title: Atoh7 Cut&Run replicate 2

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description: Cut&Run sequencing

data_processing:
Library strategy: Cut&Run
Bowtie2 v2.3.5 alignment onto the mm10 genome assembly. Samtools was used to filter out low quality (<30 MAPQ score) reads. Duplicate reads were removed using Picard v2.0.1 MarkDuplicates
MACS2 v2.2.7.1 was used to call peaks. High confidence peaks were annotated based on overlapping peaks between replicates, called using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: peak calls

source_name: Retina

extract_protocol:
Cut&Run experiements were perfored as described in Skene and Henikoff, 2018 with DNA extracted using the Qiagen Nucleotide Romval Kit.
Libraries were prepared using Manufacturer's protocols using the KAPA HyperPrep Kit (Roche)

value: Retina

tag: developmental time point

value: embryonic day 14


title: ImmatureB_HET_3

status: Public on Mar 29 2021

type: SRA

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: Rm 368 - 3649 Promenade Sir William Osler

department: Physiology

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
The high quality of sequence reads was confirmed using FastQC tool.
low-quality bases were trimmed from read extremities using Trimmomatic v.0.33.
Trimmed reads were then mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithms.
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 3 of the samples, and performed quantile normalization with the preprocessCore package to remove batch effects. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package (R version 3.4.2).
Pairwise comparisons were performed between samples across different mouse genotypes and genes with changes in expression ≥ |1.5| folds and Benjamini-Hochberg adjusted p values ≤ 0.01 were considered significant.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM values after quantile normalization
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC mm9)

molecule: total RNA

organism: Mus musculus

source_name: Immature B cells

growth_protocol: The mice were maintained under specific pathogen-free conditions. Test and control groups were bred as littermates and co-housed together.

extract_protocol:
Bone marrow was flushed in PBS supplemented with 0.1% BSA and 2mM EDTA, filtered through 40μm cell-strainers, and subjected to red blood cell lysis in ACK buffer (0.15M NH4Cl, 10mM KHCO3, 0.1mM EDTA). The samples were stained with: biotin-conjugated antibodies against lineage markers [anti-CD3ε (145-2C11, BioLegend), anti-CD11b (M1/70, BioLegend), anti-CD11c (N418, BioLegend), anti-Ly-6G/Ly-6C (Gr-1) (RB6-8C5, BioLegend), anti-NK-1.1 (PK136, BioLegend), and anti-TER-119 (TER-119, BioLegend)], followed by APC-eFluor 780-conjugated Streptavidin (eBioscience), Alexa Fluor 488-conjugated anti-IgD (11-26c.2a, BioLegend), APC-conjugated anti-CD43 (S7, BD Biosciences), PE-conjugated anti-IgM (II/41, eBioscience), PE-Cy7-conjugated anti-CD19 (6D5, BioLegend), and PerCP-Cy5.5-conjugated anti-CD45R/B220 (RA3-6B2, BioLegend) antibodies. DAPI was added immediately before sorting for dead cell exclusion. Cell sorting was performed on FACSAria and analyzed with FACS Diva software (BD Biosciences). The cells were sorted using FACS into pre-B and immature B cells, gating on B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-, and IgM-IgD-CD19+CD43- for pre-B cells, and CD19+IgM+IgD- for immature B cells.
RNA was isolated from the FACS-sorted cells using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). rRNA depletion and library preparation were performed using the SMARTer Stranded RNA-Seq kit (Takara Clontech). The libraries were sequenced on an Illumina HiSeq 4000 sequencer in paired-end 50bp configuration. Cells from multiple mice were pooled to achieve yields of >1.7ng of RNA per sample, and 3-4 independent samples were analyzed per genotype for each cell-type.

tag: strain

tag: age

tag: gender

value: m

tag: tissue

value: Bone marrow

tag: cell type

value: Immature B cells (Bone marrow cells sorted by gates B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-CD19+IgM+IgD-)

tag: genotype

value: Bap1 fl/+ mb1-Cre


title: ImmatureB_HET_2

value: f


title: CTL2

city: Brussels

first: Frederic

last: Lemaigre

address: Avenue Hippocrate, 75

department: de Duve Institute

country: Belgium

institute: UCLouvain

description: Transgenic mice

data_processing:
RNA sequencing using Illumina HiSeq 2x150bp configuration with estimated data output ≥350M raw paired-end reads per lane
Reads quality control was performed using FastQC software v0.11.7 (Babraham Institute, Cambridge, UK). Low quality reads were removed using trimmomatic-0.35.jar.
Paired-end reads were aligned using hisat2 software v2.1.0 (Johns Hopkins University School of Medicine, Center for Computational Biology, Baltimore, MD, USA)  to the Mus musculus genome Ensembl GRCm38
Gene counts were generated using HTSeq Counts software (version 0.5.4p3).
Differential expression analysis were computed using  DESeq2 version 1.22.2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include htseq count values for each sample…

source_name: Bile duct

growth_protocol: Mus musculus CD-1 model: Osteopontin-iCreERT2; RosaYFP/+; K-RASG12D or Osteopontin-iCreERT2; RosaYFP/+ mice

extract_protocol:
RNA isolation from 3 types of lesions: DP, IPNB and iCCA were microdissected using a laser capture microdissection technic (LCM) with Leica LMD7000 microscope (GIGA, Liège, Belgium) and RNA were directly extracted from the liver sections with RNAqueous®-Micro total RNA isolation AM1931 Kit (Thermo Fisher Scientific, Waltham, MA, USA) using the protocol recommended by the manufacturer.
RNA isolation of control cholangiocytes: Liver cells were dissociated using collagenase P previously described in Assi et al., 2018. Then, GFP positive cells were selected using a cell sorter (FACSAria II, BD, Franklin Lakes, USA), harvested in an individual microtube and centrifugated at 1000 rpm during 5 min. The supernatant was removed and RNA from cells pellets was extracted using RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol.
RNA libraries were generated using the TruSeq total stranded RNA-seq kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Chronic inflammation of the liver (cholangitis) using DDC (N,N'-Dicyclohexylcarbodiimide) treatment during 25 weeks.

value: Liver

value: post natal week 31

value: Osteopontin-iCreERT2; RosaYFP/+

tag: treatment

tag: group

value: FACS-purified control cholangiocytes


title: CCA1

description: Transgenic mice

value: DDC treatment 25 weeks

value: intrahepatic cholangiocarcinoma


title: PreB_HET_2

source_name: Pre B cells

value: Pre B cells (Bone marrow cells sorted by gates B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-IgM-IgD-CD19+CD43-)


title: IPNB3

description: Transgenic mice

value: intraductal papillary neoplasm of the bile duct


title: PreB_HET_1


title: IPNB2

description: Transgenic mice


title: IPNB1

description: Transgenic mice


title: Duct_Prol3

description: Transgenic mice

value: Ductular proliferations


title: ImmatureB_WT_3

value: Bap1 fl/+


title: Input_BaF3_BAP1KO4

library_source: genomic

data_processing:
Reads quality filtered according to the Illumina pipeline
Experimental and input control sequence reads were mapped to the mouse mm9 reference genome assembly with Bowtie 1.0.0 using the following settings: --best mm9.
Chromatin binding sites of BAP1 were identified using peak detection algorithm MACS (version 1.4.2, default parameters), with comparisons for read enrichment against control input DNA from the same cells.
The resulting binding sites were filtered to remove regions with < 5 fold enrichment compared to the input DNA and < 5 normalized tag counts within 200bp to the peak summit.
Genome_build: mm9

molecule: genomic DNA

source_name: Ba/F3 cell line with CRISPR-Cas9 targeted Bap1 knockout

growth_protocol: Murine B cell lineage precursor cell line Ba/F3 was maintained at 0.5-2 x10^6 cells/mL in RPMI-1640 (Wisent) with 10% Fetal Calf Serum (FCS, Wisent), 2mM L-Glutamine, 100μg/mL streptomycin, 100U/mL penicillin (Wisent), and 5% WEHI conditioned media as the source of IL-3. Ba/F3 cell lines stably expressing triple-FLAG-tagged murine BAP1 and CRISPR-Cas9 targeted Bap1 knockout cell lines were maintained under 2μg/mL puromycin selection (Wisent).

extract_protocol:
Cells were crosslinked for 10 min at room temperature with 1% formaldehyde added in culture medium. Crosslink was stopped with ice-cold PBS containing 0.125M glycine for 5min. Nuclei were prepared by sequential incubation on ice for 5min in buffer A [10mM Tris-HCl (pH 8), 10mM EDTA, 0.25% Triton X-100], and for 30min in buffer B [10mM Tris-HCl (pH 8), 1mM EDTA, 200mM NaCl] (all buffers include proteases inhibitors). Nuclei were resuspended in sonication buffer [10mM Tris-HCl (pH 8), 1mM EDTA, 0.5% SDS, 0.5% Triton X-100, 0.05% NaDOC, 140mM NaCl] and sonicated with a Branson Digital Sonifier (Branson Ultrasonics) to an average size of 250bp (12 cycles of 30 seconds  at 80%, with 30 seconds rest in cooled circulating water). Sonicated chromatin from the equivalent of 5x10^6 cells per ChIP was incubated overnight on a rotating platform at 4°C with 40μL of Dynabeads Protein G (Invitrogen, Life Technologies) conjugated with antibodies: anti-BAP1 (Cell Signaling Technology, D1W9B, 52.8 μg), anti-FLAG M2 (Sigma, F1804, 5 μg) or anti-H2AK119Ub (Cell Signaling Technology, D27C4, 5 μg). Immune complexes with anti-BAP1 and anti-H2AK119Ub antibodies were washed sequentially for 2min at room temperature with 1ml of the following buffers: Wash 1 [0.5% NP-40, 150mM KCl, 1mM EDTA, 10mM Tris-HCl pH8]; Wash 2 [0.5% Triton, 0.1% NaDOC, 100mM NaCl, 10mM Tris-HCl pH8]; Wash 3A [0.5% Triton, 0.1% NaDOC, 400mM NaCl, 10mM Tris-HCl pH8]; Wash 3B [0.5% Triton, 0.1% NaDOC, 500mM NaCl, 10mM Tris-HCl pH8]; and Wash 4 [0.5% NaDOC, 0.5% NP-40, 250mM LiCl, 1mM EDTA, 10mM Tris-HCl pH8]. Immune complexes with anti-FLAG antibody was washed sequentially for 2min at room temperature with 1ml of the following buffers: Wash B [1% Triton X-100, 0.1% SDS, 150mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8]; Wash C [1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8]; Wash D [1% NP-40, 250mM LiCl, 1mM EDTA, 10mM Tris-HCl pH 8]; and TEN buffer [50mM NaCl, 10mM Tris-HCl pH 8, 1mM EDTA]. After de-crosslinking by overnight incubation at 65°C, the ChIP and Input DNA was purified with Qiaquick PCR Cleanup kit following manufacturer’s instructions (Qiagen).
ChIP-seq libraries were prepared using the Illumina TruSeq kit and sequenced on an Illumina HiSeq 4000 sequencer in paired-end 50bp configuration, with input DNA from the same cells sequenced as negative control.

treatment_protocol: For CRISPR-Cas9 edited samples: Plasmid pSpCas9(BB)-2A-GFP (PX458) was obtained from Addgene (#48138). gRNAs targeting Bap1 were designed using the Zhang lab software (http://crispr.mit.edu): gRNA_Bap1_Exon4_ Chr14:32,066,155: gcaaatggatcgaagagcgc and gRNA_Bap1_Exon5_Chr14:32,066,654: ggcgtgagtggcacaagagt. The gRNAs were ligated into the BbsI (NEB) digested PX458 plasmid, and the resulting plasmids were transformed into DH5α competent cells, purified using PureLink HiPure Plasmid Filter Midiprep Kit (Invitrogen), and verified by Sanger sequencing. To introduce the constructed plasmid into Ba/F3 cells, nucleofection was performed using Amaxa Cell Line Nucleofector Kit V (Lonza) according to the manufacturer’s protocols.  Single GFP+ cells were sorted 48 hours after the nucleofection and then expanded over two weeks to generate single cell clones. The loss of BAP1 protein expression in the cell line clones was validated via Western blotting, with the following antibodies: anti-BAP1 (D7W7O, Cell Signaling Technology), anti-β-Actin (D6A8, Cell Signaling Technology), HRP-conjugated anti-mouse-Ig (eB144, Rockland), and HRP-conjugated anti-rabbit-Ig (eB182, Rockland).

tag: cell line

tag: chip antibody


title: Input_BaF3_WT

source_name: WT Ba/F3 cell line


title: Anti_H2AK119ub_BaF3_WT

value: anti-H2AK119Ub (Cell Signaling Technology, D27C4)


title: hy5 28 root rep3

city: Austin

first: Enamul

last: Huq

state: TX

address: Department of MBS, NHB 2.606, Stop A5000, 100 East 24th St.

country: USA

institute: The University of Texas at Austin

data_processing:
FastQC
HISAT2
Htseq
EdgeR
Genome_build: HISAT2 with TAIR10 reference
Supplementary_files_format_and_content: txt file with htseq results

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedlings

growth_protocol: Total three genotypes; Col-0, hec1hec2 and pifQ plants were used for mRNA sequencing analysis.

extract_protocol:
Total RNA was isolated using sigma plant total RNA kit(Sigma, Cat.# STRN250).
3'Tag-Seq method article was used to generate TagSeq library according to the manufacturer’s instruction. (doi: 10.1111/1755-0998.12529)

treatment_protocol: The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days in dark to induce germination. After three days, seeds were further treated 5 days in 22℃ with white light (25 µmole/s2/m2). After 5 days, seedlings were either treated with 4 hour of continuous white light (25 µmole/s2/m2) in 22 or 28.

value: light grown 5-days seedlings+4hr in 28'C

tag: ecotype

value: root


title: Col-0 28 root rep3


title: hy5 28 root rep1


title: Col-0 28 root rep2


title: Anti_H2AK119ub_BaF3_BAP1KO3


title: Anti_FLAG_BaF3_BAP1_FLAGx3

source_name: Ba/F3 cell line stably expressing triple-FLAG-tagged murine BAP1

value: anti-FLAG M2 (Sigma, F1804)


title: IgG Cut&Run

description: Cut&Run sequencing

value: Retina

value: embryonic day 14


title: hy5 28 hyp rep2

value: WT

value: hypocotyl


title: PreB_WT_4

value: m

value: Bone marrow


title: Human, treatment-naive rectal cancer, TM121

type: RNA

city: New York

first: Julio

last: Garcia-Aguilar

state: NY

department: Colorectal Surgery

institute: Memorial Sloan Kettering Cancer Center

description: gene expression from pre-treatment rectal adenocarcinoma

hyb_protocol: standard Affymetrix protocol

scan_protocol: Affymetrix

data_processing: Data were profiled by Affymetrix U133 Plus 2.0 Array platform (Affymetrix, Santa Clara, CA). A background correction using robust multi-array average (RMA) method was performed on the microarray data followed by quantile normalization. Only perfectly matched probes were taken into account and expression measure was calculated using median polish algorithm.

label: biotin

organism: Homo sapiens

source_name: Rectal cancer patients accrued through clinical trial number NCT00335833

label_protocol: standard Affymetrix protocol

growth_protocol: Not applicable

extract_protocol: Pre-treatment biopsies of patients were obtained. All the specimens were stored as formalin-fixed-paraffin-embedded (FFPE) blocks and ten slides of 10-micron thickness were cut per block. A pathologist reviewed the hematoxylin and eosin (H&E) slides of all the sections to confirm the boundaries of the malignant epithelia. The tumor enriched areas were macro-dissected from unstained slides guided by the H&E slides. DNA & RNA were extracted from FFPE sections using AllPrep DNA/RNA FFPE kit (Qiagen Inc., Valencia, CA). Total RNA was amplified to generate cDNA libraries using the Ovation FFPE WTA System (NuGEN Technologies, San Carlos, CA).

treatment_protocol: Not applicable

tag: kras_mutant or wild_type

value: KRAS-wild-type


title: Col-0 28 hyp rep3


title: Col-0 28 hyp rep2


title: hy5 22 root rep2

value: light grown 5-days seedlings+4hr in 22'C


title: Atoh7 Cut&Run replicate 1

description: Cut&Run sequencing


title: CTL3

description: Transgenic mice

value: Liver

value: post natal week 31

value: Osteopontin-iCreERT2; RosaYFP/+

value: FACS-purified control cholangiocytes


title: hy5 28 hyp rep3


title: Col-0 22 root rep3


title: Col-0 22 root rep2


title: hy5 28 hyp rep1


title: CTL1

description: Transgenic mice


title: Control ChIP-seq from K562 (ENCLB936VNC)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR298RRI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR298RRI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB936VNC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting CXXC5

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

value: 53 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Kevin White

tag: link

value: ENCBS482AXH at ENCODE; https://www.encodeproject.org/ENCBS482AXH/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: CCA2

description: Transgenic mice

tag: strain

tag: tissue

tag: age

value: DDC treatment 25 weeks

value: intrahepatic cholangiocarcinoma


title: Duct_Prol2

description: Transgenic mice

tag: genotype

tag: treatment

value: Ductular proliferations


title: CCA3

description: Transgenic mice

tag: group


title: Duct_Prol1

description: Transgenic mice


title: S_284_Meis2KO

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Illumina adapter contaminations were removed from reads using Cutadapt v1.3.
In a subsequent step, NuGen Ovation adapter sequences were eliminated by trimming 15 nucleotides from the 5' ends.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 70
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

molecule: polyA RNA

growth_protocol: Experiments were conducted using hindlimbs from E10 mouse embryos WT and Meis1KO;Meis2 KO

extract_protocol:
RNA from both hindlimbs of an embryo were isolated using RNeasy Mini Kit RNA Isolation Kit (QIAGEN)
cDNA libraries were generated using Ovation RNA-Seq System (NuGen).
RNA-seq libraries were generated using Ovation RNA-Seq System v2 kit (NuGen). Libraries were sequenced (single-end mode and length of 75 bp) on the Illumina Genome Analyzer IIx system.

tag: phenotype

value: Mut

tag: litter

tag: gender

value: Male

tag: developmental stage

value: 31-32 somites

value: Hindlimb


title: Control ChIP-seq from MCF-7 (ENCLB305DNF)

description:
https://www.encodeproject.org/experiments/ENCSR293ITU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human MCF-7
experiment encode accession: ENCSR293ITU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB305DNF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting SPDEF

tag: line

tag: biosample encode accession

value: breast cancer (adenocarcinoma)

value: 69 year

value: Michael Snyder

value: ENCBS781XRM at ENCODE; https://www.encodeproject.org/ENCBS781XRM/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: S_258_Meis2KO

value: 30-31 somites


title: Col-0 28 root rep1

value: light grown 5-days seedlings+4hr in 28'C

tag: ecotype

value: root


title: S_254_Meis2WT

value: WT

value: Female

value: 32 somites


title: hy5 28 root rep2


title: Control ChIP-seq from K562 (ENCLB184UCF)

description:
https://www.encodeproject.org/experiments/ENCSR814UCX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR814UCX
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2016-10-31
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB184UCF
size range: 200-400

source_name: Homo sapiens K562 cell line

value: cell line

tag: description

value: Control ChIP-seq in K562

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: ENCBS488ZQI at ENCODE; https://www.encodeproject.org/ENCBS488ZQI/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from K562 (ENCLB808SBV)

description:
https://www.encodeproject.org/experiments/ENCSR281WXF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF193 tagged K562 cell line.
experiment encode accession: ENCSR281WXF
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB808SBV
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZSCAN9

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF193

tag: lab

value: Kevin White, UChicago

tag: source

value: Kevin White

tag: passage number

tag: link

value: ENCBS458HON at ENCODE; https://www.encodeproject.org/ENCBS458HON/


title: Control ChIP-seq from K562 (ENCLB003INL)

description:
https://www.encodeproject.org/experiments/ENCSR814UCX/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR814UCX
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2016-10-31
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB003INL
size range: 200-400

tag: age

value: ENCBS029KIU at ENCODE; https://www.encodeproject.org/ENCBS029KIU/


title: Control ChIP-seq from HepG2 (ENCLB738PUD)

description:
https://www.encodeproject.org/experiments/ENCSR487JIM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR487JIM
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB738PUD
size range: 200-400

source_name: Homo sapiens HepG2 cell line

value: Control ChIP-seq on HepG2 cells

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS272IWF at ENCODE; https://www.encodeproject.org/ENCBS272IWF/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: Col-0 28 hyp rep1

tag: treatment

value: light grown 5-days seedlings+4hr in 28'C

tag: genotype

value: WT

tag: tissue

value: hypocotyl


title: hy5 22 root rep1

value: light grown 5-days seedlings+4hr in 22'C

value: root


title: Col-0 22 root rep1


title: hy5 22 hyp rep3


title: Control ChIP-seq from HepG2 (ENCLB312KNU)

description:
https://www.encodeproject.org/experiments/ENCSR079WWH/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR079WWH
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB312KNU
size range: 200-400

value: cell line

value: Xiang-Dong Fu, UCSD

value: ATCC

value: ENCBS751KWS at ENCODE; https://www.encodeproject.org/ENCBS751KWS/


title: Control ChIP-seq from HepG2 (ENCLB760CXR)

description:
https://www.encodeproject.org/experiments/ENCSR079WWH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR079WWH
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB760CXR
size range: 200-400

value: ENCBS704YEM at ENCODE; https://www.encodeproject.org/ENCBS704YEM/


title: hy5 22 hyp rep2


title: hy5 22 hyp rep1


title: Col-0 22 hyp rep3


title: Col-0 22 hyp rep1


title: Control ChIP-seq from K562 (ENCLB160EJZ)

description:
https://www.encodeproject.org/experiments/ENCSR018OYI/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ELK1 tagged K562 cell line.
experiment encode accession: ENCSR018OYI
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB160EJZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 cell line stably expressing N-terminal eGFP-tagged ELK1

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ELK1

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Kevin White, UChicago

value: Kevin White

value: ENCBS913AGK at ENCODE; https://www.encodeproject.org/ENCBS913AGK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Col-0 22 hyp rep2

value: WT

value: hypocotyl


title: hy5 22 root rep3

value: light grown 5-days seedlings+4hr in 22'C

value: root


title: Control ChIP-seq from A549 (ENCLB108IIV)

description:
https://www.encodeproject.org/experiments/ENCSR279OHT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR279OHT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB108IIV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line

value: cell line

value: male

value: 58 year

value: Michael Snyder, Stanford

value: ENCBS404SPY at ENCODE; https://www.encodeproject.org/ENCBS404SPY/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: A60.KS.22

city: Melbourne

first: Paul

last: Beavis

state: Victoria

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Genome_build: mm10
Supplementary_files_format_and_content: count file generated by featureCounts

source_name: activated splenocytes

growth_protocol: Mouse splenocytes were cultured in RPMI supplemented with 10% FCS, sodium pyruvate, glutamax, NEAA, HEPES and penicillin/streptomycin. Splenocytes were activated in media containing anti-CD3 (0.5 μg/ml), anti-CD28 (0.5 μg/ml) IL-2 (100 IU/ml) and IL-7 (200 pg/ml) at a concentration of 5 × 106 per milliliter. 24 hours later, T cells were isolated following a Ficoll centrifugation. Retroviral supernatant was added to retronectin-coated (10 μg/ml) plates (Takara Bio, 4ml per well of a 6 well plate). Supernatant was spun onto plates (1200 g for 30 minutes) after which T cells, resuspended in IL-2/IL-7 containing retroviral supernatants, were added to the plates to give a final volume of 5 ml/well. Final T cell concentration was between 5 × 106 and 10 × 106 per well. T cells were spun for 90 minutes (1200 g) and then incubated overnight before repeating the transduction process. At the end of the transduction process, T cells were cultured in IL-2 and IL-7 containing media. Transduced CAR T cells were used between days 6 and 8 after transduction.

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

treatment_protocol: Stimulated with plate bound anti-myc Tag (anti-CAR) antibody in the presence or absence of NECA (1 µM) for 8 hours.

tag: cell type

value: T cell

tag: glycoprotein coreceptor

value: CD4 sorted

tag: strain

tag: donor organ

value: Spleen

value: A2AR KO

tag: car

tag: stimulation

value: plate bound anti-myc TAG

tag: coculture time

value: 5 hours


title: A60.KS.24

value: NECA (1μM)


title: A60.KS.20

value: MOCK


title: A60.KS.15


title: A60.KS.23


title: A60.KS.19


title: A60.KS.18


title: Control ChIP-seq from K562 (ENCLB533TDL)

description:
https://www.encodeproject.org/experiments/ENCSR833FPN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR833FPN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB533TDL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting TCFL5

tag: line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Kevin White

value: ENCBS924IKF at ENCODE; https://www.encodeproject.org/ENCBS924IKF/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: S_280_Meis2KO

tag: phenotype

value: Mut

tag: litter

tag: gender

value: Male

tag: developmental stage

value: 32-33 somites

value: Hindlimb


title: A60.KS.13

value: T cell

value: CD4 sorted

value: Spleen

tag: genotype

tag: treatment


title: A60.KS.12

tag: cell type

value: CD8 sorted

value: A2AR KO

value: plate bound anti-myc TAG

value: 5 hours


title: S_252_Meis2WT

value: WT

value: Female

value: 30-31 somites

tag: tissue


title: Control ChIP-seq from HepG2 (ENCLB616BGE)

description:
https://www.encodeproject.org/experiments/ENCSR487JIM/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR487JIM
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB616BGE
size range: 200-400

value: cell line

tag: description

value: Control ChIP-seq on HepG2 cells

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Xiang-Dong Fu, UCSD

tag: source

value: ATCC

tag: link

value: ENCBS838SRU at ENCODE; https://www.encodeproject.org/ENCBS838SRU/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: A60.KS.14

value: T cell

tag: glycoprotein coreceptor

value: CD4 sorted

tag: strain

tag: donor organ

value: Spleen

value: MOCK

tag: car

tag: stimulation

tag: coculture time


title: A60.KS.10

value: CD8 sorted

value: A2AR KO

value: plate bound anti-myc TAG

value: 5 hours


title: A60.KS.9


title: Control ChIP-seq from K562 (ENCLB277ARZ)

description:
https://www.encodeproject.org/experiments/ENCSR275WKO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR275WKO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB277ARZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

tag: passage number

value: ENCBS469EYF at ENCODE; https://www.encodeproject.org/ENCBS469EYF/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: A60.KS.8

tag: cell type

tag: genotype

tag: treatment

value: NECA (1μM)


title: A60.KS.5

value: T cell


title: A60.KS.4


title: A60.KS.3


title: A60.KS.2


title: Control ChIP-seq from K562 (ENCLB559YAV)

description:
https://www.encodeproject.org/experiments/ENCSR785AHP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR785AHP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB559YAV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting MTF1

tag: dev stage

tag: age

tag: lab

value: Kevin White

value: ENCBS162BIW at ENCODE; https://www.encodeproject.org/ENCBS162BIW/


title: Control ChIP-seq from HepG2 (ENCLB311DDU)

description:
https://www.encodeproject.org/experiments/ENCSR792MRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR792MRQ
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB311DDU
size range: 200-400

tag: description

value: Control ChIP-seq on HepG2

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

tag: source

value: ATCC

tag: link

value: ENCBS576NFP at ENCODE; https://www.encodeproject.org/ENCBS576NFP/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: Control ChIP-seq from HepG2 (ENCLB954EAO)

description:
https://www.encodeproject.org/experiments/ENCSR792MRQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR792MRQ
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB954EAO
size range: 200-400

value: cell line

value: ENCBS040QBA at ENCODE; https://www.encodeproject.org/ENCBS040QBA/


title: Control ChIP-seq from K562 (ENCLB366AWQ)

description:
https://www.encodeproject.org/experiments/ENCSR440JAU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR440JAU
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB366AWQ
size range: 200-400

value: Control ChIP-seq in K562

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS662URL at ENCODE; https://www.encodeproject.org/ENCBS662URL/


title: Control ChIP-seq from HepG2 (ENCLB641UIY)

description:
https://www.encodeproject.org/experiments/ENCSR775ETD/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR775ETD
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB641UIY
size range: 200-400

value: Control ChIP-seq on HepG2 cells

value: ENCBS038OUO at ENCODE; https://www.encodeproject.org/ENCBS038OUO/


title: Control ChIP-seq from HepG2 (ENCLB449GDS)

description:
https://www.encodeproject.org/experiments/ENCSR775ETD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR775ETD
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB449GDS
size range: 200-400

value: male

value: hepatocellular carcinoma

value: ENCBS872AMP at ENCODE; https://www.encodeproject.org/ENCBS872AMP/


title: Control ChIP-seq from K562 (ENCLB061FSK)

description:
https://www.encodeproject.org/experiments/ENCSR440JAU/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR440JAU
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2017-02-02
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB061FSK
size range: 200-400

value: Xiang-Dong Fu, UCSD

value: ENCBS504MPM at ENCODE; https://www.encodeproject.org/ENCBS504MPM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: M00001_2_Fus1_T_CnR_031720_p300

city: Memphis

first: Stephen

middle: C

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

data_processing:
Reads were trimmed using trimGalore and quality was assessed using FastQC
The resulting reads were aligned to mm10 using Bowtie2 (v2.3.5.1)
macs2 was used for peak calling.
bigwig files were generated using deeptools
Genome_build: mm10
Supplementary_files_format_and_content: peak files
Supplementary_files_format_and_content: bigwig files

growth_protocol: Cells were grown in neural basal medium (Invitrogen) supplemented with sodium pyruvate, glutamine, B27, N2, bFGF (10 ng/mL) and rhEGF (20ng/mL). Cells were grown on treated cell culture dishes coated with Matrigel (Corning). All lines tested negative for mycoplasma contamination, as assessed using a PCR based approach. Tumor-derived cell lines were confirmed to be authentic and unique by STR fingerprinting.

extract_protocol:
CUT&RUN assay was performed as described in Skene and Henikoff. (2018)(17). Briefly, 0.5-1 million cells were captured with BioMagPlus Concanavalin A beads and incubated with primary antibody for 10-20 mins at room temperature. After washing away the EDTA in the buffer and unbound antibody with dig-wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x Complete Protease Inhibitor EDTA-Free and 0.05% Digitonin), protein A-MNase was added and incubated for 10-20mins. The cells were washed again and placed in an ice-water pre-chilled metal block at least 5mins. CaCl2 was added to the final concentration of 2 mM to activate protein A-MNase for 30mins on the ice-water chilled metal block. The reaction was stopped by addition of equal volume of 2XSTOP buffer (340 mM NaCl, 20mM EDTA, 4mM EGTA, 0.02% Digitonin, 5μL/ml RNase A, 50μg/ml glycogen and 2 pg/ml heterologous spike-in DNA). The protein-DNA complex was released and DNA was extracted with Gel and PCR Clean-up kit (Macherey-Nagel NucleoSpin®, cat. no.740609.250) or Phenol-chloroform-isoamyl alcohol precipitation (for small fragment DNA), followed by Qubit fluorometer and Agilent 4200 Tapestation quality and size distribution control.
KAPA Hyper prep kit (Cat# KK8504, KAPA Biosystems)and KAPA Dual-indexed adapter kit (Cat# KK8722 KAPA Biosystems) were used to construct the CUT&RUN DNA library for sequencing on an Illumina platform following the manufacturer’s instructions. After adaptor ligation, 2x volume of AMPure XP beads was used to recovery the small fragments. After 12-14 cycles of PCR amplification, the product was cleaned up with AMPure XP beads. 3% gel purification was performed if the PCR dimers were too much. Perform paired-end Illumina sequencing on the barcoded libraries following the manufacturer’s instructions. Briefly, the mixed libraries were denatured according to the standard protocol from Illumina. 1.3 mL of 1.8 pM diluted library pool was loaded to a NextSeq 500/550 Mid Output Kit v2 (150 cycles), and sequenced in the NextSeq 500 platform. Paired-end sequencing was then performed (2x75 bp, 8 bp index).
OTHER: CUT&RUN

treatment_protocol: No treatments were performed on these cell culture models.

tag: antibody

tag: mouse-id


title: Control ChIP-seq from MCF-7 (ENCLB780ATZ)

description:
https://www.encodeproject.org/experiments/ENCSR744FDJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF148 tagged MCF7 cell line.
experiment encode accession: ENCSR744FDJ
assay title: Control ChIP-seq
assembly: hg19, GRCh38
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB780ATZ
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens MCF-7 cell line stably expressing C-terminal eGFP-tagged ZNF148

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF148

value: breast cancer (adenocarcinoma)

value: 69 year

value: Kevin White, UChicago

value: Kevin White

value: ENCBS004ION at ENCODE; https://www.encodeproject.org/ENCBS004ION/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: A60.KS.6

value: T cell

tag: glycoprotein coreceptor

value: CD8 sorted

tag: strain

tag: donor organ

value: Spleen

value: MOCK

tag: car

tag: stimulation

value: plate bound anti-myc TAG

tag: coculture time

value: 5 hours


title: M00001_2_Fus1_T_CnR_IgG

description: IgG control

source_name: M00001 2 Fus1 T CnR IgG

value: IgG


title: M00001_2_Fus1_T_CnR_HA

description: HA-tagged CRfus1

source_name: M00001 2 Fus1 T CnR HA

value: HA


title: M00002_1_Fus1_T_CnR_ac1

source_name: M00002 1 Fus1 T CnR ac1


title: DNase-seq from islet precursor cell (ENCLB518NAO)

description:
https://www.encodeproject.org/experiments/ENCSR224FOA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR224FOA
assay title: DNase-seq
assembly: hg19, GRCh38
encode release date: 2018-01-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB518NAO

source_name: Homo sapiens female embryo (5 days) islet precursor in vitro differentiated cells

value: islet precursor cell

value: in vitro differentiated cells

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: healthy

value: embryonic

value: 5 day

value: John Stamatoyannopoulos, UW

value: Stephen Dalton

value: ENCBS587BAO at ENCODE; https://www.encodeproject.org/ENCBS587BAO/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: M00001_2_Fus1_T_CnR_031720_Cbp

value: Cbp


title: M00002_1_Fus1_T_CnR_IgG

description: IgG control

source_name: M00002 1 Fus1 T CnR IgG


title: IH.011

tag: cell type

value: T cell

value: Spleen

tag: genotype

value: A2AR KO

tag: treatment

value: NECA (1μM)

value: 8 hours


title: A60.KS.16

value: CD4 sorted

value: 5 hours


title: A60.KS.17

value: MOCK

value: plate bound anti-myc TAG


title: IH.012


title: IH.008


title: Control ChIP-seq from K562 (ENCLB563LVE)

description:
https://www.encodeproject.org/experiments/ENCSR793RRM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR793RRM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB563LVE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF408

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS410CKF at ENCODE; https://www.encodeproject.org/ENCBS410CKF/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from A549 (ENCLB140ARO)

description:
https://www.encodeproject.org/experiments/ENCSR267NPO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR267NPO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB140ARO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting FOXF2

value: male

value: 58 year

tag: source

value: Michael Snyder

tag: link

value: ENCBS668EDI at ENCODE; https://www.encodeproject.org/ENCBS668EDI/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: IH.007

value: T cell

tag: strain

value: Spleen

value: A2AR KO

value: 8 hours


title: A60.KS.11

tag: glycoprotein coreceptor

value: CD8 sorted

tag: donor organ

value: plate bound anti-myc TAG

value: NECA (1μM)

value: 5 hours


title: A60.KS.21

value: CD4 sorted

tag: car

tag: stimulation


title: A60.KS.1

value: MOCK

tag: coculture time


title: A60.KS.7


title: M00001_2_Fus1_T_CnR_031720_Rpb1_S5

tag: antibody

tag: mouse-id


title: IH.003

tag: cell type


title: M00001_2_Fus1_T_CnR_031720_Rpb1_S2


title: IH.004

tag: genotype


title: IH.009

tag: treatment


title: M00002_1_Fus1_T_CnR_p65

source_name: M00002 1 Fus1 T CnR p65


title: Control ChIP-seq from K562 (ENCLB575YWC)

description:
https://www.encodeproject.org/experiments/ENCSR257RVS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR257RVS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB575YWC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF79

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS125PFR at ENCODE; https://www.encodeproject.org/ENCBS125PFR/


title: M00002_1_Fus1_T_CnR_HA

description: HA-tagged CRfus1

source_name: M00002 1 Fus1 T CnR HA

value: HA


title: M00001_2_Fus1_T_CnR_031720_Brd4


title: IH.005

value: T cell

value: Spleen


title: IH.006

value: 8 hours


title: M00002_1_Fus1_T_CnR_ac2

source_name: M00002 1 Fus1 T CnR ac2


title: IH.002


title: IH.010

value: A2AR KO

value: plate bound anti-myc TAG


title: Control ChIP-seq from K562 (ENCLB686QJE)

description:
https://www.encodeproject.org/experiments/ENCSR251EHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR251EHJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB686QJE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting RREB1

tag: dev stage

tag: age

tag: lab

tag: source

value: ENCBS668EOK at ENCODE; https://www.encodeproject.org/ENCBS668EOK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: PB-010

source_name: Activated splenocytes

growth_protocol: Mouse splenocytes were cultured in RPMI supplemented with 10% FCS, sodium pyruvate, glutamax, NEAA, HEPES and penicillin/streptomycin. Splenocytes were activated in media containing anti-CD3 (0.5 μg/ml), anti-CD28 (0.5 μg/ml) IL-2 (100 IU/ml) and IL-7 (200 pg/ml) at a concentration of 5 × 106 per milliliter. 24 hours later, T cells were isolated following a Ficoll centrifugation. Retroviral supernatant was added to retronectin-coated (10 μg/ml) plates (Takara Bio, 4ml per well of a 6 well plate). Supernatant was spun onto plates (1200 g for 30 minutes) after which T cells, resuspended in IL-2/IL-7 containing retroviral supernatants, were added to the plates to give a final volume of 5 ml/well. Final T cell concentration was between 5 × 106 and 10 × 106 per well. T cells were spun for 90 minutes (1200 g) and then incubated overnight before repeating the transduction process. At the end of the transduction process, T cells were cultured in IL-2 and IL-7 containing media. Transduced CAR T cells were used at day 7 after transduction.

treatment_protocol: Stimulated with plate bound anti-myc Tag (anti-CAR) antibody in the presence or absence of NECA (1 µM) or SCH58261 (1 µM) for 8 hours.

tag: strain

tag: donor organ

value: WT


title: PB-011

tag: car

tag: stimulation


title: PB-001

tag: coculture time


title: PB-005


title: PB-004


title: PB-008

value: NECA (1μM)


title: PB-003


title: PB-002


title: PB-009


title: IH.001

source_name: activated splenocytes

value: MOCK


title: PB-012


title: PB-007


title: PB-006


title: Control ChIP-seq from K562 (ENCLB792PJU)

description:
https://www.encodeproject.org/experiments/ENCSR257URH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR257URH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB792PJU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF354B

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS972MXN at ENCODE; https://www.encodeproject.org/ENCBS972MXN/


title: Control ChIP-seq from K562 (ENCLB670YPO)

description:
https://www.encodeproject.org/experiments/ENCSR248LOQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR248LOQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB670YPO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ARID4B

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS170UXE at ENCODE; https://www.encodeproject.org/ENCBS170UXE/


title: Yac1_singlecell_4-Q

city: Boston

first: Volker

last: Hovestadt

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: XRBS library

data_processing:
library strategy: Bisulfite-Seq (extended representation); XRBS
Raw sequencing reads were demultiplexed by the first 8bp of read 2 (representing the adapter barcode sequence). Up to one mismatch to expected barcode sequences was allowed. Barcode sequences were cut from sequencing reads and appended to read identifiers.
Similarly, the first 6bp of read 1 (representing the hexamer sequence) were also cut and appended to read identifiers. Files for read 1 and read 2 were switched to allow compatibility with downstream alignment tools. Resulting fastq files are shared on GEO/SRA.
Genomic alignment of bisulfite-converted reads was perfomed using methylCtools version 1.0.0 (Hovestadt et al., 2014, https://github.com/hovestadt/methylCtools) and bwa mem version 0.7.17.
Alignments were futher filtered to only include reads that are uniquely aligned, map to an MspI cut site, and do not represent PCR duplicates (taking into account the hexamer sequence as a unique molecular identifier).
Methylation calls were generated using methylCtools. Resulting text files are shared on GEO.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Tab-delimited text file containing methylation calls of covered CpGs. Columns: Chromosome, Position, Strand, Context, Methylated, Unmethylated.

source_name: Yac1 cells

growth_protocol: Cells were maintained in exponential phase growth by passaging every 3 to 4 days. Cells were grown in RPMI supplemented with 10% heat inactivated fetal bovine serum and 1% penicillin/streptomycin. All cell lines were routinely tested for mycoplasma contamination and maintained in a 37C humidity-controlled incubator with 5.0% CO2.

extract_protocol:
Cells were collected and washed in cold PBS twice and then the pellet was snap frozen in liquid nitrogen. DNA was harvested by thawing the cell pellets at room temperature and resuspending in PBS, as directed by the Qiagen DNA Mini Blood Kit (51104). For experiment performed on sorted cells, cells were counterstained with 1:1000 µL of PI in PB and sorted in Sony SH800 sorter. Viable single cells were gated and used for sorting into 96 well plates preloaded with 3 uL of lysis buffer (40 mM Tris-Ac, 1mM EDTA, and 1 mM DTT). Incubation at 75°C for 30 minutes is followed by adding 0.5 µL of Qiagen Protease and a 4 hour incubation at 55°C and a 30 minute incubation at 75°C to inactivate the proteinase (Chen et al. 2017).
Here we present a novel extended representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design draws a balance between expanding coverage of regulatory elements and enriching for informative CpG dinucleotides. Barcoded DNA fragments are pooled prior to bisulfite conversion, allowing multiplex processing, improving consistency, and reducing cost and labor. Linear amplification of single stranded bisulfite-treated DNA enables library generation from fragmented and low input DNA samples.

treatment_protocol: HL-60 and OCI-AML3 cells were treated with 300 nM decitabine in 6 well plates. Cells were harvested after 5 days.

tag: cell line

value: Yac1 cells

tag: input

value: 1 cell


title: Yac1_singlecell_3-E

description: XRBS library

tag: treatment


title: Yac1_singlecell_3-B

description: XRBS library


title: Yac1_singlecell_3-G

description: XRBS library


title: Yac1_singlecell_4-R

description: XRBS library


title: Yac1_singlecell_3-C

description: XRBS library


title: Yac1_singlecell_4-T

description: XRBS library


title: Yac1_singlecell_4-S

description: XRBS library


title: Yac1_singlecell_3-D

description: XRBS library


title: Yac1_singlecell_4-V

description: XRBS library


title: Yac1_singlecell_4-W

description: XRBS library


title: Yac1_singlecell_4-X

description: XRBS library


title: Yac1_singlecell_3-F

description: XRBS library


title: Yac1_singlecell_2-W

description: XRBS library


title: Yac1_singlecell_2-V

description: XRBS library


title: Yac1_singlecell_2-S

description: XRBS library


title: Yac1_singlecell_2-X

description: XRBS library


title: Yac1_singlecell_4-U

description: XRBS library


title: Yac1_singlecell_2-T

description: XRBS library


title: Yac1_singlecell_2-U

description: XRBS library


title: Yac1_singlecell_2-R

description: XRBS library


title: Yac1_singlecell_3-A

description: XRBS library


title: Yac1_singlecell_2-Q

description: XRBS library


title: Yac1_singlecell_1-P

description: XRBS library


title: Yac1_singlecell_1-O

description: XRBS library


title: Yac1_singlecell_3-H

description: XRBS library


title: Yac1_singlecell_1-M

description: XRBS library


title: Yac1_singlecell_1-N

description: XRBS library


title: Yac1_singlecell_1-L

description: XRBS library


title: Yac1_singlecell_1-K

description: XRBS library


title: Control ChIP-seq from brain (ENCLB503AQM)

description:
https://www.encodeproject.org/experiments/ENCSR292BUB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR292BUB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503AQM
size range: 200-600

source_name: Homo sapiens female embryo (5 days) brain organoid

value: brain

value: organoid

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS327MWD at ENCODE; https://www.encodeproject.org/ENCBS327MWD/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Control ChIP-seq from brain (ENCLB199VJT)

description:
https://www.encodeproject.org/experiments/ENCSR292BUB/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR292BUB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB199VJT
size range: 200-600

value: female


title: Control ChIP-seq from GM12878 (ENCLB772ELA)

description:
https://www.encodeproject.org/experiments/ENCSR279VWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR279VWA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: Yijun Ruan, JAX
library encode accession: ENCLB772ELA

source_name: Homo sapiens GM12878 cell line

tag: line

value: cell line

value: unknown

value: adult

value: Yijun Ruan, JAX

value: Coriell

value: ENCBS601OYE at ENCODE; https://www.encodeproject.org/ENCBS601OYE/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: Yac1_singlecell_1-I

description: XRBS library

value: Yac1 cells

value: 1 cell


title: Control ChIP-seq from K562 (ENCLB964VIA)

description:
https://www.encodeproject.org/experiments/ENCSR426BBS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR426BBS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB964VIA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line

tag: biosample encode accession

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

tag: passage number

value: ENCBS345JTG at ENCODE; https://www.encodeproject.org/ENCBS345JTG/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from K562 (ENCLB132KCS)

description:
https://www.encodeproject.org/experiments/ENCSR233HNT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR233HNT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB132KCS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: Sex

tag: health state

value: ENCBS692SHF at ENCODE; https://www.encodeproject.org/ENCBS692SHF/


title: Control ChIP-seq from brain (ENCLB308HCX)

description:
https://www.encodeproject.org/experiments/ENCSR292BUB/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR292BUB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB308HCX
size range: 200-600

value: brain

value: organoid

value: female

value: healthy

tag: dev stage

value: embryonic

tag: age

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS534SGR at ENCODE; https://www.encodeproject.org/ENCBS534SGR/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Control ChIP-seq from nephron (ENCLB421RRB)

description:
https://www.encodeproject.org/experiments/ENCSR846POB/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on nephron female embryo (5 days)
experiment encode accession: ENCSR846POB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB421RRB
size range: 200-600

source_name: Homo sapiens female embryo (5 days) nephron organoid

value: nephron

tag: lab

tag: source

value: Joseph Bonventre

value: ENCBS165DBC at ENCODE; https://www.encodeproject.org/ENCBS165DBC/


title: Control ChIP-seq from brain (ENCLB836ERF)

description:
https://www.encodeproject.org/experiments/ENCSR292BUB/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR292BUB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB836ERF
size range: 200-600


title: Control ChIP-seq from progenitor cell of endocrine pancreas (ENCLB584JAK)

description:
https://www.encodeproject.org/experiments/ENCSR077RBB/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR077RBB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB584JAK
size range: 200-600

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells originated from progenitor cell of endocrine pancreas

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

tag: description

value: WA09 derived pancreatic progenitor cells

value: SESCC

value: ENCBS825BIV at ENCODE; https://www.encodeproject.org/ENCBS825BIV/


title: Control ChIP-seq from K562 (ENCLB428LAR)

description:
https://www.encodeproject.org/experiments/ENCSR080NUS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR080NUS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB428LAR
fragmentation methods: sonication (generic)

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS662EJZ at ENCODE; https://www.encodeproject.org/ENCBS662EJZ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from K562 (ENCLB892YJL)

description:
https://www.encodeproject.org/experiments/ENCSR733QVR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR733QVR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB892YJL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF134

value: female

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS797UET at ENCODE; https://www.encodeproject.org/ENCBS797UET/


title: Control ChIP-seq from GM12878 (ENCLB543VIF)

description:
https://www.encodeproject.org/experiments/ENCSR422KXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-ZBTB17 fusion protein.
experiment encode accession: ENCSR422KXZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB543VIF
size range: 450-650

source_name: Homo sapiens GM12878 cell line genetically modified (insertion) using CRISPR targeting ZBTB17

value: GM12878 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB17.

value: unknown

value: ENCBS954ALC at ENCODE; https://www.encodeproject.org/ENCBS954ALC/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: Control ChIP-seq from MCF-7 (ENCLB717FHO)

description:
https://www.encodeproject.org/experiments/ENCSR730RCJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human MCF-7
experiment encode accession: ENCSR730RCJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB717FHO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens MCF-7 cell line

value: breast cancer (adenocarcinoma)

value: 69 year

value: ATCC

value: ENCBS730EDM at ENCODE; https://www.encodeproject.org/ENCBS730EDM/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: Control ChIP-seq from K562 (ENCLB260ZGP)

description:
https://www.encodeproject.org/experiments/ENCSR025GHD/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-JunB fusion protein.
experiment encode accession: ENCSR025GHD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB260ZGP
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting JUNB

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to JunB.

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS224JZT at ENCODE; https://www.encodeproject.org/ENCBS224JZT/


title: Control ChIP-seq from K562 (ENCLB538JNO)

description:
https://www.encodeproject.org/experiments/ENCSR032KPU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR032KPU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB538JNO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting KLF10

value: female

value: Michael Snyder, Stanford

value: ENCBS319HOM at ENCODE; https://www.encodeproject.org/ENCBS319HOM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from nephron (ENCLB479WUO)

description:
https://www.encodeproject.org/experiments/ENCSR846POB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on nephron female embryo (5 days)
experiment encode accession: ENCSR846POB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB479WUO
size range: 200-600

value: nephron

value: organoid

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: ENCBS165DBC at ENCODE; https://www.encodeproject.org/ENCBS165DBC/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Yac1_singlecell_1-J

description: XRBS library

value: Yac1 cells

value: 1 cell


title: Control ChIP-seq from MCF-7 (ENCLB225INE)

description:
https://www.encodeproject.org/experiments/ENCSR734XLI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human MCF-7
experiment encode accession: ENCSR734XLI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB225INE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

value: ATCC

value: ENCBS548RRH at ENCODE; https://www.encodeproject.org/ENCBS548RRH/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: Control ChIP-seq from K562 (ENCLB670RWR)

description:
https://www.encodeproject.org/experiments/ENCSR028NPT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR028NPT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB670RWR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting NFIX

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS616FJW at ENCODE; https://www.encodeproject.org/ENCBS616FJW/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from progenitor cell of endocrine pancreas (ENCLB002MNK)

description:
https://www.encodeproject.org/experiments/ENCSR077RBB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR077RBB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB002MNK
size range: 200-600

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS825BIV at ENCODE; https://www.encodeproject.org/ENCBS825BIV/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Control ChIP-seq from brain (ENCLB673WPQ)

description:
https://www.encodeproject.org/experiments/ENCSR076IYM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on brain male adult (53 years)
experiment encode accession: ENCSR076IYM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB673WPQ
size range: 200-600

source_name: Homo sapiens male adult (53 years) brain organoid

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: male

value: adult

value: Paola Arlotta

value: ENCBS858UKR at ENCODE; https://www.encodeproject.org/ENCBS858UKR/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Control ChIP-seq from brain (ENCLB972AYV)

description:
https://www.encodeproject.org/experiments/ENCSR076IYM/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on brain male adult (53 years)
experiment encode accession: ENCSR076IYM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB972AYV
size range: 200-600

value: 53 year


title: Control ChIP-seq from K562 (ENCLB538ERS)

description:
https://www.encodeproject.org/experiments/ENCSR721XZK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR721XZK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB538ERS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting TCF15

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS942JTM at ENCODE; https://www.encodeproject.org/ENCBS942JTM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: GCN5_knockout, biological rep1

city: Ottawa

first: Goutham

last: Vasam

state: ON

address: 451 Smyth Rd

department: Faculty of Health Sciences

institute: University of Ottawa

description:
Gene expression data from Gcn5skm-/- mouse gastrocnemius muscle.
KO1

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner

data_processing:
Samples were analyzed using Affymetrix Expression Console.
Samples were normalized in Affymetrix Expression Console using RMA-sketch

source_name: Mouse gastrocnemius muscle tissue from Gcn5skm-/- animals

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Mice are housed 5 per cage in IVC GM500 cages (Tecniplast, 500 cm2) according to the Swiss cantonal rules.

extract_protocol: Trizol extraction of total RNA was performed for each sample. Sample concentrations were then measured by Nanodrop and cleaned up with a Qiagen RNEasy kit prior to preparation for microarray.

treatment_protocol: chow diet (Harlan 2018) fed 6-months-old mice were fasted for 5hrs before isoflurane anesthezia and sacrifice. Gastrocnemius skeletal muscle was immediately excised and snap-frozen in liquid nitrogen for RNA extraction.

tag: tissue

value: gastrocnemius muscle

tag: genotype


title: GCN5_knockout, biological rep2

description:
Gene expression data from Gcn5skm-/- mouse gastrocnemius muscle.
KO2


title: GCN5_knockout, biological rep4

description:
Gene expression data from Gcn5skm-/- mouse gastrocnemius muscle.
KO4


title: GCN5_knockout, biological rep3

description:
Gene expression data from Gcn5skm-/- mouse gastrocnemius muscle.
KO3


title: GCN5_wildtype, biological rep4

description:
Gene expression data from Gcn5skm+/+ mouse gastrocnemius muscle.
WT4

source_name: Mouse gastrocnemius muscle tissue from Gcn5skm+/+ animals


title: GCN5_wildtype, biological rep3

description:
Gene expression data from Gcn5skm+/+ mouse gastrocnemius muscle.
WT3


title: Ctl Tet2-/- 5hmC input

city: Hanzhou

first: Lei

last: Gu

address: 79 Qingchun Rd

country: China

institute: First Affiliated Hospital, Zhejiang University School of Medicine

description:
T2-8 input
none
19149FL-16-02-03_S75_L008

data_processing:
RNA-seq reads were aligned using STAR v2.7 (--sjdbInsertSave All --chimSegmentMin  10 --chimJunctionOverhangMin 10 ) reference genome GRCm38. and differential expression values were extracted using DESeq2 v1.26.0 . Genes with absolute fold change > 1.8 (WT group absolute fold change >1.4) and p-value < 0.05 were defined as differentially expressed genes.
5hmC captured sequencing: All sequencing libraries were run on Illumina Hi-seq 2000 machines. FASTQ sequence files from biological replicates were concatenated and aligned to the M. musculus reference genome (GRCm38/mm10) using Bowtie2 v2.3.5.1 (--no-mixed --no-discordant),  keeping unique non-duplicate genomic matches with no more than 2 mismatches within the first 25 bp.
MACS2 v2.2.6 was used to find candidate peak location (tag size = 38, bandwidth = 300, P value cutoff = 1.00 * 105). All the candidate peak loci were summarized and binned the whole genome. We then used R to count sample’s read number in each candidate loci, then used DESeq2 v1.26.0 to find DhMR (any peak loci which was p-value <0.05 and absolute fold change > 1.8).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-seq: DESeq2 normalized seq counts output for each genome type
Supplementary_files_format_and_content: ChIP-seq: MACS2 peak calling output for each sample

source_name: Ctl Tet2-/- 5hmC input

extract_protocol:
RNA-seq: Nasal mucosa samples were homogenized in TRIzol (Invitrogen, cat# 15596026) and processed according to the manufacturer’s instructions.
RNA-seq: RNA was then reverse transcribed using a SuperScript III First-Strand Synthesis System (Thermo Fisher, cat# 18080051). cDNA was quantified by qPCR using TaqMan Universal PCR Master Mix (Thermo Fisher, cat# 4304437) and SYBR Green PCR Master Mix (Thermo Fisher, cat# 4309155). Each reaction was run in triplicate and analyzed following the ΔΔCT method using glyceralde-hyde-3-phosphate dehydrogenase (Gapdh) as normalization control.
ChIP-seq: Genomic DNA was isolated from nasal tissues in 550μl of digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl), then treated with Proteinase K (Thermo) at 55 °C overnight. The second day, 550μl of phenol: chloroform: isoamyl alcohol (25:24:1 saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (P-3803, Sigma) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer was transferred into a new Eppendorf tube and precipitated with 600μl of isopropanol. The pellet was washed with 75% ethanol, air-dried, and resuspended with Nuclease-Free Water (Ambion). DNA samples were treated extensively with an RNase cocktail (Ambion) to remove contaminating RNA.
ChIP-seq: DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25–50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. All sequencing libraries were run on Illumina Hi-seq 2000 machines. FASTQ sequence files from biological replicates were concatenated and aligned to the M. musculus reference genome (GRCm38/mm10) using Bowtie2 v2.3.5.139, keeping unique non-duplicate genomic matches with no more than 2 mismatches within the first 25 bp.

treatment_protocol:
RNA-seq: Mice were sensitized by administration of an intraperitoneal injection of ovalbumin (OVA, 75ug) in 200ul of phosphate-buffered solution (PBS) containing 2mg of aluminum hydroxide (sigma Aldrich, St. Louis, MO, USA) in a total volume of 200ul on days 0, 7, 14. After initial sensitization, mice were challenged with nasal instillation of OVA 500ug in 20ul of PBS into bilateral nasal cavities on day16-25. The control group was challenged with PBS instead of OVA.
ChIP-seq: Mice were sensitized by administration of an intraperitoneal injection of ovalbumin (OVA, 75ug) in 200ul of phosphate-buffered solution (PBS) containing 2mg of aluminum hydroxide (sigma Aldrich, St. Louis, MO, USA) in a total volume of 200ul on days 0, 7, 14. After initial sensitization, mice were challenged with nasal instillation of OVA 500ug in 20ul of PBS into bilateral nasal cavities on day16-25. The control group was challenged with PBS instead of OVA.

tag: strain background

value: No

value: nasal mucosa


title: Ctl Tet2+/- 5hmC input

description:
T2-10 input
none
19149FL-16-02-04_S76_L008

source_name: Ctl Tet2+/- 5hmC input


title: A375_FOXD1 OE_rep1

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

country: Germany

institute: German Cancer Research Center

description:
A375 cells transfected with  FOXD1 plasmid replicate 1
SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Chipster software (Chipster 3.16.3)

source_name: Human melanoma cell line, were tranduced with FOXD1 plasmid

label_protocol: FOXD1 silenced cell lines and its control cell lines, FOXD1 overepressed cell lines and its control cell lines.

growth_protocol: Melanoma cell lines were cultivated in DMEM medium supplemented with heat-inactivated FCS, non-essential amino acids solution (NEAA), β-mercaptoethanol and antibotics. All cell lines were cultured in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit purchased from QIAGEN followed by clean-up and DNase I treatment according to the manufacturer’s instructions

value: A375 cell line (BRAF mutation)


title: AR Tet2+/- 5hmC input

description:
T2-25 input
none
19149FL-16-02-02_S74_L008

source_name: AR Tet2+/- 5hmC input

value: OVA-treatment


title: GCN5_wildtype, biological rep2

description:
Gene expression data from Gcn5skm+/+ mouse gastrocnemius muscle.
WT2


title: Control ChIP-seq from endodermal cell (ENCLB547YJN)

description:
https://www.encodeproject.org/experiments/ENCSR273FER/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on endodermal cell originated from endodermal cell
experiment encode accession: ENCSR273FER
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB547YJN
size range: 200-600

source_name: Homo sapiens female embryo (5 days) endodermal in vitro differentiated cells originated from endodermal cell

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

tag: link

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: WM266-4_FOXD1 KD1_rep3

description:
WM266-4 cells treated with siFOXD1–1 (UACUGCUAGGAUUUCCAAUUGUUAA)  replicate 3
SAMPLE 6

source_name: Human melanoma cell line, treated with siFOXD1

tag: cell line

value: WM266-4 cell line (BRAF mutation )


title: A375_Control_rep1

description:
A375 cells transfected with empty vector backbone of FOXD1 plasmid replicate 1
SAMPLE 10

source_name: Human melanoma cell line, were tranduced with empty vector backbone of FOXD1 plasmid


title: GCN5_wildtype, biological rep1

description:
Gene expression data from Gcn5skm+/+ mouse gastrocnemius muscle.
WT1


title: Control ChIP-seq from endodermal cell (ENCLB497YRO)

description:
https://www.encodeproject.org/experiments/ENCSR273FER/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on endodermal cell originated from endodermal cell
experiment encode accession: ENCSR273FER
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB497YRO
size range: 200-600

value: female

value: ENCBS958FWY at ENCODE; https://www.encodeproject.org/ENCBS958FWY/


title: WM266-4_FOXD1 KD1_rep1

description:
WM266-4 cells treated with siFOXD1–1 (UACUGCUAGGAUUUCCAAUUGUUAA)  replicate 1
SAMPLE 4


title: WM266-4_FOXD1 KD2_rep3

description:
WM266-4 cells treated with siFOXD1–2 (GCCGAGGAAAC  AGACAUCGACGUGG)  replicate 3
SAMPLE 9

source_name: Human melanoma cell line, treated with siFOXD2


title: WM266-4_FOXD1 KD2_rep1

description:
WM266-4 cells treated with siFOXD1–2 (GCCGAGGAAAC  AGACAUCGACGUGG)  replicate 1
SAMPLE 7


title: WM266-4_Control_rep1

description:
WM266-4 cells treated with control siRNA (Stealth  RNAi™ siRNA negative control hi GC)  replicate 1
SAMPLE 1

source_name: Human melanoma cell line, treated with control siRNA (Stealth  RNAi™ siRNA negative control hi GC)


title: AR Tet2-/- 5hmC input

description:
T2-1 input
none
19149FL-16-02-01_S73_L008

source_name: AR Tet2-/- 5hmC input


title: Ctl Tet2-/- 5hmC rep3

description:
T2-12
19149FL-16-01-09_S69_L007

source_name: Ctl Tet2-/- 5hmC_nasal musosa

value: No

tag: molecule subtype

value: 5hmC captured DNA


title: Control ChIP-seq from endodermal cell (ENCLB556BII)

description:
https://www.encodeproject.org/experiments/ENCSR273FER/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on endodermal cell originated from endodermal cell
experiment encode accession: ENCSR273FER
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB556BII
size range: 200-600


title: WM266-4_Control_rep3

description:
WM266-4 cells treated with control siRNA (Stealth  RNAi™ siRNA negative control hi GC)  replicate 3
SAMPLE 3


title: A375_Control_rep2

description:
A375 cells transfected with  empty vector backbone of FOXD1 plasmid replicate 2
SAMPLE 11

value: A375 cell line (BRAF mutation)


title: WM266-4_FOXD1 KD2_rep2

description:
WM266-4 cells treated with siFOXD1–2 (GCCGAGGAAAC  AGACAUCGACGUGG)  replicate 2
SAMPLE8


title: WM266-4_Control_rep2

description:
WM266-4 cells treated with control siRNA (Stealth  RNAi™ siRNA negative control hi GC)  replicate 2
SAMPLE 2


title: Control ChIP-seq from K562 (ENCLB824KUT)

description:
https://www.encodeproject.org/experiments/ENCSR415ETK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR415ETK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB824KUT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF507

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS613XID at ENCODE; https://www.encodeproject.org/ENCBS613XID/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: A375_FOXD1 OE_rep2

description:
A375 cells transfected with  FOXD1 plasmid replicate 2
SAMPLE 13


title: Ctl Tet2-/- 5hmC rep2

description:
T2-9
19149FL-16-01-08_S68_L007

tag: treatment

value: nasal mucosa


title: Control ChIP-seq from endodermal cell (ENCLB830UCP)

description:
https://www.encodeproject.org/experiments/ENCSR273FER/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on endodermal cell originated from endodermal cell
experiment encode accession: ENCSR273FER
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB830UCP
size range: 200-600

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/


title: Ctl Tet2-/- 5hmC rep1

description:
T2-8
19149FL-16-01-07_S67_L007

value: No

value: 5hmC captured DNA


title: A375_FOXD1 OE_rep3

description:
A375 cells transfected with  FOXD1 plasmid replicate 3
SAMPLE14

value: A375 cell line (BRAF mutation)


title: WM266-4_FOXD1 KD1_rep2

description:
WM266-4 cells treated with siFOXD1–1 (UACUGCUAGGAUUUCCAAUUGUUAA)  replicate 2
SAMPLE 5

value: WM266-4 cell line (BRAF mutation )


title: Ctl Tet2+/- 5hmC rep2

description:
T2-11
19149FL-16-01-11_S71_L007

source_name: Ctl Tet2+/- 5hmC_nasal musosa


title: Ctl Tet2+/- 5hmC rep1

description:
T2-10
19149FL-16-01-10_S70_L007


title: AR Tet2-/- 5hmC rep1

description:
T2-1
19149FL-16-01-01_S61_L007

source_name: AR Tet2-/- 5hmC_nasal musosa

value: OVA-treatment


title: AR Tet2+/- 5hmC rep1

description:
T2-4
19149FL-16-01-04_S64_L007

source_name: AR Tet2+/- 5hmC_nasal musosa


title: Ctl WT 5hmC rep3

source_name: Ctl WT 5hmC_nasal musosa

value: WT


title: WT 5hmC input

description:
WT input
none
N6NS

source_name: WT 5hmC input


title: AR Tet2+/- 5hmC rep2

description:
T2-24
19149FL-16-01-05_S65_L007


title: Ctl WT 5hmC rep2


title: Ctl WT 5hmC rep1


title: AR WT 5hmC rep1

source_name: AR WT 5hmC_nasal musosa


title: AR WT 5hmC rep2


title: Ctl Tet2-/- RNA rep2

description:
T2-9
processed data file: TET2_HO_AR_DESeq.csv (column V5)
19149R-10-01V8_S48_L003

source_name: Ctl Tet2-/- RNA_nasal musosa


title: Ctl Tet2-/- RNA rep3

description:
T2-12
processed data file: TET2_HO_AR_DESeq.csv (column V6)
19149R-10-01V9_S49_L003


title: Ctl Tet2+/- 5hmC rep3

description:
T2-13
19149FL-16-01-12_S72_L007


title: Control ChIP-seq from MCF-7 (ENCLB356XTG)

description:
https://www.encodeproject.org/experiments/ENCSR716YEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human MCF-7
experiment encode accession: ENCSR716YEJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB356XTG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting MSX2

tag: line

value: cell line

value: female

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS532FKW at ENCODE; https://www.encodeproject.org/ENCBS532FKW/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: AR Tet2-/- RNA rep3

description:
T2-18
processed data file: TET2_HO_AR_DESeq.csv (column V3)
19149R-10-01V3_S43_L003

source_name: AR Tet2-/- RNA_nasal musosa

value: nasal mucosa


title: AR Tet2-/- RNA rep2

description:
T2-17
processed data file: TET2_HO_AR_DESeq.csv (column V2)
19149R-10-01V2_S42_L003


title: Ctl Tet2+/- RNA rep2

description:
T2-11
processed data file: TET2_HY_AR_DESeq.csv (column V5)
19149R-10-11_S51_L003

source_name: Ctl Tet2+/- RNA_nasal musosa


title: Ctl Tet2+/- RNA rep3

description:
T2-13
processed data file: TET2_HY_AR_DESeq.csv (column V6)
19149R-10-12_S52_L003


title: AR Tet2-/- RNA rep1

description:
T2-1
processed data file: TET2_HO_AR_DESeq.csv (column V1)
19149R-10-01V1_S41_L003


title: Control ChIP-seq from K562 (ENCLB902VXZ)

description:
https://www.encodeproject.org/experiments/ENCSR412OEE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR412OEE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB902VXZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting TSHZ1

tag: biosample encode accession

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Kevin White

value: ENCBS626IAB at ENCODE; https://www.encodeproject.org/ENCBS626IAB/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Ctl Tet2-/- RNA rep1

description:
T2-8
processed data file: TET2_HO_AR_DESeq.csv (column V4)
19149R-10-01V7_S47_L003

value: No


title: Control ChIP-seq from K562 (ENCLB919BNA)

description:
https://www.encodeproject.org/experiments/ENCSR712UUA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR712UUA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB919BNA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ESRRB

value: ENCBS554EXL at ENCODE; https://www.encodeproject.org/ENCBS554EXL/


title: Control ChIP-seq from pancreas (ENCLB873FFA)

description:
https://www.encodeproject.org/experiments/ENCSR067CHO/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on pancreas female child (16 years)
experiment encode accession: ENCSR067CHO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB873FFA
size range: 200-600

source_name: Homo sapiens female child (16 years) pancreas tissue, preserved by flash-freezing

value: pancreas

value: tissue

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Yiing Lin, MD, PhD

value: ENCBS375CIT at ENCODE; https://www.encodeproject.org/ENCBS375CIT/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: AR Tet2+/- RNA rep3

description:
T2-25
processed data file: TET2_HY_AR_DESeq.csv (column V3)
19149R-10-01V6_S46_L003

source_name: AR Tet2+/- RNA_nasal musosa

value: OVA-treatment


title: Ctl Tet2+/- RNA rep1

description:
T2-10
processed data file: TET2_HY_AR_DESeq.csv (column V4)
19149R-10-01V10_S50_L003

value: nasal mucosa


title: AR Tet2+/- RNA rep2

description:
T2-24
processed data file: TET2_HY_AR_DESeq.csv (column V2)
19149R-10-01V5_S45_L003


title: AR Tet2+/- RNA rep1

description:
T2-4
processed data file: TET2_HY_AR_DESeq.csv (column V1)
19149R-10-01V4_S44_L003


title: Control ChIP-seq from pancreas (ENCLB209NHB)

description:
https://www.encodeproject.org/experiments/ENCSR067CHO/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on pancreas female child (16 years)
experiment encode accession: ENCSR067CHO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB209NHB
size range: 200-600

value: female

value: Michael Snyder, Stanford


title: Ctl WT RNA rep3

description:
processed data file: TET2_WT_AR_DESeq.csv (column V6)
WT_N3

source_name: Ctl WT RNA_nasal musosa

value: WT


title: Control ChIP-seq from nephron progenitor cell (ENCLB483MPM)

description:
https://www.encodeproject.org/experiments/ENCSR795YGE/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on nephron progenitor cell
experiment encode accession: ENCSR795YGE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB483MPM
size range: 200-600

source_name: Homo sapiens female embryo (5 days) nephron progenitor in vitro differentiated cells

value: nephron progenitor cell

value: in vitro differentiated cells

value: H9 NPC (Day 8):Nephron progenitor cells derived from H9 ES cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: ENCBS491YOI at ENCODE; https://www.encodeproject.org/ENCBS491YOI/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Ctl WT RNA rep2

description:
processed data file: TET2_WT_AR_DESeq.csv (column V5)
WT_N2

value: No


title: Control ChIP-seq from nephron progenitor cell (ENCLB250UET)

description:
https://www.encodeproject.org/experiments/ENCSR795YGE/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on nephron progenitor cell
experiment encode accession: ENCSR795YGE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB250UET
size range: 200-600


title: Ctl WT RNA rep1

description:
processed data file: TET2_WT_AR_DESeq.csv (column V4)
WT_N1


title: AR WT RNA rep3

description:
processed data file: TET2_WT_AR_DESeq.csv (column V3)
WT_AR3

source_name: AR WT RNA_nasal musosa


title: AR WT RNA rep2

description:
processed data file: TET2_WT_AR_DESeq.csv (column V2)
WT_AR2


title: Control ChIP-seq from nephron progenitor cell (ENCLB648EHO)

description:
https://www.encodeproject.org/experiments/ENCSR795YGE/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on nephron progenitor cell
experiment encode accession: ENCSR795YGE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB648EHO
size range: 200-600

value: ENCBS835ZTQ at ENCODE; https://www.encodeproject.org/ENCBS835ZTQ/


title: Control ChIP-seq from nephron progenitor cell (ENCLB766PVO)

description:
https://www.encodeproject.org/experiments/ENCSR795YGE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on nephron progenitor cell
experiment encode accession: ENCSR795YGE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB766PVO
size range: 200-600


title: Control ChIP-seq from MCF-7 (ENCLB737IXQ)

description:
https://www.encodeproject.org/experiments/ENCSR712GVO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human MCF-7
experiment encode accession: ENCSR712GVO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB737IXQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens MCF-7 cell line

value: cell line

value: breast cancer (adenocarcinoma)

value: adult

value: 69 year

value: ATCC

value: ENCBS838FEA at ENCODE; https://www.encodeproject.org/ENCBS838FEA/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/