title: intact Hi-C from CD4-positive, alpha-beta T cell (ENCLB224WKE)

description:
https://www.encodeproject.org/experiments/ENCSR335JYP/
***************
biological replicate number: 1
technical replicate number: 2
description: CD4+ intact Hi-C
experiment encode accession: ENCSR335JYP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB224WKE
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (20 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS296ZES at ENCODE; https://www.encodeproject.org/ENCBS296ZES/

value: derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: intact Hi-C from pancreas (ENCLB029FWJ)

status: Public on Jul 24 2023

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR387RQD/
***************
biological replicate number: 1
technical replicate number: 2
description: w73 pancreas intact dnase
experiment encode accession: ENCSR387RQD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB029FWJ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens female adult (59 years) pancreas tissue, preserved by flash-freezing

value: pancreas

value: tissue

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: health state

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

tag: dev stage

value: adult

tag: age

value: 59 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS799RGS at ENCODE; https://www.encodeproject.org/ENCBS799RGS/

value: derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: intact Hi-C from pancreas (ENCLB047PFN)

description:
https://www.encodeproject.org/experiments/ENCSR387RQD/
***************
biological replicate number: 1
technical replicate number: 1
description: w73 pancreas intact dnase
experiment encode accession: ENCSR387RQD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB047PFN
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from CD4-positive, alpha-beta T cell (ENCLB987FCG)

description:
https://www.encodeproject.org/experiments/ENCSR335JYP/
***************
biological replicate number: 1
technical replicate number: 3
description: CD4+ intact Hi-C
experiment encode accession: ENCSR335JYP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB987FCG
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: CD4-positive, alpha-beta T cell

value: male


title: 8861G iPSC, WT control, replicate 2

city: Cambridge

first: Richard

last: She

state: Massachusetts

address: 455 Main St Rm 639, Whitehead Institute

institute: Whitehead Institute

library_source: transcriptomic

data_processing:
Adapters were removed using cutadapt with option -b AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
Reads were then pseudo-aligned to species-specific transcriptomes using kallisto with options --single -l 200 -s 20
Transcriptomes were extracted from species-specific gtf annotations using the gffread utility using the -w output option
Human transcripts were obtained from the Gencode comprehensive gene annotation v36 (GTF), using genome assembly hg38.
Chimpanzee annotations were obtained from a recent study that produced a hierarchical alignment of primate genome assemblies and annotated the assemblies using the Comparative Annotation Toolkit
Assembly: hg38
Supplementary files format and content: tab-delimited text files are VST-transformed counts for each sample
Supplementary files format and content: using the function vst with option blind=TRUE and ran the DESeq linear model fitting using the function DESeq with betaPrior=TRUE

molecule: total RNA

organism: Pan troglodytes

source_name: Pluripotent stem cells

growth_protocol: Pluripotent stem cells were maintained in StemFlex media and Accutase passaged with ROCK inhibitor

extract_protocol:
High quality RNA was extracted by adding RNAse-free Trizol to each pellet and processing with the Zymo Research Direct-zol RNA miniprep kit
RNA-seq library prep was performed using the Illumina TruSeq Stranded Total RNA kit .

tag: tissue

value: Pluripotent stem cells

tag: cell line

tag: cell type

value: induced pluripotent stem cells

tag: genotype

value: WT

tag: treatment

value: Growth in StemFlex media


title: 8861G iPSC, WT control, replicate 3


title: 40290F iPSC, WT control, replicate 3


title: intact Hi-C from CD4-positive, alpha-beta T cell (ENCLB814JNY)

description:
https://www.encodeproject.org/experiments/ENCSR335JYP/
***************
biological replicate number: 1
technical replicate number: 4
description: CD4+ intact Hi-C
experiment encode accession: ENCSR335JYP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB814JNY
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: primary cell

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS296ZES at ENCODE; https://www.encodeproject.org/ENCBS296ZES/

value: derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: 8861G iPSC, WT control, replicate 1


title: intact Hi-C from stomach (ENCLB751ERR)

description:
https://www.encodeproject.org/experiments/ENCSR569OBN/
***************
biological replicate number: 1
technical replicate number: 1
description: entex stomach intact dnase hic
experiment encode accession: ENCSR569OBN
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB751ERR
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) stomach tissue

value: stomach

value: tissue

value: female

value: adult

value: 53 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS012INU at ENCODE; https://www.encodeproject.org/ENCBS012INU/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: intact Hi-C from CD4-positive, alpha-beta T cell (ENCLB343YPK)

description:
https://www.encodeproject.org/experiments/ENCSR335JYP/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4+ intact Hi-C
experiment encode accession: ENCSR335JYP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB343YPK
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: CD4-positive, alpha-beta T cell

value: male


title: 40290F iPSC, WT control, replicate 2

value: Pluripotent stem cells

value: induced pluripotent stem cells

value: WT

value: Growth in StemFlex media


title: 40280L iPSC, WT control, replicate 2


title: intact Hi-C from heart right ventricle (ENCLB410QUN)

description:
https://www.encodeproject.org/experiments/ENCSR462CIE/
***************
biological replicate number: 1
technical replicate number: 2
description: w73 heart right ventricle intact dnase hic
experiment encode accession: ENCSR462CIE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB410QUN
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (59 years) heart right ventricle tissue, preserved by flash-freezing

value: heart right ventricle

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS217QWS at ENCODE; https://www.encodeproject.org/ENCBS217QWS/

value: derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: intact Hi-C from left ventricle myocardium superior (ENCLB894AKT)

description:
https://www.encodeproject.org/experiments/ENCSR333BMU/
***************
biological replicate number: 1
technical replicate number: 1
description: w78-leftventmyosup intact Mnase HiC
experiment encode accession: ENCSR333BMU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB894AKT
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (60 years) left ventricle myocardium superior tissue, preserved by flash-freezing

value: left ventricle myocardium superior

value: tissue

tag: note

value: Superior wall of left ventricle.

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: ENCBS072DDV at ENCODE; https://www.encodeproject.org/ENCBS072DDV/

value: derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: intact Hi-C from heart right ventricle (ENCLB881ZFC)

description:
https://www.encodeproject.org/experiments/ENCSR462CIE/
***************
biological replicate number: 1
technical replicate number: 1
description: w73 heart right ventricle intact dnase hic
experiment encode accession: ENCSR462CIE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB881ZFC
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: female


title: intact Hi-C from left ventricle myocardium superior (ENCLB981CFQ)

description:
https://www.encodeproject.org/experiments/ENCSR333BMU/
***************
biological replicate number: 1
technical replicate number: 4
description: w78-leftventmyosup intact Mnase HiC
experiment encode accession: ENCSR333BMU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB981CFQ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: male


title: 3624K iPSC, WT control, replicate 3

value: Pluripotent stem cells

value: induced pluripotent stem cells

value: WT

value: Growth in StemFlex media


title: intact Hi-C from heart right ventricle (ENCLB396WJA)

description:
https://www.encodeproject.org/experiments/ENCSR812PIJ/
***************
biological replicate number: 1
technical replicate number: 2
description: UW036 heart right ventricle intact dnase hic
experiment encode accession: ENCSR812PIJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB396WJA
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (61 years) heart right ventricle tissue

value: heart right ventricle

value: nonischemic (EF 11% LVEDD 7.7; RV severe dilation, severe dysfunction)

value: 61 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS798YMJ at ENCODE; https://www.encodeproject.org/ENCBS798YMJ/

value: derived from ENCODE donor ENCDO808ASZ; https://www.encodeproject.org/ENCDO808ASZ/


title: endothelial_ATACseq_1dpa_rep1

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

data_processing:
ATAC-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2(2.2.5, with parameters --very-sensitive) to zebrafish genome (danRer10).
The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and Bigwig files were generated by kentUtils.
Supplementary files format and content: danRer10
Supplementary files format and content: bigwig file coverted from coverage output by macs2

organism: Danio rerio

source_name: Heart

extract_protocol:
Heart ventricular resections are performed on adult Tg(fli1:EGFP) zebrafish. Hearts were collected at 1 dpa and 3dpa. Uninjured zebrafish hearts were used as control.
Hearts are dissociated dissociated using Liberase DH (Roche) and EGFP+  cells were isolated by FACS. 100,000 cells/nuclei were used for library preparation.
ATAC library preparation was performed as described in (Buenrostro et al., 2013).

treatment_protocol: Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult fish between 4~12 month old were used in this study.

value: Heart

value: endothelial cells

value: 1 day post vetricular apex amputation


title: Pt5c iPSC, WT control, replicate 2


title: 40290F iPSC, WT control, replicate 1


title: intact Hi-C from left ventricle myocardium superior (ENCLB451PHD)

description:
https://www.encodeproject.org/experiments/ENCSR333BMU/
***************
biological replicate number: 1
technical replicate number: 2
description: w78-leftventmyosup intact Mnase HiC
experiment encode accession: ENCSR333BMU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB451PHD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: left ventricle myocardium superior

value: tissue

value: Superior wall of left ventricle.

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: Yiing Lin, MD, PhD

value: ENCBS072DDV at ENCODE; https://www.encodeproject.org/ENCBS072DDV/

value: derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: 3624K iPSC, WT control, replicate 2

value: Pluripotent stem cells

value: induced pluripotent stem cells

value: WT

value: Growth in StemFlex media


title: 3624K iPSC, WT control, replicate 1


title: intact Hi-C from heart right ventricle (ENCLB938GBS)

description:
https://www.encodeproject.org/experiments/ENCSR812PIJ/
***************
biological replicate number: 1
technical replicate number: 1
description: UW036 heart right ventricle intact dnase hic
experiment encode accession: ENCSR812PIJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB938GBS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: heart right ventricle

value: male

value: nonischemic (EF 11% LVEDD 7.7; RV severe dilation, severe dysfunction)

value: 61 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS798YMJ at ENCODE; https://www.encodeproject.org/ENCBS798YMJ/

value: derived from ENCODE donor ENCDO808ASZ; https://www.encodeproject.org/ENCDO808ASZ/


title: Pt5c iPSC, WT control, replicate 3


title: Pt5c iPSC, WT control, replicate 1


title: intact Hi-C from left ventricle myocardium superior (ENCLB947LSY)

description:
https://www.encodeproject.org/experiments/ENCSR333BMU/
***************
biological replicate number: 1
technical replicate number: 3
description: w78-leftventmyosup intact Mnase HiC
experiment encode accession: ENCSR333BMU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB947LSY
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: left ventricle myocardium superior

value: tissue

value: Superior wall of left ventricle.

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult


title: intact Hi-C from HCT116 (ENCLB942PIE)

description:
https://www.encodeproject.org/experiments/ENCSR565SZK/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116-SUPT16H-treated intact HIC
experiment encode accession: ENCSR565SZK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB942PIE
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS114XMP at ENCODE; https://www.encodeproject.org/ENCBS114XMP/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: C3649 iPSC, WT control, replicate 2

value: Pluripotent stem cells

value: induced pluripotent stem cells

value: WT

value: Growth in StemFlex media


title: intact Hi-C from HCT116 (ENCLB445URU)

description:
https://www.encodeproject.org/experiments/ENCSR565SZK/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-SUPT16H-treated intact HIC
experiment encode accession: ENCSR565SZK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB445URU
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: biosample encode accession

value: male


title: C3649 iPSC, WT control, replicate 3


title: C3649 iPSC, WT control, replicate 1


title: intact Hi-C from HCT116 (ENCLB028CWU)

description:
https://www.encodeproject.org/experiments/ENCSR565SZK/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116-SUPT16H-treated intact HIC
experiment encode accession: ENCSR565SZK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB028CWU
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: encode accession


title: intact Hi-C from breast epithelium (ENCLB814ODZ)

description:
https://www.encodeproject.org/experiments/ENCSR326YHP/
***************
biological replicate number: 1
technical replicate number: 3
description: entex breast intact dnase hic
experiment encode accession: ENCSR326YHP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB814ODZ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) breast epithelium tissue

value: breast epithelium

value: tissue

tag: Sex

value: female

value: 53 year

value: Kristin Ardlie

value: ENCBS712PKE at ENCODE; https://www.encodeproject.org/ENCBS712PKE/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: 40280L iPSC, WT control, replicate 3


title: intact Hi-C from breast epithelium (ENCLB840OOK)

description:
https://www.encodeproject.org/experiments/ENCSR326YHP/
***************
biological replicate number: 1
technical replicate number: 2
description: entex breast intact dnase hic
experiment encode accession: ENCSR326YHP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB840OOK
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: adult

value: Erez Aiden, Baylor


title: 40280L iPSC, WT control, replicate 1


title: intact Hi-C from breast epithelium (ENCLB561FEI)

description:
https://www.encodeproject.org/experiments/ENCSR326YHP/
***************
biological replicate number: 1
technical replicate number: 4
description: entex breast intact dnase hic
experiment encode accession: ENCSR326YHP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB561FEI
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from HCT116 (ENCLB034PEO)

description:
https://www.encodeproject.org/experiments/ENCSR565SZK/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116-SUPT16H-treated intact HIC
experiment encode accession: ENCSR565SZK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB034PEO
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

tag: health state

value: colorectal carcinoma

value: 48 year

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;


title: intact Hi-C from breast epithelium (ENCLB569VZZ)

description:
https://www.encodeproject.org/experiments/ENCSR326YHP/
***************
biological replicate number: 1
technical replicate number: 1
description: entex breast intact dnase hic
experiment encode accession: ENCSR326YHP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB569VZZ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

tag: dev stage


title: Adipocyte + SKOV3ip1 co-culture  [EL12]

type: RNA

city: Chicago

first: Abir

last: Mukherjee

state: Illinois

address: 929 E 57th street, Gordon center for integrative sciences, room w107K

institute: university of Chicago

description:
Replicate 3
EL12

hyb_protocol: Direct Hybridization Assay

scan_protocol: Arrays were scanned on an Illumina’s Bead Station 500GX Genetic Analysis System

data_processing: The raw data were processed by Illumina Genome Studio v2011.1 and Partek Genomics suite v6.6.

label: Biotin

source_name: Adipose tissue

label_protocol: Biotinylated cRNA was generated using Illumina Total Prep RNA Amplification Kit

growth_protocol: Cells were grown in DMEM:F12 media supplemented with 0.1% fatty acids-free bovine serum albumin, 100 U/ml penicillin, and 100 µg/ml streptomycin .

extract_protocol: Total RNA was isolated using RNeasy kit after in-column DNase digestion.

treatment_protocol: Cancer cells were co-cultured with primary human omental adipocytes at 1:3 (packed cell volume)

value: Benign Tissue


title: intact Hi-C from heart left ventricle (ENCLB886LXC)

description:
https://www.encodeproject.org/experiments/ENCSR385MKW/
***************
biological replicate number: 1
technical replicate number: 3
description: uw040-heart-left-ventricle-intact Dnase
experiment encode accession: ENCSR385MKW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB886LXC
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (69 years) heart left ventricle tissue

value: heart left ventricle

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

tag: age

value: 69 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS653TLO at ENCODE; https://www.encodeproject.org/ENCBS653TLO/

value: derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: intact Hi-C from heart left ventricle (ENCLB279COQ)

description:
https://www.encodeproject.org/experiments/ENCSR385MKW/
***************
biological replicate number: 1
technical replicate number: 2
description: uw040-heart-left-ventricle-intact Dnase
experiment encode accession: ENCSR385MKW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB279COQ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: male

tag: lab


title: intact Hi-C from CD14-positive monocyte (ENCLB018HFK)

description:
https://www.encodeproject.org/experiments/ENCSR444SKT/
***************
biological replicate number: 1
technical replicate number: 1
description: Monocytes CD14+ LP23 intact Mnase HiC
experiment encode accession: ENCSR444SKT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB018HFK
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (51 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

value: adult

value: 51 year

value: Charles Lee

tag: source

value: AllCells

value: ENCBS407NOU at ENCODE; https://www.encodeproject.org/ENCBS407NOU/

value: derived from ENCODE donor ENCDO346BRO; https://www.encodeproject.org/ENCDO346BRO/


title: intact Hi-C from heart left ventricle (ENCLB163XVT)

description:
https://www.encodeproject.org/experiments/ENCSR385MKW/
***************
biological replicate number: 1
technical replicate number: 1
description: uw040-heart-left-ventricle-intact Dnase
experiment encode accession: ENCSR385MKW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB163XVT
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: heart left ventricle

tag: link


title: intact Hi-C from esophagus muscularis mucosa (ENCLB768HMK)

description:
https://www.encodeproject.org/experiments/ENCSR274FJN/
***************
biological replicate number: 1
technical replicate number: 1
description: entex esophagus muscularis intact dnase hic
experiment encode accession: ENCSR274FJN
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB768HMK
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: female

value: 53 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS241VZQ at ENCODE; https://www.encodeproject.org/ENCBS241VZQ/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: intact Hi-C from esophagus muscularis mucosa (ENCLB632IQW)

description:
https://www.encodeproject.org/experiments/ENCSR274FJN/
***************
biological replicate number: 1
technical replicate number: 2
description: entex esophagus muscularis intact dnase hic
experiment encode accession: ENCSR274FJN
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB632IQW
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue


title: intact Hi-C from HCT116 (ENCLB515ANV)

description:
https://www.encodeproject.org/experiments/ENCSR176ICO/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-SUPT16H-auxin-untreated-intact HiC
experiment encode accession: ENCSR176ICO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB515ANV
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Dr. Masato Kanemaki

value: ENCBS690BSF at ENCODE; https://www.encodeproject.org/ENCBS690BSF/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from transverse colon (ENCLB615LDP)

description:
https://www.encodeproject.org/experiments/ENCSR258OVY/
***************
biological replicate number: 1
technical replicate number: 2
description: entex transverse colon intact dnase hic
experiment encode accession: ENCSR258OVY
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB615LDP
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) transverse colon tissue

value: transverse colon

value: adult

value: ENCBS191BSQ at ENCODE; https://www.encodeproject.org/ENCBS191BSQ/


title: intact Hi-C from transverse colon (ENCLB436WRS)

description:
https://www.encodeproject.org/experiments/ENCSR258OVY/
***************
biological replicate number: 1
technical replicate number: 1
description: entex transverse colon intact dnase hic
experiment encode accession: ENCSR258OVY
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB436WRS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: female


title: intact Hi-C from transverse colon (ENCLB694FOB)

description:
https://www.encodeproject.org/experiments/ENCSR258OVY/
***************
biological replicate number: 1
technical replicate number: 3
description: entex transverse colon intact dnase hic
experiment encode accession: ENCSR258OVY
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB694FOB
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: 53 year


title: intact Hi-C from HCT116 (ENCLB468WRS)

description:
https://www.encodeproject.org/experiments/ENCSR176ICO/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116-SUPT16H-auxin-untreated-intact HiC
experiment encode accession: ENCSR176ICO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB468WRS
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: Erez Aiden, Baylor


title: Wild-type, E8.5 embryo, biol rep 2

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

data_processing:
The bcl files were converted to fastq files using Illumina bcl2fastq2 Conversion Software and Samples were demultiplexed using Casava (v1.8, Illumina).
Bamfiles were generated using tophat version 2.0.8b against the mm9 build of the mouse reference genome
Processed summary data were generated using htseq data using the gtf file
Assembly: mm9
Supplementary files format and content: text
Supplementary files format and content: Text files with RPKM values

organism: Mus musculus

source_name: Whole E8.5 embryo

extract_protocol:
Whole Sox7-/- embryos and their wild-type littermates were isolated at E8.5. The Ambion RNAqueous-micro Kit; was used for isolating total RNA from three Sox7-/- embryos and three wild-type controls, according to manufacturer’s instructions.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 Kit, Low Throughput (LT) Protocol, Illumina Inc, San Diego CA. This process purifies the poly-A containing mRNA using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented and primed for cDNA synthesis. The cDNA fragments were subjected to an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. Post ligation cleanup was performed using AMpure XP beads (Agencourt, Beverly, MA, USA).  The products then enriched with PCR to create final cDNA library. The quality of the amplified libraries was checked on an BioRad Experion Bioanalyzer System (BioRad, Hercules CA, USA) using the BioRad DNA 1K Analysis Kit. The libraries were normalized to 2nM and pooled in equal volumes and sequenced using 50 bp reads on the Illumina HiSeq 2000 platform (Illumina Inc., San Diego, CA, USA).

tag: tissue

value: Whole E8.5 embryo

value: Wild-type

value: genotype


title: Adipocyte + SKOV3ip1 co-culture  [EL11]

description:
Replicate 2
EL11

value: Benign Tissue


title: Sox7-/-, E8.5 embryo, biol rep 2


title: Wild-type, E8.5 embryo, biol rep 3


title: intact Hi-C from HCT116 (ENCLB430YQC)

description:
https://www.encodeproject.org/experiments/ENCSR176ICO/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116-SUPT16H-auxin-untreated-intact HiC
experiment encode accession: ENCSR176ICO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB430YQC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line


title: Sox7-/-, E8.5 embryo, biol rep 1


title: Sox7-/-, E8.5 embryo, biol rep 3


title: intact Hi-C from CD4-positive, alpha-beta memory T cell (ENCLB094VRW)

description:
https://www.encodeproject.org/experiments/ENCSR379TIE/
***************
biological replicate number: 1
technical replicate number: 2
description: Memory CD4+ T cell (CD45RO+CCR7+/-) LP11 resting Intact mnase
experiment encode accession: ENCSR379TIE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB094VRW
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (43 years) CD4-positive, alpha-beta memory T primary cell

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: male

value: 43 year

value: Charles Lee

value: AllCells

value: ENCBS210OZB at ENCODE; https://www.encodeproject.org/ENCBS210OZB/

value: derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: SKOV3ip1 control [EL5]

description:
Replicate 3
EL5

source_name: Cancer cell line

value: Ovarian cancer


title: Adipocyte control  [EL3]

description:
Replicate 1
EL3


title: Adipocyte + SKOV3ip1 co-culture  [EL6]

description:
Replicate 1
EL6


title: intact Hi-C from CD14-positive monocyte (ENCLB000HTS)

description:
https://www.encodeproject.org/experiments/ENCSR444SKT/
***************
biological replicate number: 1
technical replicate number: 2
description: Monocytes CD14+ LP23 intact Mnase HiC
experiment encode accession: ENCSR444SKT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB000HTS
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: CD14-positive monocyte

value: adult

value: 51 year

value: ENCBS407NOU at ENCODE; https://www.encodeproject.org/ENCBS407NOU/

value: derived from ENCODE donor ENCDO346BRO; https://www.encodeproject.org/ENCDO346BRO/


title: SKOV3ip1 + Adipocyte co-culture [EL9]

description:
Replicate 3
EL9


title: SKOV3ip1 control [EL2]

description:
Replicate 2
EL2


title: Wild-type, E8.5 embryo, biol rep 1

value: Whole E8.5 embryo

value: Wild-type

value: genotype


title: SKOV3ip1 + Adipocyte co-culture [EL7]

description:
Replicate 2
EL7


title: SKOV3ip1 control [EL1]

description:
Replicate 1
EL1


title: Adipocyte control  [EL10]

description:
Replicate 3
EL10

value: Benign Tissue


title: SKOV3ip1 + Adipocyte co-culture [EL4]

description:
Replicate 1
EL4


title: Adipocyte control  [EL8]

description:
Replicate 2
EL8


title: ChIP-seq Grg iTNmut day4 progenitors rep2

city: Aurora

first: Elena

last: Abarinov

state: Colorado

address: 1775 Aurora Ct

institute: University of Colorado at Denver

description:
Grg_GEM_events.txt
Grg_logCPM.txt
RawCounts_Grg.txt
SigGrg.txt

data_processing:
RNA-seq: Reads were mapped to the mouse genome (mm10) using the RNA-seq alignment algorithm in the STAR (Spliced Transcripts Alignment to a Reference) software package (version 2.3.1) (Dobin et al., 2013).
RNA-seq: To estimate the relative abundances of transcripts, Cufflinks software was used (version 2.2.1) (Trapnell et al., 2013). FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) were calculated per individual gene.
RNA-seq: Differential RNA expression across cohorts was assessed using EdgeR (version 3.20.9) and limma (version 3.34.9) software (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010). Specifically, raw counts of all replicate samples in the pMN, iNkx2.2, and iTNmut groups were analyzed together, and all genes which did not have a count of 10 in at least two samples were excluded and considered to be not expressed. Read counts in each replicate were normalized to their new respective library size, and the data were normalized using the trimmed mean of M-values (TMM) method with the calcNormFactors function (Robinson and Oshlack, 2010).
RNA-seq: Significant differences were then determined in EdgeR/limma through linear modeling with precision weights (Law et al., 2014) and were based on adjusted p-values obtained through Benjamini and Hochberg’s method to control false discovery rate set at 5% (Benjamini and Hochberg, 1995).
Supplementary_files_format_and_content: RNA-seq: raw readcount text file used as input into EdgeR/limma
Supplementary_files_format_and_content: RNA-seq: test file of results of EdgeR/limma analysis
Supplementary_files_format_and_content: RNA-seq: text file of abundance measurements (FPKM values)
ChIP-seq: All sequencing data sets were aligned using Bowtie (version 0.12.7) (Langmead et al., 2009) to the mm10 genome assembly.
ChIP-seq: Peak calling of Sox2, Flag, Grg, Med1, and p300 was carried out using the GEM algorithm (Guo et al., 2012) with multi-condition settings to simultaneously identify all regions enriched over background in pMN, iNkx2.2, and iTNmut progenitors. Peak calling of H3K27ac, H3K4me1, H3K27me3, and HDAC2 was performed with the MACS software (“--- broad”; version2.0.9) (Zhang et al., 2008).
ChIP-seq: Read-count intensity was obtained within +/- 500bp of all GEM identified peaks and +/- 1kb around the midpoints of all MACS-defined regions. Read counts of individual replicates were then normalized to their respective sequencing library size, and only loci above a given threshold in both replicates (when n = 2) were used for subsequent analysis.
ChIP-seq: GEM peaks were then further processed as follows. After filtering out very low-occupied regions, each ChIP-seq dataset (e.g. Grg) contained loci that were bound in at least one of the three cell types (e.g. iNkx2.2, iTNmut, and pMN progenitors). If multiple ChIP-seq peaks resided within 500bp of each other in a given cell type, they were merged into one peak using Bedtools (version 2.17.0) (Quinlan, 2010). The locus with the highest read density (+/- 100bp) was identified using Tidyverse (version 1.2.1) (Wickham H., 2019) and utilized as the center of the occupied region. Read counts for all replicates across the three cell types were obtained within +/- 500bp from the center of all merged peaks as defined above, regardless of their cell-type origin. These datasets were then imported into the EdgeR (version 3.20.9) and limma (version 3.34.9) software packages (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010) to globally identify all significantly altered occupancy regions among pMN, iNkx2.2, and iTNmut progenitors for ChIP-seq datasets with an n = 2. Read counts in each replicate were normalized to their new respective library size and additionally quantile normalized to account for variations in ChIP-seq quality using the voom function (Hansen et al., 2012; Law et al., 2014). Significant differences in occupancy were then determined through linear modeling with precision weights (Law et al., 2014) and were based on adjusted p-values obtained through Benjamini and Hochberg’s method to control false discovery rate set at 5% (Benjamini and Hochberg, 1995).
ChIP-seq: MACS-defined peaks were similarly processed. After filtering out very low-occupied regions, the remaining peaks in each individual replicate were merged into one peak if they resided within 1kb of each other. Peaks that overlapped with each other in both replicates were then further merged into one peak to create the dataset for each cell type (e.g. pMN H3K27ac) and the midpoint of the newly merged peak was defined as the center. To globally identify all differential occupancy loci as described above for GEM-defined regions, peaks that overlapped among the three cell types (e.g. H3K27ac sites overlapping in pMN, iNkx2.2, iTNmut) were merged into one peak and the midpoint of the newly merged peak was defined as the center. These shared peaks and the remaining cell-type specific peaks were combined into one dataset, and read counts for all replicates across the three cell types were obtained within +/- 1kb from the center of the peaks regardless of their cell-type origin (e.g. pMN H3K27ac ChIP-seq signal was recorded at not only pMN-specific and shared coordinates but also iNkx2.2- and iTNmut-specific loci). These datasets were then further analyzed in EdgeR (version 3.20.9) and limma (version 3.34.9) software packages (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010), as described above for GEM-identified loci.
ChIP-seq: Final readcounts for all peaks of each ChIP-seq were converted to counts per million (CPM), quantile-normalized, and log2 transformed (logCPM). These logCPM values were then extracted to calculate significant differences in occupancy at specific regions (e.g. subsets of enhancers bound by Nkx2.2). Significance was determined using the Mann-Whitney test or the Kruskal-Wallis test with Dunn's post hoc analysis.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: peak text files generated by GEM or MACS software
Supplementary_files_format_and_content: ChIP-seq: raw readcount text files for peaks used as input into EdgeR/limma software and to make logCPM files
Supplementary_files_format_and_content: ChIP-seq: text file of results of EdgeR/limma analysis
Supplementary_files_format_and_content: ChIP-seq: logCPM text files for all peaks used in EdgeR/limma analysis

source_name: motor neuron progenitor cells

growth_protocol: Motor neuron differentiation of ESCs was performed as previously described (Rhee et al., 2016; Tan et al., 2016), with slight modifications. Briefly, ESCs were trypsinized (Thermo Fisher Scientific, SC25300054) and seeded at 5 x 105 cells in 12mL of medium (Advanced DMEM/F12:Neurobasal (1:1) Medium; Thermo Fisher Scientific, 12634-010, 21103-049) supplemented with 10% Knockout Serum Replacement (Thermo Fisher Scientific, 10828-028), 2 mM Glutamax (Invitrogen, 35050061), and 0.1 mM b-mercaptoethanol (Sigma-Aldrich, M3148) to initiate formation of embryoid bodies (day0). Embryoid bodies were split 1:4 on day2 of differentiation, and patterning was induced by supplementing fresh media with 1μM all-trans retinoic acid (RA, Sigma, R2625) and 0.5μM Smoothened agonist of hedgehog signaling (SAG, EMD Millipore, 566660). Doxycycline (DOX; Thermo Fisher Scientific, NC0424034) was added to the cultures at 1μg/mL on late day3 of differentiation for 24hrs. DAPT (Selleck, S2215) was added to the culture medium at 5μM on early day4 (~12hrs after DOX addition). DOX was washed on late day4 by replacing medium in both treated and control conditions. Fresh RA, SAG, and DAPT were re-added to this medium. On day5, the medium was again replaced, and only DAPT was re-added to the cultures. Embryoid bodies were collected on day4 (~16hrs post DOX induction) and day6 for analysis. For ChIP experiments, the same conditions were used but scaled to seed 4 x 106 cells on day0, and 1X Penicillin-Streptomycin (Thermo Fisher Scientific, 15140-122) was maintained in the cultures throughout the differentiation. DAPT was not added to cells collected on day4.

extract_protocol:
40-50 million cells were fixed with 2mM DSG, followed by 1% formaldehyde. Lysates were clarified from sonicated nuclei, and Grg-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

treatment_protocol: Selected samples were treated with doxycycline (DOX) for 14-16hrs prior to collection. See SAMPLES section.

value: ES-derived motor neuron progenitors

tag: cell line

value: mES iTNmut

value: treated with DOX for 14-16hrs

tag: differentiation stage

tag: chip antibody

value: goat anti TLE/Grg1-4 (Santa Cruz, sc-13373)


title: ChIP-seq Med1 iTNmut day4 progenitors rep2

description:
Med1_logCPM.txt
RawCounts_Med1.txt

extract_protocol:
40-50 million cells were fixed in 1% formaldehyde. Lysates were clarified from sonicated nuclei, and Med1-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

tag: cell type

tag: treatment

value: rabbit anti CRSP1/TRAP220/Med1 (Bethyl Laboratories, A300-793A)


title: ChIP-seq Grg iTNmut day4 progenitors rep1


title: intact Hi-C from CD4-positive, alpha-beta memory T cell (ENCLB978HGC)

description:
https://www.encodeproject.org/experiments/ENCSR379TIE/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD4+ T cell (CD45RO+CCR7+/-) LP11 resting Intact mnase
experiment encode accession: ENCSR379TIE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB978HGC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: male

value: 43 year

value: Charles Lee

value: AllCells

value: ENCBS210OZB at ENCODE; https://www.encodeproject.org/ENCBS210OZB/


title: intact Hi-C from HCT116 (ENCLB009JSZ)

description:
https://www.encodeproject.org/experiments/ENCSR176ICO/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116-SUPT16H-auxin-untreated-intact HiC
experiment encode accession: ENCSR176ICO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB009JSZ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: line

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS690BSF at ENCODE; https://www.encodeproject.org/ENCBS690BSF/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from heart left ventricle (ENCLB736GLT)

description:
https://www.encodeproject.org/experiments/ENCSR324EJR/
***************
biological replicate number: 1
technical replicate number: 2
description: uw38-heart-left-ventricle intact HiC
experiment encode accession: ENCSR324EJR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB736GLT
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (55 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: ischemic (EF 25% LVEDD 6.9; RV normal size, moderate dysfunction)

value: 55 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS814SXM at ENCODE; https://www.encodeproject.org/ENCBS814SXM/

value: derived from ENCODE donor ENCDO439CAZ; https://www.encodeproject.org/ENCDO439CAZ/


title: intact Hi-C from heart left ventricle (ENCLB733DJB)

description:
https://www.encodeproject.org/experiments/ENCSR324EJR/
***************
biological replicate number: 1
technical replicate number: 3
description: uw38-heart-left-ventricle intact HiC
experiment encode accession: ENCSR324EJR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB733DJB
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: male


title: ChIP-seq Grg iNkx2.2 day4 progenitors rep2

value: ES-derived motor neuron progenitors

value: mES iNkx2.2

value: treated with DOX for 14-16hrs

value: goat anti TLE/Grg1-4 (Santa Cruz, sc-13373)


title: ChIP-seq Grg pMN day4 progenitors rep2

value: mES A2lox.Cre

value: untreated


title: ChIP-seq Grg iNkx2.2 day4 progenitors rep1


title: intact Hi-C from heart left ventricle (ENCLB972QNN)

description:
https://www.encodeproject.org/experiments/ENCSR324EJR/
***************
biological replicate number: 1
technical replicate number: 1
description: uw38-heart-left-ventricle intact HiC
experiment encode accession: ENCSR324EJR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB972QNN
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 12
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: adult


title: ChIP-seq Grg pMN day4 progenitors rep1


title: ChIP-seq H3K4me1 iNkx2.2 day4 progenitors rep2

description:
H3K4me1_logCPM.txt
RawCounts_H3K4me1.txt
SigH3K4me1.txt

extract_protocol:
40-50 million cells were fixed in 1% formaldehyde. Lysates were clarified from sonicated nuclei, and histone-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

value: mouse anti H3K4me1 (Abcam, ab8895)


title: ChIP-seq H3K4me1 iTNmut day4 progenitors rep1

value: mES iTNmut


title: ChIP-seq H3K4me1 iTNmut day4 progenitors rep2


title: intact Hi-C from colonic mucosa (ENCLB634BAS)

description:
https://www.encodeproject.org/experiments/ENCSR439ILZ/
***************
biological replicate number: 1
technical replicate number: 1
description: w61 colonic mucosa
experiment encode accession: ENCSR439ILZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB634BAS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (41 years) colonic mucosa tissue, preserved by flash-freezing

value: colonic mucosa

value: tissue

value: female

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

value: 41 year

value: Yiing Lin, MD, PhD

value: ENCBS052DYV at ENCODE; https://www.encodeproject.org/ENCBS052DYV/

value: derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: intact Hi-C from colonic mucosa (ENCLB538FAA)

description:
https://www.encodeproject.org/experiments/ENCSR439ILZ/
***************
biological replicate number: 1
technical replicate number: 2
description: w61 colonic mucosa
experiment encode accession: ENCSR439ILZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB538FAA
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: Michael Snyder, Stanford


title: ChIP-seq H3K4me1 iNkx2.2 day4 progenitors rep1

value: ES-derived motor neuron progenitors

value: mES iNkx2.2


title: intact Hi-C from CD14-positive monocyte (ENCLB797VOO)

description:
https://www.encodeproject.org/experiments/ENCSR236EYO/
***************
biological replicate number: 1
technical replicate number: 1
description: Monocytes intact Hi-C
experiment encode accession: ENCSR236EYO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB797VOO
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (30 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

value: male

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS451PTV at ENCODE; https://www.encodeproject.org/ENCBS451PTV/

value: derived from ENCODE donor ENCDO544CHQ; https://www.encodeproject.org/ENCDO544CHQ/


title: intact Hi-C from CD14-positive monocyte (ENCLB115NEZ)

description:
https://www.encodeproject.org/experiments/ENCSR236EYO/
***************
biological replicate number: 1
technical replicate number: 2
description: Monocytes intact Hi-C
experiment encode accession: ENCSR236EYO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB115NEZ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: adult


title: intact Hi-C from heart right ventricle (ENCLB526TBZ)

description:
https://www.encodeproject.org/experiments/ENCSR374OJL/
***************
biological replicate number: 1
technical replicate number: 1
description: uw067-heart-right-ventricleintactHiC
experiment encode accession: ENCSR374OJL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB526TBZ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (66 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: 66 year

value: Shin Lin

value: ENCBS195FTJ at ENCODE; https://www.encodeproject.org/ENCBS195FTJ/

value: derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: intact Hi-C from heart right ventricle (ENCLB165FJF)

description:
https://www.encodeproject.org/experiments/ENCSR374OJL/
***************
biological replicate number: 1
technical replicate number: 2
description: uw067-heart-right-ventricleintactHiC
experiment encode accession: ENCSR374OJL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB165FJF
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: Michael Snyder, Stanford


title: intact Hi-C from CD14-positive monocyte (ENCLB527QDI)

description:
https://www.encodeproject.org/experiments/ENCSR236EYO/
***************
biological replicate number: 1
technical replicate number: 3
description: Monocytes intact Hi-C
experiment encode accession: ENCSR236EYO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB527QDI
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: CD14-positive monocyte


title: ChIP-seq H3K27ac sMN day6 neurons rep1

description:
H3K27ac_sMN_day6_logCPM.txt
RawCounts_sMN_H3K27ac.txt

source_name: postmitotic motor neurons

value: ES-derived motor neurons

value: mES A2lox.Cre

value: untreated

value: mouse anti H3K27ac (Abcam, ab4729)


title: ChIP-seq H3K27ac sMN day6 neurons rep2


title: ChIP-seq H3K4me1 pMN day4 progenitors rep2

value: ES-derived motor neuron progenitors

value: mouse anti H3K4me1 (Abcam, ab8895)


title: intact Hi-C from CD14-positive monocyte (ENCLB092SBI)

description:
https://www.encodeproject.org/experiments/ENCSR236EYO/
***************
biological replicate number: 1
technical replicate number: 4
description: Monocytes intact Hi-C
experiment encode accession: ENCSR236EYO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB092SBI
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: primary cell

value: male

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS451PTV at ENCODE; https://www.encodeproject.org/ENCBS451PTV/

value: derived from ENCODE donor ENCDO544CHQ; https://www.encodeproject.org/ENCDO544CHQ/


title: intact Hi-C from right cardiac atrium (ENCLB230VSH)

description:
https://www.encodeproject.org/experiments/ENCSR173VDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: w73-right-cardiac-atrium intact hic dnase
experiment encode accession: ENCSR173VDQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB230VSH
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (59 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

value: tissue

value: female

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

value: adult

value: 59 year

value: Yiing Lin, MD, PhD

value: ENCBS988KDP at ENCODE; https://www.encodeproject.org/ENCBS988KDP/

value: derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: ChIP-seq H3K27ac iTNmut day4 progenitors rep2

description:
H3K27ac_day4_logCPM.txt
RawCounts_day4_H3K27ac.txt
SigH3K27ac_day4.txt

value: ES-derived motor neuron progenitors

value: mES iTNmut

value: treated with DOX for 14-16hrs

value: mouse anti H3K27ac (Abcam, ab4729)


title: intact Hi-C from CD8-positive, alpha-beta T cell (ENCLB965XTL)

description:
https://www.encodeproject.org/experiments/ENCSR321BHC/
***************
biological replicate number: 1
technical replicate number: 2
description: CD8+ intact Hi-C
experiment encode accession: ENCSR321BHC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB965XTL
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: 21 year

value: Yijun Ruan, JAX

value: ENCBS651TFQ at ENCODE; https://www.encodeproject.org/ENCBS651TFQ/

value: derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: ChIP-seq H3K4me1 pMN day4 progenitors rep1

value: mES HBG3

value: untreated

value: mouse anti H3K4me1 (Abcam, ab8895)


title: intact Hi-C from CD8-positive, alpha-beta T cell (ENCLB141UXD)

description:
https://www.encodeproject.org/experiments/ENCSR321BHC/
***************
biological replicate number: 1
technical replicate number: 4
description: CD8+ intact Hi-C
experiment encode accession: ENCSR321BHC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB141UXD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: adult

value: AllCells


title: ChIP-seq H3K27ac iTNmut day4 progenitors rep1


title: intact Hi-C from CD8-positive, alpha-beta T cell (ENCLB307UFI)

description:
https://www.encodeproject.org/experiments/ENCSR321BHC/
***************
biological replicate number: 1
technical replicate number: 3
description: CD8+ intact Hi-C
experiment encode accession: ENCSR321BHC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB307UFI
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: ChIP-seq H3K27ac iNkx2.2 day4 progenitors rep1

value: mES iNkx2.2


title: intact Hi-C from MCF 10A (ENCLB039JNC)

description:
https://www.encodeproject.org/experiments/ENCSR370TFL/
***************
biological replicate number: 2
technical replicate number: 5
description: MCF10A intact Hi-C
experiment encode accession: ENCSR370TFL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB039JNC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1300000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: cell line

value: female

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS436GYV at ENCODE; https://www.encodeproject.org/ENCBS436GYV/

value: derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: intact Hi-C from right cardiac atrium (ENCLB152NPU)

description:
https://www.encodeproject.org/experiments/ENCSR173VDQ/
***************
biological replicate number: 1
technical replicate number: 2
description: w73-right-cardiac-atrium intact hic dnase
experiment encode accession: ENCSR173VDQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB152NPU
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: right cardiac atrium

value: tissue

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS988KDP at ENCODE; https://www.encodeproject.org/ENCBS988KDP/

value: derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: ChIP-seq H3K27ac iNkx2.2 day4 progenitors rep2

value: ES-derived motor neuron progenitors

value: mES iNkx2.2

value: treated with DOX for 14-16hrs

value: mouse anti H3K27ac (Abcam, ab4729)


title: intact Hi-C from CD8-positive, alpha-beta T cell (ENCLB239ZGG)

description:
https://www.encodeproject.org/experiments/ENCSR321BHC/
***************
biological replicate number: 1
technical replicate number: 1
description: CD8+ intact Hi-C
experiment encode accession: ENCSR321BHC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB239ZGG
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS651TFQ at ENCODE; https://www.encodeproject.org/ENCBS651TFQ/

value: derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: ChIP-seq H3K27ac pMN day4 progenitors rep2

value: mES A2lox.Cre

value: untreated


title: intact Hi-C from MCF 10A (ENCLB671RYC)

description:
https://www.encodeproject.org/experiments/ENCSR370TFL/
***************
biological replicate number: 2
technical replicate number: 3
description: MCF10A intact Hi-C
experiment encode accession: ENCSR370TFL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB671RYC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1300000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: MCF 10A

value: cell line

value: female

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS436GYV at ENCODE; https://www.encodeproject.org/ENCBS436GYV/

value: derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: ChIP-seq H3K27ac pMN day4 progenitors rep1

value: ES-derived motor neuron progenitors

value: mES HBG3

value: mouse anti H3K27ac (Abcam, ab4729)


title: intact Hi-C from MCF 10A (ENCLB845HTW)

description:
https://www.encodeproject.org/experiments/ENCSR370TFL/
***************
biological replicate number: 2
technical replicate number: 2
description: MCF10A intact Hi-C
experiment encode accession: ENCSR370TFL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB845HTW
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1300000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: adult


title: ChIP-seq H3K27me3 iNkx22 day4 progenitors rep1

description:
H3K27me3_logCPM.txt
RawCounts_H3K27me3.txt

value: mES iNkx2.2

value: treated with DOX for 14-16hrs

value: rabbit anti H3K27me3 (Millipore, 07-449)


title: ChIP-seq H3K27me3 pMN day4 progenitors rep1

value: mES A2lox.Cre

value: untreated


title: intact Hi-C from MCF 10A (ENCLB919LSP)

description:
https://www.encodeproject.org/experiments/ENCSR370TFL/
***************
biological replicate number: 1
technical replicate number: 1
description: MCF10A intact Hi-C
experiment encode accession: ENCSR370TFL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB919LSP
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1950000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: MCF 10A

value: cell line

value: ENCBS820QZE at ENCODE; https://www.encodeproject.org/ENCBS820QZE/


title: intact Hi-C from MCF 10A (ENCLB014JCP)

description:
https://www.encodeproject.org/experiments/ENCSR370TFL/
***************
biological replicate number: 2
technical replicate number: 4
description: MCF10A intact Hi-C
experiment encode accession: ENCSR370TFL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB014JCP
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1300000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: female

value: fibrocystic disease

value: 36 year


title: intact Hi-C from MCF 10A (ENCLB819VPQ)

description:
https://www.encodeproject.org/experiments/ENCSR370TFL/
***************
biological replicate number: 2
technical replicate number: 1
description: MCF10A intact Hi-C
experiment encode accession: ENCSR370TFL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB819VPQ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1300000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS436GYV at ENCODE; https://www.encodeproject.org/ENCBS436GYV/


title: ChIP-seq HDAC2 iTNmut day4 progenitors rep2

description:
HDAC2_logCPM.txt
RawCounts_HDAC2.txt
SigHDAC2.txt

extract_protocol:
40-50 million cells were fixed with 2mM DSG, followed by 1% formaldehyde. Lysates were clarified from sonicated nuclei, and HDAC2-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

value: ES-derived motor neuron progenitors

value: mES iTNmut

value: rabbit anti HDAC2 (Abcam, ab7029)


title: intact Hi-C from HCT116 (ENCLB629WFB)

description:
https://www.encodeproject.org/experiments/ENCSR233DHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 BRD4 degron untreated intact mnase
experiment encode accession: ENCSR233DHQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB629WFB
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS241GOH at ENCODE; https://www.encodeproject.org/ENCBS241GOH/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: ChIP-seq HDAC2 iNkx2.2 day4 progenitors rep2

value: mES iNkx2.2

value: treated with DOX for 14-16hrs


title: intact Hi-C from HCT116 (ENCLB687MSQ)

description:
https://www.encodeproject.org/experiments/ENCSR233DHQ/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 BRD4 degron untreated intact mnase
experiment encode accession: ENCSR233DHQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB687MSQ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line


title: intact Hi-C from HCT116 (ENCLB803JSG)

description:
https://www.encodeproject.org/experiments/ENCSR233DHQ/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116 BRD4 degron untreated intact mnase
experiment encode accession: ENCSR233DHQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB803JSG
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: ChIP-seq HDAC2 pMN day4 progenitors rep2

value: mES A2lox.Cre

value: untreated


title: ChIP-seq HDAC2 iNkx2.2 day4 progenitors rep1


title: ChIP-seq Med1 iTNmut day4 progenitors rep1

description:
Med1_logCPM.txt
RawCounts_Med1.txt

value: rabbit anti CRSP1/TRAP220/Med1 (Bethyl Laboratories, A300-793A)


title: ChIP-seq HDAC2 pMN day4 progenitors rep1

value: ES-derived motor neuron progenitors


title: intact Hi-C from MCF 10A (ENCLB960LGC)

description:
https://www.encodeproject.org/experiments/ENCSR370TFL/
***************
biological replicate number: 1
technical replicate number: 2
description: MCF10A intact Hi-C
experiment encode accession: ENCSR370TFL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB960LGC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1950000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: MCF 10A

value: female

value: fibrocystic disease

value: 36 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS820QZE at ENCODE; https://www.encodeproject.org/ENCBS820QZE/

value: derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: ChIP-seq Input

extract_protocol:
40-50 million cells were fixed in 1% formaldehyde. Lysates were clarified from sonicated nuclei. No antibody was added.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.


title: ChIP-seq Med1 iNkx22 day4 progenitors rep1

description:
Med1_logCPM.txt
RawCounts_Med1.txt


title: ChIP-seq Nkx2.2-Flag iTNmut day4 progenitors rep2

description:
Nkx2.2-Flag_GEM_events.txt
Nkx2.2_logCPM.txt
RawCounts_Nkx2.2-Flag.txt
SigNkx2.2.txt

extract_protocol:
40-50 million cells were fixed in 1% formaldehyde. Lysates were clarified from sonicated nuclei, and FLAG-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

value: mES iTNmut

value: mouse anti Flag (Sigma-Aldrich, F1804)


title: intact Hi-C from HCT116 (ENCLB049WND)

description:
https://www.encodeproject.org/experiments/ENCSR218URU/
***************
biological replicate number: 1
technical replicate number: 5
description: HCT116 Pol2RA auxin treated degron intact mnase hic
experiment encode accession: ENCSR218URU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB049WND
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS749WJM at ENCODE; https://www.encodeproject.org/ENCBS749WJM/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from left cardiac atrium (ENCLB883SZK)

description:
https://www.encodeproject.org/experiments/ENCSR434MBR/
***************
biological replicate number: 1
technical replicate number: 1
description: w73 left cardiac atrium intact dnase hic
experiment encode accession: ENCSR434MBR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB883SZK
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (59 years) left cardiac atrium tissue, preserved by flash-freezing

value: left cardiac atrium

value: tissue

tag: biosample encode accession

value: female

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS059VPO at ENCODE; https://www.encodeproject.org/ENCBS059VPO/

value: derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: intact Hi-C from heart right ventricle (ENCLB070AWW)

description:
https://www.encodeproject.org/experiments/ENCSR315OOJ/
***************
biological replicate number: 1
technical replicate number: 1
description: UW040-heart-right-ventricle intact HiC
experiment encode accession: ENCSR315OOJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB070AWW
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (69 years) heart right ventricle tissue

value: heart right ventricle

tag: encode accession

value: male

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 69 year

value: Shin Lin

value: ENCBS419EHR at ENCODE; https://www.encodeproject.org/ENCBS419EHR/

value: derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: intact Hi-C from left cardiac atrium (ENCLB570FLK)

description:
https://www.encodeproject.org/experiments/ENCSR434MBR/
***************
biological replicate number: 1
technical replicate number: 2
description: w73 left cardiac atrium intact dnase hic
experiment encode accession: ENCSR434MBR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB570FLK
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

tag: Sex

value: adult


title: intact Hi-C from heart right ventricle (ENCLB659VUO)

description:
https://www.encodeproject.org/experiments/ENCSR315OOJ/
***************
biological replicate number: 1
technical replicate number: 2
description: UW040-heart-right-ventricle intact HiC
experiment encode accession: ENCSR315OOJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB659VUO
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

tag: health state


title: ChIP-seq Nkx2.2-Flag iTNmut day4 progenitors rep1

value: ES-derived motor neuron progenitors

value: mES iTNmut

value: treated with DOX for 14-16hrs

value: mouse anti Flag (Sigma-Aldrich, F1804)


title: ChIP-seq HDAC2 iTNmut day4 progenitors rep1

value: rabbit anti HDAC2 (Abcam, ab7029)


title: intact Hi-C from HCT116 (ENCLB097MJW)

description:
https://www.encodeproject.org/experiments/ENCSR218URU/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 Pol2RA auxin treated degron intact mnase hic
experiment encode accession: ENCSR218URU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB097MJW
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: colorectal carcinoma

tag: dev stage

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS749WJM at ENCODE; https://www.encodeproject.org/ENCBS749WJM/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from HCT116 (ENCLB378QGB)

description:
https://www.encodeproject.org/experiments/ENCSR218URU/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116 Pol2RA auxin treated degron intact mnase hic
experiment encode accession: ENCSR218URU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB378QGB
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: male

tag: age


title: intact Hi-C from HCT116 (ENCLB524BTF)

description:
https://www.encodeproject.org/experiments/ENCSR218URU/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116 Pol2RA auxin treated degron intact mnase hic
experiment encode accession: ENCSR218URU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB524BTF
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: lab


title: ChIP-seq Med1 pMN day4 progenitors rep1

description:
Med1_logCPM.txt
RawCounts_Med1.txt

value: mES HBG3

value: untreated

value: rabbit anti CRSP1/TRAP220/Med1 (Bethyl Laboratories, A300-793A)


title: ChIP-seq Nkx2.2-Flag iNkx2.2 day4 progenitors rep1

value: ES-derived motor neuron progenitors

value: mES iNkx2.2


title: ChIP-seq p300 iTNmut day4 progenitors rep1

description:
p300_GEM_events.txt
p300_logCPM.txt
RawCounts_p300.txt
Sigp300.txt

extract_protocol:
40-50 million cells were fixed in 1% formaldehyde. Lysates were clarified from sonicated nuclei, and p300-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

value: mES iTNmut

value: treated with DOX for 14-16hrs

value: rabbit anti p300 (Santa Cruz, sc-584)


title: intact Hi-C from HCT116 (ENCLB447YSR)

description:
https://www.encodeproject.org/experiments/ENCSR233DHQ/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116 BRD4 degron untreated intact mnase
experiment encode accession: ENCSR233DHQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB447YSR
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: adult

tag: source

value: ENCBS241GOH at ENCODE; https://www.encodeproject.org/ENCBS241GOH/


title: ChIP-seq p300 iNkx2.2 day4 progenitors rep2


title: intact Hi-C from HCT116 (ENCLB599KIO)

description:
https://www.encodeproject.org/experiments/ENCSR218URU/
***************
biological replicate number: 1
technical replicate number: 6
description: HCT116 Pol2RA auxin treated degron intact mnase hic
experiment encode accession: ENCSR218URU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB599KIO
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

tag: link


title: intact Hi-C from HCT116 (ENCLB035ISN)

description:
https://www.encodeproject.org/experiments/ENCSR218URU/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 Pol2RA auxin treated degron intact mnase hic
experiment encode accession: ENCSR218URU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB035ISN
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS749WJM at ENCODE; https://www.encodeproject.org/ENCBS749WJM/


title: intact Hi-C from psoas muscle (ENCLB181ZVI)

description:
https://www.encodeproject.org/experiments/ENCSR173QPK/
***************
biological replicate number: 1
technical replicate number: 4
description: w61-psoas-muscle intact HiC
experiment encode accession: ENCSR173QPK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB181ZVI
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (41 years) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

value: tissue

value: female

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

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS192WLC at ENCODE; https://www.encodeproject.org/ENCBS192WLC/

value: derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: intact Hi-C from psoas muscle (ENCLB583SGV)

description:
https://www.encodeproject.org/experiments/ENCSR173QPK/
***************
biological replicate number: 1
technical replicate number: 2
description: w61-psoas-muscle intact HiC
experiment encode accession: ENCSR173QPK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB583SGV
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: adult


title: ChIP-seq p300 iNkx2.2 day4 progenitors rep1

value: ES-derived motor neuron progenitors

value: mES iNkx2.2

value: treated with DOX for 14-16hrs

value: rabbit anti p300 (Santa Cruz, sc-584)


title: ChIP-seq Sox2 iTNmut day4 progenitors rep1

description:
Sox2_GEM_events.txt
Sox2_logCPM.txt
RawCounts_Sox2.txt

extract_protocol:
40-50 million cells were fixed in 1% formaldehyde. Lysates were clarified from sonicated nuclei, and Sox2-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

value: mES iTNmut

value: goat anti Sox2 (R&D systems, AF2018-SP)


title: ChIP-seq p300 pMN day4 progenitors rep2

value: mES A2lox.Cre

value: untreated


title: intact Hi-C from psoas muscle (ENCLB444IHT)

description:
https://www.encodeproject.org/experiments/ENCSR173QPK/
***************
biological replicate number: 1
technical replicate number: 1
description: w61-psoas-muscle intact HiC
experiment encode accession: ENCSR173QPK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB444IHT
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: psoas muscle

value: tissue


title: ChIP-seq p300 pMN day4 progenitors rep1

value: mES HBG3


title: ChIP-seq H3K27me3 iTNmut day4 progenitors rep1

description:
H3K27me3_logCPM.txt
RawCounts_H3K27me3.txt

value: rabbit anti H3K27me3 (Millipore, 07-449)


title: intact Hi-C from left ventricle myocardium inferior (ENCLB381XPI)

description:
https://www.encodeproject.org/experiments/ENCSR352EGR/
***************
biological replicate number: 1
technical replicate number: 1
description: W78 left ventricle myocardium inferior intact Hi-C
experiment encode accession: ENCSR352EGR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB381XPI
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (60 years) left ventricle myocardium inferior tissue, preserved by flash-freezing

value: left ventricle myocardium inferior

tag: note

value: Inferior wall of left ventricle.

value: male

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: 60 year

value: Michael Snyder, Stanford

value: ENCBS244SGP at ENCODE; https://www.encodeproject.org/ENCBS244SGP/

value: derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: intact Hi-C from left ventricle myocardium inferior (ENCLB206RNR)

description:
https://www.encodeproject.org/experiments/ENCSR352EGR/
***************
biological replicate number: 1
technical replicate number: 2
description: W78 left ventricle myocardium inferior intact Hi-C
experiment encode accession: ENCSR352EGR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB206RNR
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: adult

value: Yiing Lin, MD, PhD


title: intact Hi-C from left ventricle myocardium inferior (ENCLB301ZZG)

description:
https://www.encodeproject.org/experiments/ENCSR352EGR/
***************
biological replicate number: 1
technical replicate number: 3
description: W78 left ventricle myocardium inferior intact Hi-C
experiment encode accession: ENCSR352EGR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB301ZZG
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: ChIP-seq p300 iTNmut day4 progenitors rep2

value: ES-derived motor neuron progenitors

tag: cell line

value: mES iTNmut

value: treated with DOX for 14-16hrs

value: rabbit anti p300 (Santa Cruz, sc-584)


title: RNA-seq iTNmut day4 progenitors rep3

description:
RNAseq_FPKM.txt
RNAseq_readcounts.txt
RNAseq_SigGenes.txt

extract_protocol:
RNA was extracted using Trizol Reagent (Life Technologies, SC: 15596-018) in combination with RNeasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing using Illumina Trueseq RNA Prep Kit.

tag: differentiation stage


title: intact Hi-C from left ventricle myocardium inferior (ENCLB065UHV)

description:
https://www.encodeproject.org/experiments/ENCSR352EGR/
***************
biological replicate number: 1
technical replicate number: 4
description: W78 left ventricle myocardium inferior intact Hi-C
experiment encode accession: ENCSR352EGR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB065UHV
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue


title: intact Hi-C from psoas muscle (ENCLB053IKJ)

description:
https://www.encodeproject.org/experiments/ENCSR173QPK/
***************
biological replicate number: 1
technical replicate number: 3
description: w61-psoas-muscle intact HiC
experiment encode accession: ENCSR173QPK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB053IKJ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: psoas muscle

value: female

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

value: 41 year

value: ENCBS192WLC at ENCODE; https://www.encodeproject.org/ENCBS192WLC/

value: derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: intact Hi-C from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB302LBG)

description:
https://www.encodeproject.org/experiments/ENCSR215PTV/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD4+ T cell Th0 effector resting intact mnase
experiment encode accession: ENCSR215PTV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB302LBG
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (35 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: male

value: 35 year

value: Charles Lee

value: AllCells

value: ENCBS562INO at ENCODE; https://www.encodeproject.org/ENCBS562INO/

value: derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: RNA-seq iNkx2.2 day4 progenitors rep3

value: ES-derived motor neuron progenitors

value: mES iNkx2.2


title: intact Hi-C from sciatic nerve (ENCLB054OBZ)

description:
https://www.encodeproject.org/experiments/ENCSR119TFS/
***************
biological replicate number: 1
technical replicate number: 1
description: w61 sciatic nerve intact dnase hic
experiment encode accession: ENCSR119TFS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB054OBZ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (41 years) sciatic nerve tissue, preserved by flash-freezing

value: sciatic nerve

value: adult

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS936RHZ at ENCODE; https://www.encodeproject.org/ENCBS936RHZ/


title: intact Hi-C from sciatic nerve (ENCLB413JMN)

description:
https://www.encodeproject.org/experiments/ENCSR119TFS/
***************
biological replicate number: 1
technical replicate number: 2
description: w61 sciatic nerve intact dnase hic
experiment encode accession: ENCSR119TFS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB413JMN
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: female

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

value: 41 year


title: RNA-seq iTNmut day4 progenitors rep2

source_name: motor neuron progenitor cells

value: mES iTNmut

value: treated with DOX for 14-16hrs


title: intact Hi-C from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB957OTG)

description:
https://www.encodeproject.org/experiments/ENCSR215PTV/
***************
biological replicate number: 1
technical replicate number: 2
description: naive CD4+ T cell Th0 effector resting intact mnase
experiment encode accession: ENCSR215PTV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB957OTG
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: primary cell

value: male

value: 35 year

value: Charles Lee


title: RNA-seq iTNmut day4 progenitors rep1

value: ES-derived motor neuron progenitors


title: RNA-seq iNkx2.2 day4 progenitors rep2

value: mES iNkx2.2


title: ChIP-seq Sox2 pMN day4 progenitors rep1

extract_protocol:
See Peterson et al., 2012
See Peterson et al., 2012

value: See Peterson et al., 2012

value: untreated

tag: chip antibody

value: goat anti Sox2 (R&D systems, AF2018-SP)