enrichment. Initial quantification was performed using Qubit2.0, and the insert size of the library was detected using Agilent 2100. After passing the library test, different libraries are merged based on the amount of target data and sequenced using the Illumina HiSeq platform.

value: endometrium

tag: body weight


title: E1


title: P1

source_name: rabbit placenta

value: placenta


title: P3


title: P2


title: SR54_Psoriasis_Psoriasis_NON-LESION Agilent_251485039392_S01_GE2-v5_95_Feb07_1_3

city: South San Francisco

first: David

middle: Fong

last: Choy

address: 1 DNA Way

institute: Genentech, Inc.

description:
SR54_Psoriasis_Psoriasis_NON-LESION
SR54_Psoriasis_Psoriasis_NON-LESION

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: vsn/Bioconductor

label_protocol: standard Agilent protocol

extract_protocol: Qiagen RNeasy Fibrous Tissue extraction kit

tag: diagnosis

value: Psoriasis

tag: lesion

value: FALSE

source_name: Universal Human Reference RNA

tag: sample type

value: reference


title: RC14_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039226_S01_GE2-v5_95_Feb07_1_1

description:
RC14_Contact Dermatitis_Contact Dermatitis_NON-LESION
RC14_Contact Dermatitis_Contact Dermatitis_NON-LESION

value: Contact Dermatitis


title: RC14_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039225_S01_GE2-v5_95_Feb07_1_4

value: TRUE


title: TW31_Control_Control_NON-LESION Agilent_251485039379_S01_GE2-v5_95_Feb07_1_4

description:
TW31_Control_Control_NON-LESION
TW31_Control_Control_NON-LESION

value: Control


title: PM74_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485037731_S01_GE2-v5_95_Feb07_1_4

description:
PM74_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
PM74_Atopic Dermatitis_Atopic Dermatitis_NON-LESION

value: Atopic Dermatitis


title: MP63_Psoriasis_Psoriasis_NON-LESION Agilent_251485039394_S01_GE2-v5_95_Feb07_1_1

description:
MP63_Psoriasis_Psoriasis_NON-LESION
MP63_Psoriasis_Psoriasis_NON-LESION


title: SS47_Psoriasis_Psoriasis_NON-LESION Agilent_251485039379_S01_GE2-v5_95_Feb07_1_2

description:
SS47_Psoriasis_Psoriasis_NON-LESION
SS47_Psoriasis_Psoriasis_NON-LESION


title: ML65_Psoriasis_Psoriasis_NON-LESION Agilent_251485039397_S01_GE2-v5_95_Feb07_1_3

description:
ML65_Psoriasis_Psoriasis_NON-LESION
ML65_Psoriasis_Psoriasis_NON-LESION


title: SS47_Psoriasis_Psoriasis_NON-LESION Agilent_251485039379_S01_GE2-v5_95_Feb07_1_3


title: MM55_Psoriasis_Psoriasis_NON-LESION Agilent_251485039393_S01_GE2-v5_95_Feb07_1_2

description:
MM55_Psoriasis_Psoriasis_NON-LESION
MM55_Psoriasis_Psoriasis_NON-LESION


title: MB19_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039227_S01_GE2-v5_95_Feb07_1_1

description:
MB19_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
MB19_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: MP63_Psoriasis_Psoriasis_NON-LESION Agilent_251485039393_S01_GE2-v5_95_Feb07_1_4


title: 1812_1_WT_Cold4h

city: Albany

first: Sneha

last: Damal Villivalam

address: 485 Ohlone Ave, Apt 210

department: NST

institute: UC Berkeley

data_processing:
RNA-seq reads were aligned to UCSC mm10 using STAR aligner and uniquely aligned reads were retained for downstream analysis. After filtering rRNA and mitochondrial reads, gene expression levels were measured using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing raw read count and RPKM-normalized count for each gene

source_name: Inguinal white adipose tissue

growth_protocol: Tet floxed mice or Tet1 KO mice were maintained on chow diet

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen. For RNA seq,  RNA was harvested using Trizol reagent. Qiagen Rneasy mini kit Sample Prep Kit (Cat#74106) was used with 1 ug of total RNA for the construction of sequencing libraries.  and sequencing was performed on the BGISEQ.
Libraries were prepared by the genome sequencing facility following manufacturers instructions for BGILibrary prep kit for RNA seq.

treatment_protocol: Mice were kept at room temperture or exposed to cold temperature 4 C for 4 hours.

value: C57BL/6 Tet1 adipose specific Floxed WT control mice

tag: genotype

value: WT

value: Inguinal white adipose tissue


title: LB38_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039225_S01_GE2-v5_95_Feb07_1_3

description:
LB38_Contact Dermatitis_Contact Dermatitis_NON-LESION
LB38_Contact Dermatitis_Contact Dermatitis_NON-LESION


title: SR54_Psoriasis_Psoriasis_NON-LESION Agilent_251485039392_S01_GE2-v5_95_Feb07_1_2


title: MM55_Psoriasis_Psoriasis_NON-LESION Agilent_251485039393_S01_GE2-v5_95_Feb07_1_3


title: LE71_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485037731_S01_GE2-v5_95_Feb07_1_1

description:
LE71_Contact Dermatitis_Contact Dermatitis_NON-LESION
LE71_Contact Dermatitis_Contact Dermatitis_NON-LESION


title: ML73_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485037732_S01_GE2-v5_95_Feb07_1_1

description:
ML73_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
ML73_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: MR18_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039085_S01_GE2-v5_95_Feb07_1_3

description:
MR18_Contact Dermatitis_Contact Dermatitis_NON-LESION
MR18_Contact Dermatitis_Contact Dermatitis_NON-LESION


title: MR18_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039085_S01_GE2-v5_95_Feb07_1_4


title: ML73_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485037731_S01_GE2-v5_95_Feb07_1_3


title: PM74_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485037732_S01_GE2-v5_95_Feb07_1_2


title: MB19_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039226_S01_GE2-v5_95_Feb07_1_4


title: LE71_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485037731_S01_GE2-v5_95_Feb07_1_2


title: ML65_Psoriasis_Psoriasis_NON-LESION Agilent_251485039397_S01_GE2-v5_95_Feb07_1_2


title: KK62_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039396_S01_GE2-v5_95_Feb07_1_3

description:
KK62_Contact Dermatitis_Contact Dermatitis_NON-LESION
KK62_Contact Dermatitis_Contact Dermatitis_NON-LESION


title: KR69_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039390_S01_GE2-v5_95_Feb07_1_3

description:
KR69_Contact Dermatitis_Contact Dermatitis_NON-LESION
KR69_Contact Dermatitis_Contact Dermatitis_NON-LESION


title: KS66_Control_Control_NON-LESION Agilent_251485039395_S01_GE2-v5_95_Feb07_1_3

description:
KS66_Control_Control_NON-LESION
KS66_Control_Control_NON-LESION


title: LB38_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039225_S01_GE2-v5_95_Feb07_1_2


title: KR69_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039390_S01_GE2-v5_95_Feb07_1_2


title: KK62_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039396_S01_GE2-v5_95_Feb07_1_2


title: JR34_Psoriasis_Psoriasis_NON-LESION Agilent_251485039085_S01_GE2-v5_95_Feb07_1_2

description:
JR34_Psoriasis_Psoriasis_NON-LESION
JR34_Psoriasis_Psoriasis_NON-LESION


title: JS57_Control_Control_NON-LESION Agilent_251485039390_S01_GE2-v5_95_Feb07_1_1

description:
JS57_Control_Control_NON-LESION
JS57_Control_Control_NON-LESION


title: JM37_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039228_S01_GE2-v5_95_Feb07_1_2

description:
JM37_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
JM37_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: JG40_Psoriasis_Psoriasis_NON-LESION Agilent_251485039229_S01_GE2-v5_95_Feb07_1_3

description:
JG40_Psoriasis_Psoriasis_NON-LESION
JG40_Psoriasis_Psoriasis_NON-LESION


title: JD48_Psoriasis_Psoriasis_NON-LESION Agilent_251485039392_S01_GE2-v5_95_Feb07_1_1

description:
JD48_Psoriasis_Psoriasis_NON-LESION
JD48_Psoriasis_Psoriasis_NON-LESION


title: JR34_Psoriasis_Psoriasis_NON-LESION Agilent_251485039085_S01_GE2-v5_95_Feb07_1_1


title: KJ04_KY04_Psoriasis_Psoriasis_NON-LESION Agilent_251485039086_S01_GE2-v5_95_Feb07_1_2

description:
KJ04_KY04_Psoriasis_Psoriasis_NON-LESION
KJ04_KY04_Psoriasis_Psoriasis_NON-LESION


title: JC50_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039225_S01_GE2-v5_95_Feb07_1_1

description:
JC50_Contact Dermatitis_Contact Dermatitis_NON-LESION
JC50_Contact Dermatitis_Contact Dermatitis_NON-LESION


title: JD48_Psoriasis_Psoriasis_NON-LESION Agilent_251485039391_S01_GE2-v5_95_Feb07_1_4


title: JG40_Psoriasis_Psoriasis_NON-LESION Agilent_251485039229_S01_GE2-v5_95_Feb07_1_2


title: JM37_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039228_S01_GE2-v5_95_Feb07_1_3


title: JD03_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039226_S01_GE2-v5_95_Feb07_1_2

description:
JD03_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
JD03_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: EY24_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039227_S01_GE2-v5_95_Feb07_1_2

description:
EY24_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
EY24_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: JC50_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039086_S01_GE2-v5_95_Feb07_1_4


title: GA70_Psoriasis_Psoriasis_NON-LESION Agilent_251485039394_S01_GE2-v5_95_Feb07_1_4

description:
GA70_Psoriasis_Psoriasis_NON-LESION
GA70_Psoriasis_Psoriasis_NON-LESION


title: GA70_Psoriasis_Psoriasis_NON-LESION Agilent_251485039395_S01_GE2-v5_95_Feb07_1_1


title: GP27_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039084_S01_GE2-v5_95_Feb07_1_4

description:
GP27_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
GP27_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: DW60_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039391_S01_GE2-v5_95_Feb07_1_3

description:
DW60_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
DW60_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: GP27_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039084_S01_GE2-v5_95_Feb07_1_3


title: EY24_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039227_S01_GE2-v5_95_Feb07_1_3


title: DP07_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039082_S01_GE2-v5_95_Feb07_1_1

description:
DP07_Contact Dermatitis_Contact Dermatitis_NON-LESION
DP07_Contact Dermatitis_Contact Dermatitis_NON-LESION


title: DP17_Psoriasis_Psoriasis_NON-LESION Agilent_251485039083_S01_GE2-v5_95_Feb07_1_2

description:
DP17_Psoriasis_Psoriasis_NON-LESION
DP17_Psoriasis_Psoriasis_NON-LESION


title: DP07_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039082_S01_GE2-v5_95_Feb07_1_2


title: DW60_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039391_S01_GE2-v5_95_Feb07_1_2


title: DL32_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039083_S01_GE2-v5_95_Feb07_1_4

description:
DL32_Contact Dermatitis_Contact Dermatitis_NON-LESION
DL32_Contact Dermatitis_Contact Dermatitis_NON-LESION


title: DP17_Psoriasis_Psoriasis_NON-LESION Agilent_251485039083_S01_GE2-v5_95_Feb07_1_1


title: DL32_Contact Dermatitis_Contact Dermatitis_NON-LESION Agilent_251485039083_S01_GE2-v5_95_Feb07_1_3


title: DH68_Psoriasis_Psoriasis_NON-LESION Agilent_251485039394_S01_GE2-v5_95_Feb07_1_2

description:
DH68_Psoriasis_Psoriasis_NON-LESION
DH68_Psoriasis_Psoriasis_NON-LESION


title: DD26_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039228_S01_GE2-v5_95_Feb07_1_1

description:
DD26_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
DD26_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: CM22_Control_Control_NON-LESION Agilent_251485039395_S01_GE2-v5_95_Feb07_1_4

description:
CM22_Control_Control_NON-LESION
CM22_Control_Control_NON-LESION


title: AT06_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039084_S01_GE2-v5_95_Feb07_1_2

description:
AT06_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
AT06_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: DD26_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039227_S01_GE2-v5_95_Feb07_1_4


title: DH68_Psoriasis_Psoriasis_NON-LESION Agilent_251485039394_S01_GE2-v5_95_Feb07_1_3


title: AH36_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039391_S01_GE2-v5_95_Feb07_1_1

description:
AH36_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
AH36_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: MDA-MB-231_CTRL_rep1

city: Trieste

first: Giannino

last: Del Sal

state: TS

address: Padriciano 99 - ed. F3 - Area Science Park

country: Italy

institute: LNCIB

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.9 was used and cubic spline normalization was applied to the data. The average signal was used for performing the analysis (AVG_Signal) using limma in the Biocondoctor.

source_name: MDA-MB-231 stably transduced with TW3-GFP control vector

label_protocol: Standard labeling protocol with biotin with Cy3-streptavidin

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptomycin in a 37 °C, 5% CO2 incubator.

extract_protocol: RNA was extracted with Qiazol reagent (Qiagen), following the protocol provided by the manufacturer. RNA integrity was checked by agarose gel electrophoresis. Purity and concentration were determined on a Nanodrop spectrophotometer.

treatment_protocol: For lentivirus production, low-confluence HEK-293T packaging cells were transfected using calcium phosphate with the decoy-30d and matching control vectors in combination with the pMD2.G and psPAX2 packaging vectors. After 48–72 h the virus-containing medium was collected and filtered with 0.20 syringe filter to remouve cellular debris, and was added to the target cells, which were then selected and mantained in culture with puromycin (2 μg/ml).

tag: cell line


title: AH36_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039390_S01_GE2-v5_95_Feb07_1_4


title: MDA-MB-231_dy_30d_rep3

source_name: MDA-MB-231 stably transduced with TW3-GFP-decoy-30d vector


title: MDA-MB-231_dy_30d_rep2


title: JO56_Control_Control_NON-LESION Agilent_251485039396_S01_GE2-v5_95_Feb07_1_1

description:
JO56_Control_Control_NON-LESION
JO56_Control_Control_NON-LESION


title: pcHiC_Reactivated_rep1

city: Rehovot

first: Asaf

last: Marco

address: Herzl 229

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Illumina Casava1.7 software used for basecalling.
The HiCUP pipeline was employed to process the raw fastq sequencing reads. This pipeline was used to map the read pairs against the mouse (mm9) genome, to filter experimental artefacts (such as circularized reads and re-ligations) and to remove duplicate reads.
For the pc-HiC data, the resulting BAM files were downsampled and processed using CHiCAGO version 1.2.079, following the default settings to call significant interactions.
Genome_build: mm9
Supplementary_files_format_and_content: interaction score

source_name: Sorted neuronal nuclei

extract_protocol:
Hippocampal tissue was extracted and flash frozen. After extraction, samples were immediately homogenized in 0.5 mL ice cold PBS with protease inhibitors (Pi) (11836170001, Roche). The suspension was fixed with 2% paraformaldehyde for 10 min, quenched with Glycine 2.5M for 5 min and washed twice with 5 mL of PBS. The suspension was centrifuged at 1200 g, 4°C, for 5 minutes and the pellet was resuspended in 5 mL NF-1 hypotonic buffer (0.5% Triton X-100/0.1M Sucrose/5mM MgCl2/1mM EDTA/10mM Tris-HCl, pH 8.0, Pi). Pelleted nuclei were resuspended in and incubated with NeuN and GFP primary antibodies for overnight in 4°C. Unbound antibodies were washed out twice and nuclei were filtered with 40 µm mesh filter for FACS sorting.
Hi-C libraries were prepared from 10,000 cells /per group (N=3-4), as previously described (Nagano, T. et al. Nat. Protoc. 2015), with some modification. First restriction digestion was carried as described in the original protocol with 1,500 U of HindIII (R3104L, New England Biolabs, USA), as the 6-base cutter (instead of BglII in the original protocol). After Biotin labeling and overnight ligation, samples were spun down (4°C, 1,600 x g for 15 min) and the pellet was resuspended in 25 μl of PBS. The suspension was incubated in 65c with 3 μl of proteinase K for 12-16h. Purification of Hi-C DNA was carried as described in the original protocol with 100 μl of streptavidin-beads. For the second restriction enzyme we used the 4-base cutter Hpych4V (10 U /per sample, R0620S, New England Biolabs, USA). After A-tailing reaction (see original protocol for details), samples were amplified using PCR (17 cycles) and purified with AMPure XP beads. Hi-C libraries were eluted in 20 ul of 10 mM Tris-HCl (pH 8.5). Bait capture system design for Promoter Capture Hi-C – A list of 5000 mouse gene promoters was obtained from the previously published protocol in Schoenfelder, S. et al. Genome Res. 2015.  Selected probes were synthesized by Agilent Technologies according to the SureSelect target enrichment system (Agilent Technologies). To capture Hi-C ligation products containing promoter sequences, we used the previously published protocol (Schoenfelder, S. et al. Genome Res. 2015).

treatment_protocol: In order to minimize the nonspecific eYFP label, one day prior to the contextual fear conditioning (CFC), mice were single housed in a 24h dark/dark room. In the next day, mice received one dose of 4-Hydroxytamoxifen, 1h before the CFC test. Following the behavioral task, mice were either euthanized after 1.5-2 h and brain were collected, or placed back into the dark room for the following 48 hr. After mice were taken out of the dark, they were returned to normal 12 hr (06:00–18:00) light-dark cycle, in the same room. 3 days later (total of 5 days after the CFC), half of the mice cohort were euthanized and brain were collected, while the other half returned to the testing room, where they exposed to the fear inducing cue (tone and context).

tag: tissue

value: Hippocampus

value: ArcCreERT2 x R26R-STOP-floxed- yellow fluorescent protein (eYFP)

value: Foot shock day 0, No recall, tissue collection day 11


title: pcHiC_Reactivated_rep4

tag: treatment

value: Foot shock day 0, No recall, tissue collection day 14


title: pcHiC_Reactivated_rep2

value: Foot shock day 0, No recall, tissue collection day 12


title: pcHiC_Reactivated_rep3

value: Foot shock day 0, No recall, tissue collection day 13


title: CC23_Psoriasis_Psoriasis_NON-LESION Agilent_251485039229_S01_GE2-v5_95_Feb07_1_1

description:
CC23_Psoriasis_Psoriasis_NON-LESION
CC23_Psoriasis_Psoriasis_NON-LESION


title: AT06_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039084_S01_GE2-v5_95_Feb07_1_1


title: AB53_Psoriasis_Psoriasis_NON-LESION Agilent_251485039392_S01_GE2-v5_95_Feb07_1_4

description:
AB53_Psoriasis_Psoriasis_NON-LESION
AB53_Psoriasis_Psoriasis_NON-LESION


title: CC23_Psoriasis_Psoriasis_NON-LESION Agilent_251485039228_S01_GE2-v5_95_Feb07_1_4


title: MDA-MB-231_CTRL_rep3


title: AD29_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039082_S01_GE2-v5_95_Feb07_1_4

description:
AD29_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
AD29_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: MDA-MB-231_CTRL_rep2


title: AB53_Psoriasis_Psoriasis_NON-LESION Agilent_251485039393_S01_GE2-v5_95_Feb07_1_1


title: AD29_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039082_S01_GE2-v5_95_Feb07_1_3


title: JD03_Atopic Dermatitis_Atopic Dermatitis_NON-LESION Agilent_251485039226_S01_GE2-v5_95_Feb07_1_3

description:
JD03_Atopic Dermatitis_Atopic Dermatitis_NON-LESION
JD03_Atopic Dermatitis_Atopic Dermatitis_NON-LESION


title: pcHiC_Late_rep3

value: Foot shock day 0, No recall, tissue collection day 9


title: pcHiC_Late_rep4

value: Foot shock day 0, No recall, tissue collection day 10


title: pcHiC_Late_rep1

value: Foot shock day 0, No recall, tissue collection day 7


title: pcHiC_Late_rep2

value: Foot shock day 0, No recall, tissue collection day 8


title: MDA-MB-231_dy_30d_rep1


title: pcHiC_Early_rep2

value: Foot shock day 0, No recall, tissue collection day 4


title: pcHiC_Early_rep1

value: Foot shock day 0, No recall, tissue collection day 3


title: pcHiC_Basal_rep3

value: Foot shock day 0, No recall, tissue collection day 2


title: pcHiC_Basal_rep1

value: Foot shock day 0, No recall, tissue collection day 0


title: pcHiC_Basal_rep2

value: Foot shock day 0, No recall, tissue collection day 1


title: pcHiC_Early_rep4

value: Foot shock day 0, No recall, tissue collection day 6


title: HiC_Basal_rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
HOMER Hi-C pipeline was used to filter experimental artefacts such as circularization, self-ligations and PCR duplicates.
Filtered reads were aligned to the reference mouse genome (mm9) and further processed using HOMER HI-C pipeline.
HOMER’s Hi-C tools were used to perform principal component analysis (PCA) on the Hi-C data to identify sub-nuclear compartments (A and B) at 50 Kb resolution.
Genome_build: mm9
Supplementary_files_format_and_content: first principal component (PC1) score
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Hippocampal tissue was extracted and flash frozen. After extraction, samples were immediately homogenized in 0.5 mL ice cold PBS with protease inhibitors (Pi) (11836170001, Roche). The suspension was fixed with 1% paraformaldehyde for 10 min, quenched with Glycine 2.5M for 5 min and washed twice with 5 mL of PBS. The suspension was centrifuged at 1200 g, 4°C, for 5 minutes and the pellet was resuspended in 5 mL NF-1 hypotonic buffer (0.5% Triton X-100/0.1M Sucrose/5mM MgCl2/1mM EDTA/10mM Tris-HCl, pH 8.0, Pi). Pelleted nuclei were resuspended in and incubated with NeuN and GFP primary antibodies for overnight in 4°C. Unbound antibodies were washed out twice and nuclei were filtered with 40 µm mesh filter for FACS sorting.
Nuclei from fixed cells were sorted into 1.5 mL eppendorf tubes containing 500 µl fresh ice-cold lysis buffer (10mM Tris pH=8, 10mM NaCl, 0.2% Igepal CA-630, Pi and PCR grade water) and frozen on dry ice and stored at -80c until they were used. Hi-C libraries were prepared from 100,000 cells/per group (collected from two animals) in two biological replicates, using DovetailTM Hi-C kit manual (v.1.03, Dovetail Genomics, Chicago, USA).


title: HiC_Early_rep1


title: HiC_Basal_rep1


title: HiC_Late_rep1


title: HiC_Late_rep2


title: pcHiC_Early_rep3

value: Foot shock day 0, No recall, tissue collection day 5


title: Dppa_WT_Mc3B-2

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
Sampe 188
RNA-seq
Processed_data_Samples_172_189.txt.gz

data_processing:
EB RNA-seq raw FastQ data were trimmed with Trim Galore (version 0.4.4, default parameters) and mapped to the mouse GRCm38 genome assembly using Hisat2 version 2.1.0. Stable overexpression clone data used Trim Galore v0.5.0_dev and HiSat2 v2.1.0.
ChIP-seq Raw FastQ data were trimmed with Trim Galore v0.6.1 and aligned to mouse GRCm38 genome using Bowtie 2 v 2.3.2.
ATAC-seq Raw FastQ data were trimmed with Trim Galore (v0.5.0_dev) using standard parameters and aligned using Bowtie 2 v2.3.2.
NOME-seq Raw fastQ data were trimmed using Trim Galore version 0.4.4 using standard parameters, reads aligned using Bismark v0.18.2
All downstream data processing was performed using SeqMonk software (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Amplicon-bisulfite-seq: As first step in the processing, the first 8 bp of Read 2 were removed and written into the readID of both reads as an in-line barcode, or UMI (Unique Molecular Identifier). This UMI was then later used during the de-duplication step with "deduplicate bismark --barcode mapped_file.bam".Raw sequence reads were then trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.5 www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 2.3, parameters: --paired).
Genome_build: mm10
Supplementary_files_format_and_content: The ChIP and ATAC is enrichment RPM over 1kb running windows. The RNA-seq is all genes RPM and the NOME-seq is 100CpG running window % methylation.  The files were generated using SeqMonk (exporting an annotated probe report).

source_name: Dppa2/4 WT parental line (no CRISPR)

growth_protocol: E14 mouse ESCs were grown using standard serum/LIF culture conditions (DMEM, 4,500 mg/L glucose, 4 mM L-glutamine, 110 mg/L sodium pyruvate, 15% fetal bovine serum, 1 U/mL penicillin, 1 mg/mL streptomycin, 0.1 mM nonessential amino acids, 50 mM b-mercaptoethanol, 103 U/mL LIF) at 37 degrees Celsius in normal oxygen, feeder-free on gelatin coated plates.

extract_protocol:
RNAseq: Total RNA was isolated using TriReagent (Sigma) or RNA-DNA allprep columns (Qiagen) 0.5-1mg DNAse treated (Thermo Fisher EN0525).
ChIPseq: Ten million cells were fixed in 1% formaldehyde (Fisher Scientific 28906) in DMEM (Invitrogen 41966-052) for 10 minutes, quenched in 0.125M glycine, and scraped off cell culture dishes using cell scrapers. Cells were lysed with buffers LB1 (50mM Hepes-KOH (pH 7.5), 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% Igepal CA-630, 0.25% Triton-X 100), LB2 (10mM Tris-HCl (pH 8.0), 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and LB3 (10mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x Protease Inhibitors (Roche)) consecutively, before fragmenting chromatin by sonicating for 30 cycles of 30s ON high /30s OFF (Diagenode Bioruptor). For each ChIP, 5µg antibody (anti-Ash2l Bethyl Labs A300-489, anti-Ezh2 CST D2C9, anti-H2A.Z Abcam ab4174, anti-H3K4me3 Abcam ab8580, anti-H3K27me3 Active Motif AM39155, anti-IgG Abcam ab125938, anti-Ring1b CST D22F2) was pre-bound to protein G dynabeads (Invitrogen) and blocked with 0.5% BSA in PBS. Sonicated DNA was added to antibody-bound beads with 10% Triton-X 100 and incubated overnight at 4°C on a rotator. Beads and DNA were washed 6 times with RIPA buffer (50mM HEPES-KOH (pH 7.6), 1mM EDTA, 0.7% Na-Deoxycholate, 1% Igepal CA-630, 0.5M LiCl), followed by one wash in 1x TBS and overnight incubation at 65°C with elution buffer (50 mM Tris- HCl, pH 8; 10 mM EDTA; 1% SDS). For precipitation of chromatin, samples were treated with RNase A and Proteinase K. DNA was purified using MinElute PCR purification columns (Qiagen 28006) and eluted in 30µL of TE. DNA was quantified using HS DNA Qubit (ThermoFisher) or PicoGreen (ThermoFisher) assays.
ATACseq: 10,000 cells were trypsinised and immediately processed for ATACseq.
NOMEseq: Cells were fixed on 15cm plates wih Fixation solution (Active-Motif) for 10minutes at room temperature then processed according to Active Motif NOME-seq kit protocol.
amplicon bisulfite: Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) or the AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s instructions and eluted into TE buffer or H2O.
RNAseq: Opposite strand-specific polyA RNA libraries were made using 1 µg of DNase- treated RNA at the Sanger Institute Illumina bespoke pipeline and sequenced using the Illumina HiSeq2 platform.
ChIPseq: libraries generated using MicroPlex Library Preparation Kit (Diagenode) following the manufacturer’s instructions. Libraries were quality controlled using bioanalyser HS DNA chips (Agilent) and single-end 50bp reads sequenced using the Illumina HiSeq2 sequencing platform.
ATACseq: ATAC-seq libraries were performed as previously described (Buenrostro, Wu, Chang, & Greenleaf, 2015) with the following modification to use on 10,000 cells: initial transposition reaction was performed with 10,000 cells, 10ml 2x TD buffer, 0.5ml Tn5 enzyme and 9.5ml H2O for 30minutes at 37 degrees Celsius. A total of 15 cycles of amplification were used. Two technical replicates were performed per clone, with 3 WT and 3 Dppa2/4 DKO clones used (total of 12 samples).
NOMEseq: Whole genome bisulfite libraries were generated using NOME-seq kit from Active Motif (103946) according to manufacturer’s instructions with 6 cycles of amplification for 2 WT clones (clones 57 and 58) and 1 Dppa2/4 DKO clone (clone 43).
amplicon bisulfite: 1μg of genomic DNA was bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) according to manufacturer’s instructions with either magnetic bead or column clean-up and eluted/resuspended in elution buffer. Amplicons of interest were amplified using 2x KAPA HiFi Uracil+ ReadyMix using primers containing UMI for deduplication and PCR adapters for a second round of PCR to adapt sample-specific barcodes and adapters for Illumina Sequencing. Libraries were sequenced using the Illumina MiSeq platform with a 10% PhIX spike-in and paired-end 250bp reads.
: RNA-seq or ChIP-seq or NOME-seq or amplicon bisulfite-seq

treatment_protocol: Stable overexpression cell lines were generated using Lipofectamine 2000 on preplated cells and resistant cells selected with appropriate antibiotics for at least 1 week before sorting single cells into 96 well plates by flow cytometry using a BD Aria III or BD Influx high-speed cell sorter, and clonal expansion. CRISPR double knockout ESC line (clone 43) was described previously (M. Eckersley-Maslin et al., 2019), and additional CRISPR double knockout ESC lines (clone 37 and clone 53) generated as previously described (M. Eckersley-Maslin et al., 2019). For embryoid bodies, 2x106 mESCs were cultured on 10cm low-attachment dishes in standard ESC medium containing all described components except LIF.

value: embryonic stem cell

tag: culture conditions

value: serum/LIF

value: E14 ESCs, contains MERVL::tdTomato reporter

tag: chip antibody


title: Dppa_WT_Mc3C-2

description:
Sampe 189
RNA-seq
Processed_data_Samples_172_189.txt.gz

tag: cell type


title: Dppa_WT_Mc3A-2

description:
Sampe 187
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_WT_58B-2

description:
Sampe 185
RNA-seq
Processed_data_Samples_172_189.txt.gz

source_name: Dppa2/4 WT clone 58

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: Dppa_WT_58C-2

description:
Sampe 186
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_WT_58A-2

description:
Sampe 184
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_WT_57C-2

description:
Sampe 183
RNA-seq
Processed_data_Samples_172_189.txt.gz

source_name: Dppa2/4 WT clone 57


title: RNA_Late_rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw fastq data were aligned to the mouse mm9 reference genome using Bowtie 2.0.
The mapped reads from gene bodies (including exons and introns reads) were processed by Cufflinks 2.2 and DEseq2 with UCSC mm9 reference gene annotation to estimate transcript abundances.
Differential gene expression and downstream analyses were performed using DEseq2 and custom R scripts.
Relative abundance of transcripts was measured by fragments per kilobase of exon per million fragments mapped (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts

extract_protocol:
Hippocampal tissue was extracted and flash frozen. After extraction, samples were immediately homogenized in 0.5 mL ice cold PBS with protease inhibitors (Pi) (11836170001, Roche). The suspension was fixed with 1% paraformaldehyde for 10 min, quenched with Glycine 2.5M for 5 min and washed twice with 5 mL of PBS. The suspension was centrifuged at 1200 g, 4°C, for 5 minutes and the pellet was resuspended in 5 mL NF-1 hypotonic buffer (0.5% Triton X-100/0.1M Sucrose/5mM MgCl2/1mM EDTA/10mM Tris-HCl, pH 8.0, Pi). Pelleted nuclei were resuspended in and incubated with NeuN, Arc and GFP primary antibodies for overnight in 4°C. Unbound antibodies were washed out twice and nuclei were filtered with 40 µm mesh filter for FACS sorting.
Immediately follow fixation and sorting, nucleic acids were recovered by RecoverAll™ protocol (Total Nucleic Acid Isolation Kit for FFPE, Life Technologies, AM1975). Next, 0.75 mL of Trizol LS and 0.2 mL of Phenol : Chloroform solution was added to each sample followed by vigorous shaking. Suspension was placed into Phase lock gel heavy tubes and spun down at 13,000rpm for 5 min. Aquatic phase with nucleic acids was extracted from the tubes to fresh  eppendorf tube with equal amount of ethanol 100%. RNA purification was carried by Direct-zol™ RNA MicroPrep kit (Zymo Research, R2060) for RNA purification, according to the manufacturer’s instruction. RNA was eluted (10 ul, DEPC) and then stored at −80 °C. SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Clontech, 635006) was used for the library preparation and amplification. Libraries were prepared according to the manufacturer’s instructions with no extra fragmentation step (FFPE, option 2, see manual), with depletion of ribosomal cDNA and final PCR amplification (15 cycles).

value: Hippocampus

value: ArcCreERT2 x R26R-STOP-floxed- yellow fluorescent protein (eYFP)


title: RNA_Late_rep2


title: RNA_Late_rep1


title: RNA_Early_rep3


title: RNA_Reactivated_rep1


title: RNA_Basal_rep1


title: RNA_Basal_rep2


title: RNA_Basal_rep3


title: RNA_Reactivated_rep2


title: RNA_Reactivated_rep3


title: RNA_Early_rep2


title: RNA_Early_rep1


title: Dppa_DKO_53C-2

description:
Sampe 180
RNA-seq
Processed_data_Samples_172_189.txt.gz

source_name: Dppa2/4 DKO clone 53


title: Dppa_WT_57A-2

description:
Sampe 181
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_DKO_53B-2

description:
Sampe 179
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_DKO_43A-2

description:
Sampe 175
RNA-seq
Processed_data_Samples_172_189.txt.gz

source_name: Dppa2/4 DKO clone 43


title: Dppa_DKO_43B-2

description:
Sampe 176
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_DKO_43C-2

description:
Sampe 177
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_DKO_53A-2

description:
Sampe 178
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_DKO_36B-2

description:
Sampe 173
RNA-seq
Processed_data_Samples_172_189.txt.gz

source_name: Dppa2/4 DKO clone 36


title: Dppa_DKO_36C-2

description:
Sampe 174
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: Dppa_DKO_36A-2

description:
Sampe 172
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: KJ04_KY04_Psoriasis_Psoriasis_NON-LESION Agilent_251485039086_S01_GE2-v5_95_Feb07_1_3

description:
KJ04_KY04_Psoriasis_Psoriasis_NON-LESION
KJ04_KY04_Psoriasis_Psoriasis_NON-LESION

value: Psoriasis

value: FALSE

value: reference


title: Dppa_WT_57B-2

description:
Sampe 182
RNA-seq
Processed_data_Samples_172_189.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa4_plusDox_2

description:
Sampe 168
ChIP-seq
Processed_data_Samples_130-171.txt.gz

source_name: inducible shRNA cells treated with dox for 7 days

value: E14 ESCs containing inducible shRNA hairpin against Dppa4

value: anti-H3K4me3 Abcam ab8580


title: H3K4me3_ChIP_shRNA_Dppa4_recovery_2

description:
Sampe 167
ChIP-seq
Processed_data_Samples_130-171.txt.gz

source_name: inducible shRNA cells treated with dox for 7 days then dox washout for 14 days


title: H3K4me3_ChIP_shRNA_Dppa4_noDox_3

description:
Sampe 169
ChIP-seq
Processed_data_Samples_130-171.txt.gz

source_name: inducible shRNA cells untreated


title: H3K4me3_ChIP_shRNA_Dppa4_recovery_1

description:
Sampe 164
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa2_noDox_2

description:
Sampe 157
ChIP-seq
Processed_data_Samples_130-171.txt.gz

value: E14 ESCs containing inducible shRNA hairpin against Dppa2


title: H3K4me3_ChIP_shRNA_Dppa2_plusDox_2

description:
Sampe 159
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa2_plusDox_3

description:
Sampe 162
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa2_noDox_3

description:
Sampe 160
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa4_noDox_1

description:
Sampe 163
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa4_noDox_2

description:
Sampe 166
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa4_plusDox_1

description:
Sampe 165
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa2_recovery_2

description:
Sampe 158
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa4_plusDox_3

description:
Sampe 171
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa2_recovery_3

description:
Sampe 161
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa4_recovery_3

description:
Sampe 170
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa2_plusDox_1

description:
Sampe 156
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa2_noDox_1

description:
Sampe 154
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K4me3_ChIP_shRNA_Dppa2_recovery_1

description:
Sampe 155
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa4_plusDox_3

description:
Sampe 153
ChIP-seq
Processed_data_Samples_130-171.txt.gz

value: anti-H3K27me3 Active Motif AM39155


title: H3K27me3_ChIP_shRNA_Dppa4_recovery_3

description:
Sampe 152
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa4_noDox_2

description:
Sampe 148
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa4_plusDox_2

description:
Sampe 150
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa4_plusDox_1

description:
Sampe 147
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa4_noDox_1

description:
Sampe 145
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa4_recovery_1

description:
Sampe 146
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa2_plusDox_3

description:
Sampe 144
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa2_noDox_3

description:
Sampe 142
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa4_noDox_3

description:
Sampe 151
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa4_recovery_2

description:
Sampe 149
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: MC2494 rep4

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

description:
replicate 4
SAMPLE 12

scan_protocol: chip were scanned with Illumina BeadArray Reader, BeadScan software version 3.5.49

data_processing: The data were normalised using quantile normalisation with limma package in R

source_name: acute myeloid leukemia

label_protocol: 3000ng of total RNA were converted in cDNA and then in cRNA following manufacturer's instruction.

growth_protocol: U937 cells were cultured in RPMI medium supplemented with 2 mM glutamine, 100 IU/ml penicillin, 100 µg/ml streptomycin

extract_protocol: Total RNA extracted using TRIZOL  (Invitrogen) reagent  following manufacturer's instructions.

treatment_protocol: U937 clls were treated with the compounds for 24h


title: EX527 rep4

description:
replicate 4
SAMPLE 8


title: EX527 rep1

description:
replicate 1
SAMPLE 5


title: MCF7, BLRP-ER Wild type (ChIP-Seq)

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

growth_protocol: MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody or by HA antibody conjugated magnet beads pull-down.
The extracted ChIP DNA was ligated to specific adaptors of ThruPLEX DNA-seq kit (R400427), according to the manufacturer’s instructions.ER_pbox/WT ChIP library was constructed by KAPA Hyper Prep system (KK8504)

treatment_protocol: For MCF7 cells with different ER truncations, MCF7 cells were first infected with lentivirus-based ER truncations, and then transiently infected shER targeting 3'UTR to knock down endogenous ER. Cells were kept in hormone stripped condition for at least three days before treating with 100 nM estradiol or corresponding condition of ethanol for 30 min.ER_pbox/WT ChIP was done in full medium condition.

tag: transfection

value: Wild type ER

value: full medium

value: Biotin-ChIP using Streptavidin Magnetic beads (Solulink)


title: H3K27me3_ChIP_shRNA_Dppa2_plusDox_2

description:
Sampe 141
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: MC2494 rep3

description:
replicate 3
SAMPLE 11


title: MC2494 rep2

description:
replicate 2
SAMPLE 10


title: MC2494 rep1

description:
replicate 1
SAMPLE 9


title: EX527 rep3

description:
replicate 3
SAMPLE 7


title: H3K27me3_ChIP_shRNA_Dppa2_recovery_2

description:
Sampe 140
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: U937 rep4

description:
replicate 4
SAMPLE 4

value: control


title: U937 rep3

description:
replicate 3
SAMPLE 3


title: MCF7, WT_ER_Veh (ChIP-Seq)

value: WT ER

value: Veh

value: HA (Thermofisher, 88837)


title: H3K27me3_ChIP_shRNA_Dppa2_recovery_3

description:
Sampe 143
ChIP-seq
Processed_data_Samples_130-171.txt.gz

value: embryonic stem cell

value: serum/LIF


title: U937 rep1

description:
replicate 1
SAMPLE 1


title: EX527 rep2

description:
replicate 2
SAMPLE 6


title: U937 rep2

description:
replicate 2
SAMPLE 2


title: MCF7, WT_ER_E2 (ChIP-Seq)


title: H3K27me3_ChIP_shRNA_Dppa2_noDox_2

description:
Sampe 139
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: MCF7, BLRP-ER pBOX (ChIP-Seq)

value: pBox mutant ER


title: ChR2(+)LIGHT_Mouse2

city: Aurora

first: Richard

last: Benninger

state: Colorado

address: 1775 Aurora Court, M20-4202V

department: Bioengineering

institute: University of Colorado Anschutz Medical Campus

description: Genetically Modified Mouse Islets

data_processing:
Data colllection and analsysis was performed at Novogene, Inc
Supplementary_files_format_and_content: read count, fpkm and statistics

source_name: β-cells, α-cells, δ-cells

growth_protocol: Mouse had ad libitum food in 12h light/dark cycle

extract_protocol:
Pancrease isolation followed by collagenase treatment to isolate islets
Library and RNAseq was performed at Novogene, Inc

treatment_protocol: Low glucose, high glucose, high glucose + diazoxide (membrane hyperpolarization), high glucose + FK506 (Calcineurin Inhibitor); (-) ChR2 Stimulation and (+) ChR2 Stimulation

value: islets

value: Genetically Modified:Channelrhodopsin-2 Beta-cell specific

tag: background strain

value: Differentially treated with light stimulation for 40 min using a 1.5m Light On and 5 min light off


title: H3K27me3_ChIP_shRNA_Dppa2_plusDox_1

description:
Sampe 138
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: H3K27me3_ChIP_shRNA_Dppa2_recovery_1

description:
Sampe 137
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: MCF7, Rnase_ER_Veh (ChIP-Seq)

value: No

value: Rnase+Veh

value: ERalpha (Bethyl, A300-495A)


title: ChR2(-)LIGHT_Mouse2

description: Genetically Modified Mouse Islets

value: Untreated


title: MCF7, noRnase_ER_Veh (ChIP-Seq)


title: H3K27me3_ChIP_shRNA_Dppa2_noDox_1

description:
Sampe 136
ChIP-seq
Processed_data_Samples_130-171.txt.gz

value: E14 ESCs containing inducible shRNA hairpin against Dppa2

value: anti-H3K27me3 Active Motif AM39155


title: MCF7, Rnase_ER_E2 (ChIP-Seq)


title: MCF7, noRnase_ER_E2 (ChIP-Seq)


title: 11G+FK_Mouse2

description: Wild-Type Mouse Islets

value: wildtype

value: 11 mM Glucose + FK506 treated for 4h


title: 11G+D_Mouse2

description: Wild-Type Mouse Islets

value: 11 mM Glucose + Diazoxide treated for 4h


title: ChR2(+)LIGHT_Mouse1

description: Genetically Modified Mouse Islets


title: 11G+D_Mouse1

description: Wild-Type Mouse Islets


title: ChR2(-)LIGHT_Mouse1

description: Genetically Modified Mouse Islets


title: input_shRNA_Dppa4_recovery

description:
Sampe 134
ChIP-seq
Processed_data_Samples_130-171.txt.gz

value: E14 ESCs containing inducible shRNA hairpin against Dppa4


title: MCF7, dDBD_ER_Veh (ChIP-Seq)

value: dDBD ER

value: Veh

value: HA (Thermofisher, 88837)


title: MCF7, dDBD_ER_E2 (ChIP-Seq)


title: input_shRNA_Dppa4_noDox

description:
Sampe 133
ChIP-seq
Processed_data_Samples_130-171.txt.gz

value: embryonic stem cell

value: serum/LIF


title: 11G_Mouse1

description: Wild-Type Mouse Islets

value: islets

value: 11 mM Glucose treated for 4h


title: input_shRNA_Dppa4_plusDox

description:
Sampe 135
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: input_shRNA_Dppa2_plusDox

description:
Sampe 132
ChIP-seq
Processed_data_Samples_130-171.txt.gz


title: MCF7, dAF2_ER_Veh (ChIP-Seq)

value: dAF2 ER


title: e13_5

city: Baltimore

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

data_processing:
Demultiplexing was performed based on the 8 bp sample index read to generate FASTQs for the Read1 and Read2 paired-end reads.
Reads were aligned using STAR as implemented in the CellRanger pipeline
Barcodes and UMIs were filtered.
PCR duplicates were marked if two sets of read pairs shared a barcode sequence, a UMI tag, and a gene ID (Ensembl).
Previously described processing is according to: Zheng et. al. 2017.
Genome_build: mm10 with added exogenous genes including green fluorescent protein
Supplementary_files_format_and_content: There are two anndata (annotated data matrix) h5ad files. The file contains the preprocessed and annotated count data of all four experiments (E12.5-15-5). annData_GLE_cells.h5ad contains the joint cells. annData_nonjoint_cells.h5ad contains the non-joint cells, such as immune cells, neural crest derivatives, and muscle.
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file

source_name: embryonic hindlimb

extract_protocol:
wo presumptive knee joints were isolated by transfemoral and transtibial division in a single 3 cm dish (Figure 1A) and incubated in digestion solution I (3 mg / mL collagenase D, DMEM high glucose culture medium, serum free) for 45 min at 37 °C, and then in digestion solution II (1 mg / mL collagenase D, DMEM high glucose culture medium, serum free) for 3 hrs (one embryo per dish) at 37 °C. During the period of incubation, the mice gender was identified by genotyping and only male samples were chosen for further processing. The tissues with medium were gently pipetted to disperse cell aggregates and filtered through 40 µm cell strainer, then centrifuged for 10 min at 400 g. The pellet was suspended with 0.4% BSA in PBS.
Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 30 Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) as indicated in Zheng et al 2017; PMID: 28091601) .

treatment_protocol: Mice were kept in light-reversed room (light turns on at 10 pm and turns off at 10 am). Timing was determined by putting one male mouse and two female mice in the same cage at 9 am and separating them at 4 pm on the same day. We count that midnight as E0.5 stage. On E12.5, E13.5, E14.5 and E15.5, the pregnant mice were sacrificed by CO2 at 3 am. The cells were isolated using the protocol (Primary culture and phenotyping of murine Chondrocytes) with modification: The embryos (usually n=6-8) were rinsed three times in PBS on ice.

value: hind limb

tag: developmental stage

value: embryonic hindlimb

value: synovial joint progenitor cells


title: e14_5


title: e12_5


title: Dppa_WT_Mc3B

data_processing:
EB RNA-seq raw FastQ data were trimmed with Trim Galore (version 0.4.4, default parameters) and mapped to the mouse GRCm38 genome assembly using Hisat2 version 2.1.0. Stable overexpression clone data used Trim Galore v0.5.0_dev and HiSat2 v2.1.0.
ChIP-seq Raw FastQ data were trimmed with Trim Galore v0.6.1 and aligned to mouse GRCm38 genome using Bowtie 2 v 2.3.2.
ATAC-seq Raw FastQ data were trimmed with Trim Galore (v0.5.0_dev) using standard parameters and aligned using Bowtie 2 v2.3.2.
NOME-seq Raw fastQ data were trimmed using Trim Galore version 0.4.4 using standard parameters, reads aligned using Bismark v0.18.2
All downstream data processing was performed using SeqMonk software (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: mm10
Supplementary_files_format_and_content: The ChIP and ATAC is enrichment RPM over 1kb running windows. The RNA-seq is all genes RPM and the NOME-seq is 100CpG running window % methylation.  The files were generated using SeqMonk (exporting an annotated probe report).

extract_protocol:
RNAseq: Total RNA was isolated using TriReagent (Sigma) or RNA-DNA allprep columns (Qiagen) 0.5-1mg DNAse treated (Thermo Fisher EN0525).
ChIPseq: Ten million cells were fixed in 1% formaldehyde (Fisher Scientific 28906) in DMEM (Invitrogen 41966-052) for 10 minutes, quenched in 0.125M glycine, and scraped off cell culture dishes using cell scrapers. Cells were lysed with buffers LB1 (50mM Hepes-KOH (pH 7.5), 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% Igepal CA-630, 0.25% Triton-X 100), LB2 (10mM Tris-HCl (pH 8.0), 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and LB3 (10mM Tris-HCl (pH 8.0), 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x Protease Inhibitors (Roche)) consecutively, before fragmenting chromatin by sonicating for 30 cycles of 30s ON high /30s OFF (Diagenode Bioruptor). For each ChIP, 5µg antibody (anti-Ash2l Bethyl Labs A300-489, anti-Ezh2 CST D2C9, anti-H2A.Z Abcam ab4174, anti-H3K4me3 Abcam ab8580, anti-H3K27me3 Active Motif AM39155, anti-IgG Abcam ab125938, anti-Ring1b CST D22F2) was pre-bound to protein G dynabeads (Invitrogen) and blocked with 0.5% BSA in PBS. Sonicated DNA was added to antibody-bound beads with 10% Triton-X 100 and incubated overnight at 4°C on a rotator. Beads and DNA were washed 6 times with RIPA buffer (50mM HEPES-KOH (pH 7.6), 1mM EDTA, 0.7% Na-Deoxycholate, 1% Igepal CA-630, 0.5M LiCl), followed by one wash in 1x TBS and overnight incubation at 65°C with elution buffer (50 mM Tris- HCl, pH 8; 10 mM EDTA; 1% SDS). For precipitation of chromatin, samples were treated with RNase A and Proteinase K. DNA was purified using MinElute PCR purification columns (Qiagen 28006) and eluted in 30µL of TE. DNA was quantified using HS DNA Qubit (ThermoFisher) or PicoGreen (ThermoFisher) assays.
ATACseq: 10,000 cells were trypsinised and immediately processed for ATACseq.
NOMEseq: Cells were fixed on 15cm plates wih Fixation solution (Active-Motif) for 10minutes at room temperature then processed according to Active Motif NOME-seq kit protocol.
RNAseq: Opposite strand-specific polyA RNA libraries were made using 1 µg of DNase- treated RNA at the Sanger Institute Illumina bespoke pipeline and sequenced using the Illumina HiSeq2 platform.
ChIPseq: libraries generated using MicroPlex Library Preparation Kit (Diagenode) following the manufacturer?s instructions. Libraries were quality controlled using bioanalyser HS DNA chips (Agilent) and single-end 50bp reads sequenced using the Illumina HiSeq2 sequencing platform.
ATACseq: ATAC-seq libraries were performed as previously described (Buenrostro, Wu, Chang, & Greenleaf, 2015) with the following modification to use on 10,000 cells: initial transposition reaction was performed with 10,000 cells, 10ml 2x TD buffer, 0.5ml Tn5 enzyme and 9.5ml H2O for 30minutes at 37 degrees Celsius. A total of 15 cycles of amplification were used. Two technical replicates were performed per clone, with 3 WT and 3 Dppa2/4 DKO clones used (total of 12 samples).
NOMEseq: Whole genome bisulfite libraries were generated using NOME-seq kit from Active Motif (103946) according to manufacturer?s instructions with 6 cycles of amplification for 2 WT clones (clones 57 and 58) and 1 Dppa2/4 DKO clone (clone 43).

value: Dppa2/4 WT parental line (no CRISPR)

value: E14 ESCs, contains MERVL::tdTomato reporter


title: V6.5_Neuron_MECP2-GFP_R168X_rep3

first: Charles

last: Li

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description:
V6.5_Neuron_MECP2-GFP_WT_R168X.rsem.genes.results.counts.txt
V6.5_Neuron_MECP2-GFP_WT_R168X.ERCC.DESeq2.resLFC.txt

data_processing:
RNA-seq reads were mapped using STAR aligner (v. 2.6.1a) to the murine RefSeq mm9 reference with ERCC spike-in reference sequences added. Alignment was performed using ENCODE long RNA-seq pipeline default parameters: --outFilterType BySJout, --outSAMattributes NH HI AS NM MD, --outFilterMultimapNmax 20, --outFilterMismatchNmax 999, --outFilterMismatchNoverReadLmax 0.05, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --sjdbScore 1. Gene expression values were quantified using RSEM (v. 1.2.31) with default parameters. Differential expression analysis was performed using DESeq2 (v. 1.24.0) with default parameters. Spike-in cell number normalization was performed by using ERCC spike-ins to estimate size factors used for DESeq2 library normalization. An FDR adjusted p-value cutoff of 0.1 was used to determine differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: counts_RSEM
DESeq2 file represents the output results of differential expression analysis performed using DESeq2. File is organized as a table with each row representing a different gene. Columns represent the following: geneName, baseMean, log2FoldChange(WT/R168X), lfcSE, stat, pvalue, and padj.

source_name: Neuron

growth_protocol: MeCP2-GFP WT and R168X mutant V6.5 mouse embryonic stem cells (ESCs) were cultured in serum-free 2i/LIF media comprised of DMEM/F12 (Gibco 11320) supplemented with 0.5X N2 supplement (Gibco 17502), 0.5X B27 supplement (Gibco 17504), 2 mM L-glutamine (Gibco 25030), 1X MEM non-essential amino acids (Gibco 11140), 100 U/mL penicillin-streptomycin (Gibco 15140), 0.1 mM 2-mercaptoethanol (Sigma M7522), 3 µM CHIR99021 (Stemgent 04-0004), 1 µM PD0325901 (Stemgent 04-0006), and 1000 U/mL leukemia inhibitor factor (LIF) (ESGRO ESG1107). Prior to culturing cells, all tissue culture dishes were coated with 0.2% gelatin. The cells were grown in 37°C incubator maintaining 5% CO2 in a water-saturated atmosphere. Cell culture media were exchanged every 24 hours and cells were passaged every 2-3 days.

extract_protocol:
Cells were dissociated and counted. RNA was harvested from 2 million cell aliquots using the RNeasy Mini Plus kit (QIAGEN 74134) according to manufacturer's protocol. The amount of RNA extracted was quantified using a Nanodrop spectrophotometer (Thermo Scientific). A fixed amount of ERCC RNA Spike-In (Invitrogen 4456740) was added to each sample for use in cell number normalization. Samples were treated with DNA-free DNA Removal Kit (Invitrogen AM1906).
Library construction was performed by the Whitehead Institute Genome Technology Core using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems K8562) according to manufacturer's protocol.

treatment_protocol: Neurons were derived from mESCs by expression of NGN2 to induce neuronal differentiation. A doxycycline-inducible NGN2 expression construct with a puromycin-resistance gene was integrated into mESCs using the PiggyBac transposon system. ESCs with successful integration of the expression construct were selected with puromycin (Gibco A1113803). Prior to induction of neuronal differentiation, mESCs were seeded in 2i/LIF media onto a layer of mouse astrocytes grown on either tissue culture treated plates coated with poly-L-ornithine (Sigma P4957) and laminin (Corning 354232). 24 hours after seeding mESCs, NGN2 expression was induced by changing to N2B27 media with 2 µg/mL doxycycline (Sigma D9891). Media was changed daily with 2 µg/mL doxycycline in N2B27 media. Neurons were harvested for experiments 5 days after induction of NGN2 expression.

value: neurons derived from V6.5 mESCs

value: MECP2-GFP R168X

tag: gtcid


title: input_shRNA_Dppa2_noDox

description:
Sampe 130
ChIP-seq
Processed_data_Samples_130-171.txt.gz

value: E14 ESCs containing inducible shRNA hairpin against Dppa2


title: MCF7, WT_Veh_rep2 (RNA-Seq)

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes reads counts for each Sample

extract_protocol:
total RNA was extracted by Trizol Reagent from Invitrogen (Cat no 15596026).
RNA library was prepared by the KAPA Stranded mRNA-Seq kit (KK8421), according to the manufacturer’s instructions.

treatment_protocol: MCF7 cells were first infected with lentivirus-based ER truncations, and then transiently infected shControl(for vector group) or shER(for WT and dDBD group) targeting 3'UTR to knock down endogenous ER. Cells were kept in hormone stripped condition for at least three days before treating with 100 nM estradiol or corresponding condition of ethanol for six hours.

value: Cells were infected with wild type ER


title: MCF7, dAF2_ER_E2 (ChIP-Seq)


title: V6.5_Neuron_MECP2-GFP_R168X_rep1


title: V6.5_Neuron_MECP2-GFP_R168X_rep2


title: V6.5_Neuron_MECP2-GFP_WT_rep3

value: MECP2-GFP WT


title: Dppa_WT_Mc3A


title: V6.5_Neuron_MECP2-GFP_WT_rep2


title: MCF7, WT_Veh_rep1 (RNA-Seq)

value: Veh


title: MCF7, WT_E2_rep2 (RNA-Seq)

value: 100 nM E2, 6hrs


title: Dppa_WT_58B

value: Dppa2/4 WT

value: embryonic stem cell

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: V6.5_Neuron_MECP2-GFP_WT_rep1


title: MCF7, WT_E2_rep1 (RNA-Seq)


title: 11G+FK_Mouse1

description: Wild-Type Mouse Islets

value: islets

value: wildtype

value: 11 mM Glucose + FK506 treated for 4h


title: 2G_Mouse2

description: Wild-Type Mouse Islets

value: Untreated


title: TTP KO, 9h, replicate 3

city: Wien

first: Pavel

last: Kovarik

address: Dr.-Bohr-Gasse 9/4

department: Max Perutz Labs

country: Austria

institute: University of Vienna

data_processing:
Cutadapt (https://doi.org/10.14806/ej.17.1.200) was used for barcode, adapter and quality trimming.
Quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
STAR version 2.5 (Dobin et al. 2013) was used to map all remaining reads to the GRCm38/mm10 mouse genome assembly.
Differential expression analysis was performed based on read counts using DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: excel workbook files containing default DESeq2 result tables plus calculated individual FPKMs for each replicate

source_name: Bone marrow-derived dendritic cells

growth_protocol: Bone marrow-derived dendritic cells (BMDCs) were produced from bone marrow isolated from the femurs and tibias of 9-12 week old WT and TTP-/- mice.

extract_protocol:
Total RNA was extracted using QIAzol Lysis Reagent, which was followed by chloroform extraction. RNA was precipitated using Isopropanol and GlycoBlue, and was consequently subject to DNA digestion using DNase.
Libraries were prepared using SENSE mRNA-Seq Library Prep Kit V2 (Lexogen)

treatment_protocol: BMDCs were left untreated (0 h) or stimulated with 10 ng/ml lipopolysaccharide (LPS) for 3, 6 or 9 h.

value: Bone marrow-derived dendritic cells

value: TTP-/-

value: Lipopolysaccharide 9 hours


title: Dppa_WT_58A

value: serum/LIF


title: TTP KO, 9h, replicate 1


title: MCF7, Vector_Veh_rep1 (RNA-Seq)

value: Cells were infected with vector


title: MCF7, Vector_Veh_rep2 (RNA-Seq)


title: 2G_Mouse1

description: Wild-Type Mouse Islets


title: Wild type, 9h, replicate 3

value: Wild-type


title: Wild type, 9h, replicate 2


title: Dppa_WT_57B


title: Wild type, 9h, replicate 1


title: Dppa_WT_57A


title: TTP KO, 6h, replicate 3

value: Lipopolysaccharide 6 hours


title: TTP KO, 9h, replicate 2


title: Dppa_DKO_53B

value: Dppa2/4 DKO


title: MCF7, Vector_E2_rep1 (RNA-Seq)


title: TTP KO, 6h, replicate 1


title: MCF7, Vector_E2_rep2 (RNA-Seq)


title: MCF7, dDBD_Veh_rep2 (RNA-Seq)

value: Cells were infected with dDBD ER

value: Veh


title: 11G_Mouse2

description: Wild-Type Mouse Islets

value: 11 mM Glucose treated for 4h


title: Wild type, 6h, replicate 1


title: Wild type, 6h, replicate 3


title: Dppa_DKO_53A

value: embryonic stem cell


title: Wild type, 6h, replicate 2


title: T47D-LTED 991R

type: genomic

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

description: Palbociclib-resistant

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G with AutoLoader.

data_processing:
SNPs were called using the Birdseed v2 algorithm (.CHP files), and copy number variations were called using the CN5 algorithm (.CNCHP files) using Affymetrix Genotyping Console 4.0 (Affymetrix). Sample table and .CNCHP data are based on genome build GRCh37 (hg19). HapMap samples were used as a reference.
Genotype Call (SNP call): AA, AB, BB, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: T47D-LTED, resistant to estrogen deprivation, treated with Palbociclib (CDK4/6 inhibitor) until became Palbociclib-resistant

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from target cell lines using QIAamp DNA mini kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

treatment_protocol: wt cells were treated long term with palobociclib until thay develop resistance.

value: T47D-LTED 991R

tag: compound


title: MCF7, dDBD_E2_rep2 (RNA-Seq)

value: 100 nM E2, 6hrs


title: TTP KO, 3h, replicate 2

tag: strain

value: Lipopolysaccharide 3 hours


title: wt-MCF7 991R

description: Palbociclib-resistant

source_name: MCF7 in E2 treated with Palbociclib (CDK4/6 inhibitor) until resistant

value: wt-MCF7 991R


title: TTP KO, 3h, replicate 1


title: Wild type, 3h, replicate 3


title: MCF7, dDBD_E2_rep1 (RNA-Seq)


title: Dppa_DKO_36B

value: CRISPR targetted E14 ESCs, contains MERVL::tdTomato reporter


title: Dppa_DKO_43A


title: MCF7, dDBD_Veh_rep1 (RNA-Seq)


title: e15_5

value: hind limb

value: embryonic hindlimb

value: synovial joint progenitor cells


title: Wild type, 3h, replicate 2

value: Bone marrow-derived dendritic cells


title: Wild type, 3h, replicate 1


title: TTP KO, 6h, replicate 2

value: TTP-/-


title: MCF7-LTED 991R

description: Palbociclib-resistant

source_name: MCF7-LTED, resistant to estrogen deprivation, treated with Palbociclib (CDK4/6 inhibitor) until became Palbociclib-resistant

value: MCF7-LTED 991R


title: T47D

description: basal

source_name: T47D under E2 maintenance

value: E2 maintenance


title: Dppa_58_DNAm_CpG

data_processing:
Library strategy: NOMe-seq
EB RNA-seq raw FastQ data were trimmed with Trim Galore (version 0.4.4, default parameters) and mapped to the mouse GRCm38 genome assembly using Hisat2 version 2.1.0. Stable overexpression clone data used Trim Galore v0.5.0_dev and HiSat2 v2.1.0.
ChIP-seq Raw FastQ data were trimmed with Trim Galore v0.6.1 and aligned to mouse GRCm38 genome using Bowtie 2 v 2.3.2.
ATAC-seq Raw FastQ data were trimmed with Trim Galore (v0.5.0_dev) using standard parameters and aligned using Bowtie 2 v2.3.2.
NOME-seq Raw fastQ data were trimmed using Trim Galore version 0.4.4 using standard parameters, reads aligned using Bismark v0.18.2
All downstream data processing was performed using SeqMonk software (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: mm10
Supplementary_files_format_and_content: The ChIP and ATAC is enrichment RPM over 1kb running windows. The RNA-seq is all genes RPM and the NOME-seq is 100CpG running window % methylation.  The files were generated using SeqMonk (exporting an annotated probe report).

source_name: Dppa2/4 WT clone 58

value: Dppa2/4 WT

value: serum/LIF


title: Wild type, 0h, replicate 2

value: Wild-type

value: Untreated


title: TTP KO, 0h, replicate 1


title: Wild type, 0h, replicate 3


title: input_shRNA_Dppa2_recovery

description:
Sampe 131
ChIP-seq
Processed_data_Samples_130-171.txt.gz

value: embryonic stem cell

value: E14 ESCs containing inducible shRNA hairpin against Dppa2


title: TTP KO, 0h, replicate 3


title: Wild type, 0h, replicate 1


title: Dppa_43_DNAm_CpG

value: Dppa2/4 DKO


title: Ash2l_58

value: anti-Ash2l Bethyl Labs A300-489