title: intact Hi-C from heart right ventricle (ENCLB722XKE)

description:
https://www.encodeproject.org/experiments/ENCSR908NSV/
***************
biological replicate number: 1
technical replicate number: 1
description: uw038-heart-right-ventricle intact HiC
experiment encode accession: ENCSR908NSV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB722XKE
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 right ventricle tissue

value: tissue

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

value: 55 year

value: Michael Snyder, Stanford

value: ENCBS029DZY at ENCODE; https://www.encodeproject.org/ENCBS029DZY/

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


title: intact Hi-C from right cardiac atrium (ENCLB638LLZ)

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/ENCSR503LWK/
***************
biological replicate number: 1
technical replicate number: 3
description: w78-right-cardiac-atrium-intact dnase hic
experiment encode accession: ENCSR503LWK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB638LLZ
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 male adult (60 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

tag: biosample encode accession

tag: encode accession

tag: Sex

value: male

tag: health state

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

tag: dev stage

value: adult

tag: age

value: 60 year

tag: lab

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS852VTT at ENCODE; https://www.encodeproject.org/ENCBS852VTT/

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


title: intact Hi-C from right cardiac atrium (ENCLB513JAJ)

description:
https://www.encodeproject.org/experiments/ENCSR503LWK/
***************
biological replicate number: 1
technical replicate number: 1
description: w78-right-cardiac-atrium-intact dnase hic
experiment encode accession: ENCSR503LWK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB513JAJ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from heart left ventricle (ENCLB234JHC)

description:
https://www.encodeproject.org/experiments/ENCSR518LPK/
***************
biological replicate number: 1
technical replicate number: 2
description: uw054-heart-left-ventricle-intact dnase
experiment encode accession: ENCSR518LPK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB234JHC
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 (54 years) heart left ventricle tissue

value: heart left ventricle

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: 54 year

value: Shin Lin

value: ENCBS366UGG at ENCODE; https://www.encodeproject.org/ENCBS366UGG/

value: derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: intact Hi-C from heart right ventricle (ENCLB615ELT)

description:
https://www.encodeproject.org/experiments/ENCSR771MVF/
***************
biological replicate number: 1
technical replicate number: 1
description: UW65-heart-right-ventricle intact HiC
experiment encode accession: ENCSR771MVF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB615ELT
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 (73 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: ischemic (EF 35%, LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 73 year

value: Michael Snyder, Stanford

value: ENCBS979LNP at ENCODE; https://www.encodeproject.org/ENCBS979LNP/

value: derived from ENCODE donor ENCDO804CLC; https://www.encodeproject.org/ENCDO804CLC/


title: intact Hi-C from right cardiac atrium (ENCLB179ALF)

description:
https://www.encodeproject.org/experiments/ENCSR503LWK/
***************
biological replicate number: 1
technical replicate number: 2
description: w78-right-cardiac-atrium-intact dnase hic
experiment encode accession: ENCSR503LWK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB179ALF
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: male

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

value: adult

value: 60 year


title: intact Hi-C from GM12878 (ENCLB689GXT)

description:
https://www.encodeproject.org/experiments/ENCSR916MFV/
***************
biological replicate number: 1
technical replicate number: 3
description: GM12878 intact mnase hi-c
experiment encode accession: ENCSR916MFV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB689GXT
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 GM12878 cell line

tag: line

value: cell line

value: female

value: unknown

value: Mats Ljungman, UMichigan

value: Coriell

value: ENCBS678NVO at ENCODE; https://www.encodeproject.org/ENCBS678NVO/

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


title: 110- Day 5 8H

city: Baltimore

first: Ali

last: Ahmadi

address: 855 N Wolfe Street

institute: MedRegen LLC

library_source: transcriptomic

data_processing:
Using cutadapt version 1.18 the reads of the sequencing run were scanned for adapter contaminations, continuous polyA sequences and continuous polyG sequences at the 3’ end and had the contaminations removed if found.
The reads of the samples prior to adapter trimming and after adapter trimming were analyzed with FastQC version v0.11.7
The reads were aligned to the spike-in complemented Ensembl release 94 of the Homo sapiens assembly GRCh38 from the Genome Reference Consortium. The alignment was performed with the splice-aware aligner STAR version 2.6.1a.
The alignments were quantified based on the annotations of Ensembl GRCh38.94 and the spike-in specific annotations of Lexogen with the featureCounts software program version 1.6.4 of the subread analysis package.
Functional enrichment analysis was performed and visualized with clusterProfiler 4.2.2, For gene set enrichment testing the hallmark data set of the molecular signature database has been used. The data used has been retrieved from the CRAN R package msigdbr 7.5.1.
Assembly: Ensembl release 94 of the Homo sapiens assembly GRCh38 from the Genome Reference Consortium.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

molecule: total RNA

source_name: White blood cells

growth_protocol: Cells were directly snap-fozen in liquid nitrogen after isolation and stored in -80C until further use.

extract_protocol:
RNA was harvested by using the Split 008UG005V0310_SPLIT-RNA-Extraction Kit (Lexogen). 100 ng of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using a QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (015UG009V0260) with Globin Block Module following procedures for degraded RNA.

treatment_protocol: No further treatment was provided.

tag: tissue

value: White blood cells

tag: treatment


title: 110- Day 5 24H


title: intact Hi-C from heart right ventricle (ENCLB832UPU)

description:
https://www.encodeproject.org/experiments/ENCSR908NSV/
***************
biological replicate number: 1
technical replicate number: 2
description: uw038-heart-right-ventricle intact HiC
experiment encode accession: ENCSR908NSV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB832UPU
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: tissue

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

value: 55 year

value: Shin Lin

value: ENCBS029DZY at ENCODE; https://www.encodeproject.org/ENCBS029DZY/

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


title: intact Hi-C from HCT116 (ENCLB236FAD)

description:
https://www.encodeproject.org/experiments/ENCSR777YML/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 SMARCA5 auxin untreated degron intact hic
experiment encode accession: ENCSR777YML
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB236FAD
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 SMARCA5

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS719AUN at ENCODE; https://www.encodeproject.org/ENCBS719AUN/

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


title: 110- Day 3 48H


title: 109- Day 5 12H


title: 110- Day 5 12H


title: 110- Day 5 1H


title: 110- Day 5 48H


title: 109- Day 5 48H


title: 109- Day 5 24H


title: 110- Day 5 3H


title: 109- Day 5 3H


title: 109- Day 5 1H


title: 1309- Day 1 48H


title: 1309- Day 1 24H


title: 1309- Day 1 8H


title: 109- Day 5 8H


title: 109- Day 3 48H


title: 1309- Day 1 12H


title: 312- Day 1 24H


title: 1309- Day 1 3H


title: 1309- Day 1 Predose


title: 1309- Day 1 1H


title: 312- Day 1 48H


title: 312- Day 1 8H


title: 312- Day 1 3H


title: 312- Day 1 1H


title: 312- Day 1 Predose


title: 310- Day 1 48H


title: 310- Day 1 12H


title: 310- Day 1 8H


title: 310- Day 1 24H


title: 310- Day 1 1H


title: 310- Day 1 Predose


title: 302- Day 1 8H


title: 302- Day 1 Predose


title: 302- Day 1 24H


title: 212- Day 1 24H


title: 302- Day 1 1H


title: 212- Day 1 48H


title: 212- Day 1 12H


title: 302- Day 1 12H


title: 212- Day 1 8H


title: 212- Day 1 3H


title: 312- Day 1 12H


title: 1201- Day 1 12H


title: 212- Day 1 1H


title: 212- Day 1 Predose


title: 1201- Day 1 48H


title: 1201- Day 1 8H


title: 1201- Day 1 1H


title: 1201- Day 1 24H


title: 1201- Day 1 3H


title: 1201- Day 1 Predose


title: 211- Day 1 48H


title: 310- Day 1 3H


title: 302- Day 1 3H


title: 302- Day 1 48H


title: 211- Day 1 24H


title: 211- Day 1 8H


title: 211- Day 1 3H


title: 211- Day 1 12H


title: 210- Day 1 48H


title: 211- Day 1 1H


title: 211- Day 1 Predose


title: 210- Day 1 12H


title: 210- Day 1 1H


title: 210- Day 1 Predose


title: 210- Day 1 8H


title: 311- Day 1 12H

value: Saline Placebo


title: 311- Day 1 24H

value: White blood cells


title: 210- Day 1 3H


title: 311- Day 1 8H


title: 311- Day 1 48H


title: 301- Day 1 12H


title: 301- Day 1 3H


title: 301- Day 1 24H


title: 301- Day 1 48H


title: 311- Day 1 Predose


title: 311- Day 1 1H


title: 301- Day 1 8H


title: 301- Day 1 1H


title: 301- Day 1 Predose


title: 210- Day 1 24H


title: 209- Day 1 12H


title: 209- Day 1 48H


title: 209- Day 1 24H


title: 209- Day 1 3H


title: 209- Day 1 1H


title: 209- Day 1 Predose


title: 209- Day 1 8H


title: 311- Day 1 3H


title: 202- Day 1 24H


title: 202- Day 48H


title: 202- Day 8H


title: 1111- Day 1 48H


title: 202- Day 1 1H


title: 202- Day 1 Predose


title: 202- Day 12H


title: 1111- Day 1 12H


title: 1111- Day 1 24H


title: 1111- Day 1 8H


title: 1111- Day 1 1H


title: 1111- Day 1 Predose


title: intact Hi-C from lower lobe of right lung (ENCLB439SOQ)

description:
https://www.encodeproject.org/experiments/ENCSR749PID/
***************
biological replicate number: 1
technical replicate number: 3
description: W78 lower lobe of right lung intact HIC
experiment encode accession: ENCSR749PID
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB439SOQ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (60 years) lower lobe of right lung tissue, preserved by flash-freezing

value: lower lobe of right lung

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

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS616TCG at ENCODE; https://www.encodeproject.org/ENCBS616TCG/

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


title: intact Hi-C from pancreas (ENCLB096DSP)

description:
https://www.encodeproject.org/experiments/ENCSR502GIO/
***************
biological replicate number: 1
technical replicate number: 2
description: w62-pancreas intact hic dnase
experiment encode accession: ENCSR502GIO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB096DSP
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 child (16 years) pancreas tissue, preserved by flash-freezing

value: pancreas

value: tissue

value: female

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

value: child

value: 16 year

value: ENCBS485HVN at ENCODE; https://www.encodeproject.org/ENCBS485HVN/

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


title: intact Hi-C from right lobe of liver (ENCLB377JYU)

description:
https://www.encodeproject.org/experiments/ENCSR753CKM/
***************
biological replicate number: 1
technical replicate number: 2
description: w63 right lobe of liver intact HIC
experiment encode accession: ENCSR753CKM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB377JYU
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 (47 years) right lobe of liver tissue, preserved by flash-freezing

value: right lobe of liver

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

value: adult

value: 47 year

value: ENCBS462BTB at ENCODE; https://www.encodeproject.org/ENCBS462BTB/

value: derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: intact Hi-C from pancreas (ENCLB779OUU)

description:
https://www.encodeproject.org/experiments/ENCSR502GIO/
***************
biological replicate number: 1
technical replicate number: 1
description: w62-pancreas intact hic dnase
experiment encode accession: ENCSR502GIO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB779OUU
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

value: Yiing Lin, MD, PhD


title: intact Hi-C from adrenal gland (ENCLB053KZV)

description:
https://www.encodeproject.org/experiments/ENCSR898ANZ/
***************
biological replicate number: 1
technical replicate number: 1
description: W61 adrenal gland intact dnase hic
experiment encode accession: ENCSR898ANZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB053KZV
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) adrenal gland tissue, preserved by flash-freezing

value: adrenal gland

value: 41 year

value: ENCBS947QBF at ENCODE; https://www.encodeproject.org/ENCBS947QBF/

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


title: intact Hi-C from lower lobe of right lung (ENCLB650SRG)

description:
https://www.encodeproject.org/experiments/ENCSR749PID/
***************
biological replicate number: 1
technical replicate number: 2
description: W78 lower lobe of right lung intact HIC
experiment encode accession: ENCSR749PID
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB650SRG
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: lower lobe of right lung

value: tissue

value: male

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

value: 60 year

value: ENCBS616TCG at ENCODE; https://www.encodeproject.org/ENCBS616TCG/

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


title: intact Hi-C from heart left ventricle (ENCLB691YWU)

description:
https://www.encodeproject.org/experiments/ENCSR498AFT/
***************
biological replicate number: 1
technical replicate number: 2
description: w73 heart left ventricle intact dnase hic
experiment encode accession: ENCSR498AFT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB691YWU
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 (59 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: female

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

value: adult

value: 59 year

value: ENCBS384GEM at ENCODE; https://www.encodeproject.org/ENCBS384GEM/

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


title: intact Hi-C from lower leg skin (ENCLB130OVT)

description:
https://www.encodeproject.org/experiments/ENCSR720WEB/
***************
biological replicate number: 1
technical replicate number: 2
description: entex skin (sun exposed) lower leg intact dnase hic
experiment encode accession: ENCSR720WEB
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB130OVT
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) lower leg skin tissue

value: lower leg skin

value: 53 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS221DLR at ENCODE; https://www.encodeproject.org/ENCBS221DLR/

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


title: intact Hi-C from left lung (ENCLB851FDG)

description:
https://www.encodeproject.org/experiments/ENCSR892BZA/
***************
biological replicate number: 1
technical replicate number: 2
description: w62-left-lung intact HiC
experiment encode accession: ENCSR892BZA
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB851FDG
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 child (16 years) left lung tissue, preserved by flash-freezing

value: left lung

value: tissue

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

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS740TAF at ENCODE; https://www.encodeproject.org/ENCBS740TAF/

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


title: intact Hi-C from lower leg skin (ENCLB362ZHT)

description:
https://www.encodeproject.org/experiments/ENCSR720WEB/
***************
biological replicate number: 1
technical replicate number: 1
description: entex skin (sun exposed) lower leg intact dnase hic
experiment encode accession: ENCSR720WEB
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB362ZHT
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

value: adult


title: 202- Day 1 3H

value: White blood cells

value: Saline Placebo


title: intact Hi-C from heart left ventricle (ENCLB064NYT)

description:
https://www.encodeproject.org/experiments/ENCSR498AFT/
***************
biological replicate number: 1
technical replicate number: 1
description: w73 heart left ventricle intact dnase hic
experiment encode accession: ENCSR498AFT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB064NYT
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

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

value: 59 year

value: ENCBS384GEM at ENCODE; https://www.encodeproject.org/ENCBS384GEM/

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


title: intact Hi-C from mammary epithelial cell (ENCLB555PSV)

description:
https://www.encodeproject.org/experiments/ENCSR707XVJ/
***************
biological replicate number: 1
technical replicate number: 4
description: HMEC intact Hi-C
experiment encode accession: ENCSR707XVJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB555PSV
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 female adult (19 years) mammary epithelial primary cell

value: mammary epithelial cell

value: primary cell

value: 19 year

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS131DIO at ENCODE; https://www.encodeproject.org/ENCBS131DIO/

value: derived from ENCODE donor ENCDO955XOD; https://www.encodeproject.org/ENCDO955XOD/


title: intact Hi-C from mammary epithelial cell (ENCLB057VTC)

description:
https://www.encodeproject.org/experiments/ENCSR707XVJ/
***************
biological replicate number: 1
technical replicate number: 1
description: HMEC intact Hi-C
experiment encode accession: ENCSR707XVJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB057VTC
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: intact Hi-C from HCT116 (ENCLB095OBI)

description:
https://www.encodeproject.org/experiments/ENCSR490HOI/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116-MED14-auxin untreated degon-intact
experiment encode accession: ENCSR490HOI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB095OBI
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 MED14

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS614TIF at ENCODE; https://www.encodeproject.org/ENCBS614TIF/

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


title: 1111- Day 1 3H

value: White blood cells

value: Saline Placebo


title: intact Hi-C from mammary epithelial cell (ENCLB340JHQ)

description:
https://www.encodeproject.org/experiments/ENCSR707XVJ/
***************
biological replicate number: 1
technical replicate number: 2
description: HMEC intact Hi-C
experiment encode accession: ENCSR707XVJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB340JHQ
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: mammary epithelial cell

value: female

value: adult


title: intact Hi-C from HCT116 (ENCLB455IIW)

description:
https://www.encodeproject.org/experiments/ENCSR490HOI/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116-MED14-auxin untreated degon-intact
experiment encode accession: ENCSR490HOI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB455IIW
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: intact Hi-C from right lobe of liver (ENCLB631OIA)

description:
https://www.encodeproject.org/experiments/ENCSR753CKM/
***************
biological replicate number: 1
technical replicate number: 1
description: w63 right lobe of liver intact HIC
experiment encode accession: ENCSR753CKM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB631OIA
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: right lobe of liver

value: tissue

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

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS462BTB at ENCODE; https://www.encodeproject.org/ENCBS462BTB/

value: derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: intact Hi-C from HCT116 (ENCLB338HOY)

description:
https://www.encodeproject.org/experiments/ENCSR481XZF/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 CDK7 degron untreated intact mnase
experiment encode accession: ENCSR481XZF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB338HOY
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 CDK7

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: ENCBS657VWI at ENCODE; https://www.encodeproject.org/ENCBS657VWI/


title: intact Hi-C from HCT116 (ENCLB782WPN)

description:
https://www.encodeproject.org/experiments/ENCSR490HOI/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-MED14-auxin untreated degon-intact
experiment encode accession: ENCSR490HOI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB782WPN
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: ENCBS614TIF at ENCODE; https://www.encodeproject.org/ENCBS614TIF/

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


title: intact Hi-C from HCT116 (ENCLB187KLS)

description:
https://www.encodeproject.org/experiments/ENCSR481XZF/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116 CDK7 degron untreated intact mnase
experiment encode accession: ENCSR481XZF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB187KLS
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 left lung (ENCLB184LIS)

description:
https://www.encodeproject.org/experiments/ENCSR892BZA/
***************
biological replicate number: 1
technical replicate number: 1
description: w62-left-lung intact HiC
experiment encode accession: ENCSR892BZA
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB184LIS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: left lung

value: tissue

value: female

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

value: child

value: 16 year

value: ENCBS740TAF at ENCODE; https://www.encodeproject.org/ENCBS740TAF/

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


title: intact Hi-C from HCT116 (ENCLB170HRJ)

description:
https://www.encodeproject.org/experiments/ENCSR481XZF/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 CDK7 degron untreated intact mnase
experiment encode accession: ENCSR481XZF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB170HRJ
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: male


title: intact Hi-C from adrenal gland (ENCLB992OBO)

description:
https://www.encodeproject.org/experiments/ENCSR898ANZ/
***************
biological replicate number: 1
technical replicate number: 2
description: W61 adrenal gland intact dnase hic
experiment encode accession: ENCSR898ANZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB992OBO
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: adrenal gland

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS947QBF at ENCODE; https://www.encodeproject.org/ENCBS947QBF/

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


title: intact Hi-C from spleen (ENCLB111IHF)

description:
https://www.encodeproject.org/experiments/ENCSR692QWS/
***************
biological replicate number: 1
technical replicate number: 1
description: w80 spleen permafrost intact dnase hic
experiment encode accession: ENCSR692QWS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB111IHF
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 (61 years) spleen tissue, preserved by flash-freezing

value: spleen

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: ENCBS920YAO at ENCODE; https://www.encodeproject.org/ENCBS920YAO/

value: derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: intact Hi-C from spleen (ENCLB042XAY)

description:
https://www.encodeproject.org/experiments/ENCSR692QWS/
***************
biological replicate number: 1
technical replicate number: 2
description: w80 spleen permafrost intact dnase hic
experiment encode accession: ENCSR692QWS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB042XAY
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: female


title: intact Hi-C from HepG2 (ENCLB740OBC)

description:
https://www.encodeproject.org/experiments/ENCSR888DEJ/
***************
biological replicate number: 1
technical replicate number: 2
description: HepG2 intact Hi-C
experiment encode accession: ENCSR888DEJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB740OBC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HepG2 cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS285MXI at ENCODE; https://www.encodeproject.org/ENCBS285MXI/

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


title: intact Hi-C from HepG2 (ENCLB009YAO)

description:
https://www.encodeproject.org/experiments/ENCSR888DEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: HepG2 intact Hi-C
experiment encode accession: ENCSR888DEJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB009YAO
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: male


title: intact Hi-C from HepG2 (ENCLB567NSJ)

description:
https://www.encodeproject.org/experiments/ENCSR888DEJ/
***************
biological replicate number: 1
technical replicate number: 3
description: HepG2 intact Hi-C
experiment encode accession: ENCSR888DEJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB567NSJ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: intact Hi-C from K562 (ENCLB829MAM)

description:
https://www.encodeproject.org/experiments/ENCSR479XDG/
***************
biological replicate number: 2
technical replicate number: 1
description: K562 intact Hi-C
experiment encode accession: ENCSR479XDG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB829MAM
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 800000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens K562 cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS671OWM at ENCODE; https://www.encodeproject.org/ENCBS671OWM/

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


title: intact Hi-C from mammary epithelial cell (ENCLB137IKJ)

description:
https://www.encodeproject.org/experiments/ENCSR707XVJ/
***************
biological replicate number: 1
technical replicate number: 3
description: HMEC intact Hi-C
experiment encode accession: ENCSR707XVJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB137IKJ
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: mammary epithelial cell

value: primary cell

value: adult

value: 19 year

value: Lonza

value: ENCBS131DIO at ENCODE; https://www.encodeproject.org/ENCBS131DIO/

value: derived from ENCODE donor ENCDO955XOD; https://www.encodeproject.org/ENCDO955XOD/


title: intact Hi-C from K562 (ENCLB421YRC)

description:
https://www.encodeproject.org/experiments/ENCSR479XDG/
***************
biological replicate number: 1
technical replicate number: 2
description: K562 intact Hi-C
experiment encode accession: ENCSR479XDG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB421YRC
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: female

value: Mats Ljungman, UMichigan

value: ENCBS104XTA at ENCODE; https://www.encodeproject.org/ENCBS104XTA/


title: intact Hi-C from K562 (ENCLB717SFJ)

description:
https://www.encodeproject.org/experiments/ENCSR479XDG/
***************
biological replicate number: 2
technical replicate number: 5
description: K562 intact Hi-C
experiment encode accession: ENCSR479XDG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB717SFJ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 800000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: ATCC


title: intact Hi-C from K562 (ENCLB208VEP)

description:
https://www.encodeproject.org/experiments/ENCSR479XDG/
***************
biological replicate number: 2
technical replicate number: 2
description: K562 intact Hi-C
experiment encode accession: ENCSR479XDG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB208VEP
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 800000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line


title: intact Hi-C from K562 (ENCLB045FEA)

description:
https://www.encodeproject.org/experiments/ENCSR479XDG/
***************
biological replicate number: 2
technical replicate number: 3
description: K562 intact Hi-C
experiment encode accession: ENCSR479XDG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB045FEA
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 800000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: intact Hi-C from upper lobe of right lung (ENCLB199RLJ)

description:
https://www.encodeproject.org/experiments/ENCSR673UZF/
***************
biological replicate number: 1
technical replicate number: 4
description: W78 upper lobe of right lung intact HIC
experiment encode accession: ENCSR673UZF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB199RLJ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (60 years) upper lobe of right lung tissue, preserved by flash-freezing

value: upper lobe of right lung

value: tissue

value: male

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

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS562NYH at ENCODE; https://www.encodeproject.org/ENCBS562NYH/

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


title: intact Hi-C from upper lobe of right lung (ENCLB931HPJ)

description:
https://www.encodeproject.org/experiments/ENCSR673UZF/
***************
biological replicate number: 1
technical replicate number: 2
description: W78 upper lobe of right lung intact HIC
experiment encode accession: ENCSR673UZF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB931HPJ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: adult


title: intact Hi-C from upper lobe of right lung (ENCLB738FMD)

description:
https://www.encodeproject.org/experiments/ENCSR673UZF/
***************
biological replicate number: 1
technical replicate number: 3
description: W78 upper lobe of right lung intact HIC
experiment encode accession: ENCSR673UZF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB738FMD
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from HCT116 (ENCLB572CTH)

description:
https://www.encodeproject.org/experiments/ENCSR481XZF/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116 CDK7 degron untreated intact mnase
experiment encode accession: ENCSR481XZF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB572CTH
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

value: Dr. Masato Kanemaki

value: ENCBS657VWI at ENCODE; https://www.encodeproject.org/ENCBS657VWI/

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


title: intact Hi-C from K562 (ENCLB355TSW)

description:
https://www.encodeproject.org/experiments/ENCSR479XDG/
***************
biological replicate number: 2
technical replicate number: 6
description: K562 intact Hi-C
experiment encode accession: ENCSR479XDG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB355TSW
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: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS671OWM at ENCODE; https://www.encodeproject.org/ENCBS671OWM/

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


title: intact Hi-C from vagina (ENCLB880YKH)

description:
https://www.encodeproject.org/experiments/ENCSR886JAM/
***************
biological replicate number: 1
technical replicate number: 1
description: entex vagina intact dnase hic
experiment encode accession: ENCSR886JAM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB880YKH
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) vagina tissue

value: vagina

value: tissue

value: Kristin Ardlie

value: ENCBS007TEL at ENCODE; https://www.encodeproject.org/ENCBS007TEL/

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


title: intact Hi-C from HCT116 (ENCLB431ARB)

description:
https://www.encodeproject.org/experiments/ENCSR490HOI/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116-MED14-auxin untreated degon-intact
experiment encode accession: ENCSR490HOI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB431ARB
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

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: ENCBS614TIF at ENCODE; https://www.encodeproject.org/ENCBS614TIF/


title: intact Hi-C from HCT116 (ENCLB195ADA)

description:
https://www.encodeproject.org/experiments/ENCSR669VZH/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116-CTCF auxin treated intact HIC
experiment encode accession: ENCSR669VZH
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB195ADA
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 CTCF treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

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: ENCBS131GYJ at ENCODE; https://www.encodeproject.org/ENCBS131GYJ/

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


title: intact Hi-C from vagina (ENCLB481CTE)

description:
https://www.encodeproject.org/experiments/ENCSR886JAM/
***************
biological replicate number: 1
technical replicate number: 3
description: entex vagina intact dnase hic
experiment encode accession: ENCSR886JAM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB481CTE
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

value: 53 year


title: intact Hi-C from upper lobe of right lung (ENCLB297KFG)

description:
https://www.encodeproject.org/experiments/ENCSR673UZF/
***************
biological replicate number: 1
technical replicate number: 1
description: W78 upper lobe of right lung intact HIC
experiment encode accession: ENCSR673UZF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB297KFG
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: upper lobe of right lung

value: tissue

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

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS562NYH at ENCODE; https://www.encodeproject.org/ENCBS562NYH/

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


title: intact Hi-C from HCT116 (ENCLB243IIE)

description:
https://www.encodeproject.org/experiments/ENCSR669VZH/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116-CTCF auxin treated intact HIC
experiment encode accession: ENCSR669VZH
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB243IIE
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

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor


title: intact Hi-C from MCF-7 (ENCLB761AOJ)

description:
https://www.encodeproject.org/experiments/ENCSR660LPJ/
***************
biological replicate number: 1
technical replicate number: 2
description: MCF-7 intact Hi-C
experiment encode accession: ENCSR660LPJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB761AOJ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens MCF-7 cell line

value: cell line

value: breast cancer (adenocarcinoma)

value: 69 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS885VEP at ENCODE; https://www.encodeproject.org/ENCBS885VEP/

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


title: intact Hi-C from HCT116 (ENCLB432HOR)

description:
https://www.encodeproject.org/experiments/ENCSR669VZH/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-CTCF auxin treated intact HIC
experiment encode accession: ENCSR669VZH
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB432HOR
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: ENCBS131GYJ at ENCODE; https://www.encodeproject.org/ENCBS131GYJ/

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


title: intact Hi-C from HCT116 (ENCLB518JUA)

description:
https://www.encodeproject.org/experiments/ENCSR669VZH/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116-CTCF auxin treated intact HIC
experiment encode accession: ENCSR669VZH
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB518JUA
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: intact Hi-C from vagina (ENCLB510BZA)

description:
https://www.encodeproject.org/experiments/ENCSR886JAM/
***************
biological replicate number: 1
technical replicate number: 2
description: entex vagina intact dnase hic
experiment encode accession: ENCSR886JAM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB510BZA
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: vagina

value: tissue

value: female

value: 53 year

value: Kristin Ardlie

value: ENCBS007TEL at ENCODE; https://www.encodeproject.org/ENCBS007TEL/

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


title: intact Hi-C from MCF-7 (ENCLB367TCM)

description:
https://www.encodeproject.org/experiments/ENCSR660LPJ/
***************
biological replicate number: 1
technical replicate number: 3
description: MCF-7 intact Hi-C
experiment encode accession: ENCSR660LPJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB367TCM
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: breast cancer (adenocarcinoma)

value: adult


title: intact Hi-C from HCT116 (ENCLB431WUP)

description:
https://www.encodeproject.org/experiments/ENCSR477GZK/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116 intact Hi-C
experiment encode accession: ENCSR477GZK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB431WUP
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

value: male

value: colorectal carcinoma

value: 48 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS755DRE at ENCODE; https://www.encodeproject.org/ENCBS755DRE/


title: intact Hi-C from MCF-7 (ENCLB021WOW)

description:
https://www.encodeproject.org/experiments/ENCSR660LPJ/
***************
biological replicate number: 1
technical replicate number: 4
description: MCF-7 intact Hi-C
experiment encode accession: ENCSR660LPJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB021WOW
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: 69 year

value: ENCBS885VEP at ENCODE; https://www.encodeproject.org/ENCBS885VEP/

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


title: intact Hi-C from MCF-7 (ENCLB556RWF)

description:
https://www.encodeproject.org/experiments/ENCSR660LPJ/
***************
biological replicate number: 1
technical replicate number: 1
description: MCF-7 intact Hi-C
experiment encode accession: ENCSR660LPJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB556RWF
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: female


title: intact Hi-C from K562 (ENCLB796WKU)

description:
https://www.encodeproject.org/experiments/ENCSR479XDG/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 intact Hi-C
experiment encode accession: ENCSR479XDG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB796WKU
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: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS104XTA at ENCODE; https://www.encodeproject.org/ENCBS104XTA/

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


title: intact Hi-C from HCT116 (ENCLB853SCO)

description:
https://www.encodeproject.org/experiments/ENCSR477GZK/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 intact Hi-C
experiment encode accession: ENCSR477GZK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB853SCO
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1700000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: ENCBS885PGI at ENCODE; https://www.encodeproject.org/ENCBS885PGI/

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


title: intact Hi-C from HCT116 (ENCLB925WZX)

description:
https://www.encodeproject.org/experiments/ENCSR878JLT/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 BRD4 degron treated intact mnase
experiment encode accession: ENCSR878JLT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB925WZX
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 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: adult

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: ENCBS627EDW at ENCODE; https://www.encodeproject.org/ENCBS627EDW/


title: intact Hi-C from HCT116 (ENCLB143JLL)

description:
https://www.encodeproject.org/experiments/ENCSR878JLT/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116 BRD4 degron treated intact mnase
experiment encode accession: ENCSR878JLT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB143JLL
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


title: intact Hi-C from HCT116 (ENCLB395ZZP)

description:
https://www.encodeproject.org/experiments/ENCSR878JLT/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 BRD4 degron treated intact mnase
experiment encode accession: ENCSR878JLT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB395ZZP
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: intact Hi-C from HCT116 (ENCLB353SRK)

description:
https://www.encodeproject.org/experiments/ENCSR878JLT/
***************
biological replicate number: 1
technical replicate number: 5
description: HCT116 BRD4 degron treated intact mnase
experiment encode accession: ENCSR878JLT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB353SRK
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: intact Hi-C from HCT116 (ENCLB676XCN)

description:
https://www.encodeproject.org/experiments/ENCSR642MGQ/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 SMARCA5 auxin treated degron intact hic
experiment encode accession: ENCSR642MGQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB676XCN
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 SMARCA5 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: ENCBS253RUX at ENCODE; https://www.encodeproject.org/ENCBS253RUX/


title: intact Hi-C from HCT116 (ENCLB541FXC)

description:
https://www.encodeproject.org/experiments/ENCSR642MGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 SMARCA5 auxin treated degron intact hic
experiment encode accession: ENCSR642MGQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB541FXC
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: intact Hi-C from HCT116 (ENCLB998UZH)

description:
https://www.encodeproject.org/experiments/ENCSR642MGQ/
***************
biological replicate number: 1
technical replicate number: 6
description: HCT116 SMARCA5 auxin treated degron intact hic
experiment encode accession: ENCSR642MGQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB998UZH
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: intact Hi-C from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB861RXM)

description:
https://www.encodeproject.org/experiments/ENCSR458VJJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Naive CD4+ T cell (CD45RO-CCR7+) Intact Mnase
experiment encode accession: ENCSR458VJJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB861RXM
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) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: 43 year

value: Charles Lee

value: AllCells

value: ENCBS838JAJ at ENCODE; https://www.encodeproject.org/ENCBS838JAJ/

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


title: intact Hi-C from HCT116 (ENCLB697CQX)

description:
https://www.encodeproject.org/experiments/ENCSR642MGQ/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116 SMARCA5 auxin treated degron intact hic
experiment encode accession: ENCSR642MGQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB697CQX
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 (ENCLB897HFZ)

description:
https://www.encodeproject.org/experiments/ENCSR642MGQ/
***************
biological replicate number: 1
technical replicate number: 5
description: HCT116 SMARCA5 auxin treated degron intact hic
experiment encode accession: ENCSR642MGQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB897HFZ
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: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from HCT116 (ENCLB012YVG)

description:
https://www.encodeproject.org/experiments/ENCSR642MGQ/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116 SMARCA5 auxin treated degron intact hic
experiment encode accession: ENCSR642MGQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB012YVG
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


title: intact Hi-C from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB613MJI)

description:
https://www.encodeproject.org/experiments/ENCSR458VJJ/
***************
biological replicate number: 1
technical replicate number: 2
description: Naive CD4+ T cell (CD45RO-CCR7+) Intact Mnase
experiment encode accession: ENCSR458VJJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB613MJI
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 tibial artery (ENCLB753IFC)

description:
https://www.encodeproject.org/experiments/ENCSR601RFS/
***************
biological replicate number: 1
technical replicate number: 2
description: entex tibial artery intact dnase hic
experiment encode accession: ENCSR601RFS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB753IFC
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) tibial artery tissue

value: tibial artery

value: tissue

value: female

value: 53 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS075UOY at ENCODE; https://www.encodeproject.org/ENCBS075UOY/

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


title: intact Hi-C from tibial artery (ENCLB117UVE)

description:
https://www.encodeproject.org/experiments/ENCSR601RFS/
***************
biological replicate number: 1
technical replicate number: 1
description: entex tibial artery intact dnase hic
experiment encode accession: ENCSR601RFS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB117UVE
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 (ENCLB076RRG)

description:
https://www.encodeproject.org/experiments/ENCSR477GZK/
***************
biological replicate number: 2
technical replicate number: 2
description: HCT116 intact Hi-C
experiment encode accession: ENCSR477GZK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB076RRG
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: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS755DRE at ENCODE; https://www.encodeproject.org/ENCBS755DRE/


title: Shoot, Warm, 3hours, replicate 3 [Sh_180_Warm_3]

city: West Lafayette

first: Kranthi

last: Varala

state: IN

address: 625 Agriculture Mall Dr.

department: Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
Reads aligned to ITAG 3.2 with BBMap (v37.93) with default parameters
Reads assigned to features using the featureCounts program in the subread package.
Read counts were filtered to remove features with less than 0.5 RPM in at least 3 libraries and then normalized using the TMM function in edgeR
Assembly: ITAG3.2
Supplementary files format and content: Root_wO_TMM.txt contains the filtered, normalized read counts from root samples, that was used for statistical analysis
Supplementary files format and content: Shoot_wO_TMM.txt contains the filtered, normalized read counts from shoot samples, that was used for statistical analysis

organism: Solanum lycopersicum

source_name: Shoot

growth_protocol: Tomato seeds (L. M82 cultivar, TGRC accession: LA3475) were sterilized with 20% bleach solution for 20 minutes, rinsed thoroughly with deionized water, germinated on 1/2MS-media in Petri dishes in a growth chamber set at 24°C/20°C (day/night) with a photoperiod of 16h/8h (day/night) and a PAR of 100mol m-2s-1 for 7-days. Seedlings were then transferred to a hydroponics system containing Hoagland solution. The solution was renewed every 3 or 4 days and the pots were aerated for 2h/d, for 11-days.

extract_protocol: Total RNA was extracted from 15 shoot samples (two treatments + two timepoints +  three biological replicates + three time zero samples) and 9 root samples (two treatments + three biological replicates + three time zero samples) with RNeasy Plant Mini Kit (Qiagen, USA) following the manufacturer’s protocol. The quality and quantity of RNA were checked using the Nanodrop 1000 spectrophotometer (ThermoScientific, USA). RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies). All samples had RIN values >8. The RNA samples were processed, and sequencing libraries were generated using the Illumina TruSeq RNA Sample preparation kit for cDNA library preparation and sequenced on the Illumina HiSeq or NovaSeq platforms (150 cycles, paired end)

treatment_protocol: On the 18th day, tomato plants of nearly identical size were chosen and divided into two, equal groups and moved to fresh hydroponic containers 2.5 hours after the start of light cycle (i.e., Zeitgeber time (ZT) 2.5). One group remained at 24°C and the other group was transferred to 4°C in a cold-room. Both groups were exposed to light with a PAR of 100mmol m-2s-1.

value: Shoot

tag: genotype

value: Ambient


title: intact Hi-C from head of caudate nucleus (ENCLB557DIB)

description:
https://www.encodeproject.org/experiments/ENCSR874HTT/
***************
biological replicate number: 1
technical replicate number: 2
description: rush brain anterior caudate healthy intact dnase hic
experiment encode accession: ENCSR874HTT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB557DIB
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (89 years) head of caudate nucleus tissue

value: head of caudate nucleus

value: 89 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS713GNA at ENCODE; https://www.encodeproject.org/ENCBS713GNA/

value: Derived from ENCODE donor ENCDO707TUE; https://www.encodeproject.org/ENCDO707TUE/


title: intact Hi-C from head of caudate nucleus (ENCLB902TIP)

description:
https://www.encodeproject.org/experiments/ENCSR874HTT/
***************
biological replicate number: 1
technical replicate number: 1
description: rush brain anterior caudate healthy intact dnase hic
experiment encode accession: ENCSR874HTT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB902TIP
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: female

value: adult


title: intact Hi-C from heart right ventricle (ENCLB119WPT)

description:
https://www.encodeproject.org/experiments/ENCSR591SNM/
***************
biological replicate number: 1
technical replicate number: 2
description: w76-heart-right-ventricle intact dnase hic
experiment encode accession: ENCSR591SNM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB119WPT
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 (40 years) heart right ventricle tissue, preserved by flash-freezing

value: heart right ventricle

value: male

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

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS258NPW at ENCODE; https://www.encodeproject.org/ENCBS258NPW/

value: derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: intact Hi-C from Right ventricle myocardium superior (ENCLB928OYR)

description:
https://www.encodeproject.org/experiments/ENCSR476RFQ/
***************
biological replicate number: 1
technical replicate number: 2
description: w78-right-ventricle-myocardium-superior-intact dnase hic
experiment encode accession: ENCSR476RFQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB928OYR
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 (60 years) Right ventricle myocardium superior tissue, preserved by flash-freezing

value: Right ventricle myocardium superior

tag: note

value: Superior wall of right ventricle.

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

value: 60 year

value: ENCBS387NCX at ENCODE; https://www.encodeproject.org/ENCBS387NCX/

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


title: intact Hi-C from Right ventricle myocardium superior (ENCLB718HET)

description:
https://www.encodeproject.org/experiments/ENCSR476RFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: w78-right-ventricle-myocardium-superior-intact dnase hic
experiment encode accession: ENCSR476RFQ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB718HET
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


title: intact Hi-C from heart right ventricle (ENCLB767KYD)

description:
https://www.encodeproject.org/experiments/ENCSR591SNM/
***************
biological replicate number: 1
technical replicate number: 1
description: w76-heart-right-ventricle intact dnase hic
experiment encode accession: ENCSR591SNM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB767KYD
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: Shoot, Cold, 3hours, replicate 2 [Sh_180_Cold_2]

value: Shoot

value: Cold


title: intact Hi-C from HCT116 (ENCLB793FOO)

description:
https://www.encodeproject.org/experiments/ENCSR878JLT/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116 BRD4 degron treated intact mnase
experiment encode accession: ENCSR878JLT
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB793FOO
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

value: adult

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: ENCBS627EDW at ENCODE; https://www.encodeproject.org/ENCBS627EDW/

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


title: intact Hi-C from HCT116 (ENCLB235SPA)

description:
https://www.encodeproject.org/experiments/ENCSR477GZK/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 intact Hi-C
experiment encode accession: ENCSR477GZK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB235SPA
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1700000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: male

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS885PGI at ENCODE; https://www.encodeproject.org/ENCBS885PGI/


title: Shoot, Warm, 3hours, replicate 2 [Sh_180_Warm_2]

value: Ambient


title: Shoot, Cold, 3hours, replicate 3 [Sh_180_Cold_3]


title: intact Hi-C from Panc1 (ENCLB121IFD)

description:
https://www.encodeproject.org/experiments/ENCSR584RBV/
***************
biological replicate number: 1
technical replicate number: 3
description: Panc1 intact Hi-C
experiment encode accession: ENCSR584RBV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB121IFD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens Panc1 cell line

value: pancreatic carcinoma

value: 56 year

value: ENCBS036UTR at ENCODE; https://www.encodeproject.org/ENCBS036UTR/

value: derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/


title: intact Hi-C from adrenal gland (ENCLB256MVJ)

description:
https://www.encodeproject.org/experiments/ENCSR832NED/
***************
biological replicate number: 1
technical replicate number: 1
description: entex adrenal gland intact dnase
experiment encode accession: ENCSR832NED
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB256MVJ
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 (54 years) adrenal gland tissue

value: adrenal gland

value: tissue

value: 54 year

value: Ellen Gelfand

value: ENCBS673VJU at ENCODE; https://www.encodeproject.org/ENCBS673VJU/

value: derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Shoot, pretreatment, replicate 2 [Sh_000_2]

value: Shoot


title: Shoot, pretreatment, replicate 3 [Sh_000_3]


title: Shoot, pretreatment, replicate 1 [Sh_000_1]


title: intact Hi-C from Panc1 (ENCLB913GHM)

description:
https://www.encodeproject.org/experiments/ENCSR584RBV/
***************
biological replicate number: 1
technical replicate number: 1
description: Panc1 intact Hi-C
experiment encode accession: ENCSR584RBV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB913GHM
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: adult


title: intact Hi-C from adrenal gland (ENCLB627XNE)

description:
https://www.encodeproject.org/experiments/ENCSR832NED/
***************
biological replicate number: 1
technical replicate number: 2
description: entex adrenal gland intact dnase
experiment encode accession: ENCSR832NED
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB627XNE
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: male

value: Erez Aiden, Baylor


title: Root, Warm, 3hours, replicate 2 [Rt_180_Warm_2]

source_name: Root

value: Root


title: Shoot, Cold, 3hours, replicate 1 [Sh_180_Cold_1]

value: Cold


title: intact Hi-C from Panc1 (ENCLB247SKL)

description:
https://www.encodeproject.org/experiments/ENCSR584RBV/
***************
biological replicate number: 1
technical replicate number: 2
description: Panc1 intact Hi-C
experiment encode accession: ENCSR584RBV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB247SKL
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: pancreatic carcinoma

value: Mats Ljungman, UMichigan

value: ATCC


title: Root, Warm, 3hours, replicate 3 [Rt_180_Warm_3]

value: Ambient


title: intact Hi-C from dendritic cell (ENCLB052UEN)

description:
https://www.encodeproject.org/experiments/ENCSR456QYU/
***************
biological replicate number: 1
technical replicate number: 1
description: Monocytes Dendritic cell day 4 LP23 intact mnase HiC
experiment encode accession: ENCSR456QYU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB052UEN
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) dendritic primary cell treated with 50 ng/mL granulocyte-macrophage colony-stimulating factor for 4 days, 40 ng/mL Interleukin-4 for 4 days

value: dendritic cell

value: primary cell

value: 51 year

value: Charles Lee

value: AllCells

value: treatment_term_id:UniProtKB:P04141; treatment_term_name:granulocyte-macrophage colony-stimulating factor; treatment_type:protein; duration:4; duration_units:day; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:4; duration_units:day;

value: ENCBS401CSG at ENCODE; https://www.encodeproject.org/ENCBS401CSG/

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


title: Root, Warm, 3hours, replicate 1 [Rt_180_Warm_1]


title: intact Hi-C from dendritic cell (ENCLB831ETN)

description:
https://www.encodeproject.org/experiments/ENCSR456QYU/
***************
biological replicate number: 1
technical replicate number: 2
description: Monocytes Dendritic cell day 4 LP23 intact mnase HiC
experiment encode accession: ENCSR456QYU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB831ETN
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 activated T-helper 2 cell (ENCLB430UQX)

description:
https://www.encodeproject.org/experiments/ENCSR474VTW/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD4+ T cell Th2 effector _activated intact mnase
experiment encode accession: ENCSR474VTW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB430UQX
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) activated T-helper 2 primary cell treated with Interferon-gamma ab for 36h, anti-CD3 and anti-CD28 coated beads for 24h, Interleukin-2 for 14d, anti-CD3 and anti-CD28 coated beads for 14d,  Interleukin-4 for 36h

value: activated T-helper 2 cell

value: male

value: 35 year

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; duration:36; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:14; duration_units:day; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:36; duration_units:hour;

value: ENCBS408YDW at ENCODE; https://www.encodeproject.org/ENCBS408YDW/

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


title: Root, Cold, 3hours, replicate 3 [Rt_180_Cold_3]

value: Root

value: Cold


title: intact Hi-C from A673 (ENCLB719RBU)

description:
https://www.encodeproject.org/experiments/ENCSR455KLX/
***************
biological replicate number: 1
technical replicate number: 3
description: A673 intact Hi-C
experiment encode accession: ENCSR455KLX
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB719RBU
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 A673 cell line

value: cell line

value: female

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS007DTL at ENCODE; https://www.encodeproject.org/ENCBS007DTL/

value: derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: Shoot, Warm, 3hours, replicate 1 [Sh_180_Warm_1]

value: Shoot

value: Ambient


title: Root, Cold, 3hours, replicate 2 [Rt_180_Cold_2]


title: intact Hi-C from A673 (ENCLB271ZKE)

description:
https://www.encodeproject.org/experiments/ENCSR455KLX/
***************
biological replicate number: 1
technical replicate number: 1
description: A673 intact Hi-C
experiment encode accession: ENCSR455KLX
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB271ZKE
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1300000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: Root, Cold, 3hours, replicate 1 [Rt_180_Cold_1]


title: Root, pretreatment, replicate 3 [Rt_000_3]


title: intact Hi-C from T-helper 2 cell (ENCLB197KAQ)

description:
https://www.encodeproject.org/experiments/ENCSR832CKD/
***************
biological replicate number: 1
technical replicate number: 2
description: naive CD4+ T cell Th2 effector resting intact mnase
experiment encode accession: ENCSR832CKD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB197KAQ
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) T-helper 2 primary cell treated with 100 ng/mL Interleukin-4 for 36 hours, 5ug/mL Interferon-gamma antibody for 36 hours

value: T-helper 2 cell

value: primary cell

value: male

value: adult

value: Charles Lee

value: AllCells

value: treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:36; duration_units:hour; treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS222HMB at ENCODE; https://www.encodeproject.org/ENCBS222HMB/


title: intact Hi-C from A673 (ENCLB567ODO)

description:
https://www.encodeproject.org/experiments/ENCSR455KLX/
***************
biological replicate number: 1
technical replicate number: 2
description: A673 intact Hi-C
experiment encode accession: ENCSR455KLX
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB567ODO
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: cell line

value: female


title: Root, pretreatment, replicate 2 [Rt_000_2]

value: Root


title: Root, pretreatment, replicate 1 [Rt_000_1]


title: intact Hi-C from T-helper 2 cell (ENCLB641ZCV)

description:
https://www.encodeproject.org/experiments/ENCSR832CKD/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD4+ T cell Th2 effector resting intact mnase
experiment encode accession: ENCSR832CKD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB641ZCV
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: 35 year

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


title: intact Hi-C from activated T-helper 2 cell (ENCLB988VJC)

description:
https://www.encodeproject.org/experiments/ENCSR474VTW/
***************
biological replicate number: 1
technical replicate number: 2
description: naive CD4+ T cell Th2 effector _activated intact mnase
experiment encode accession: ENCSR474VTW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB988VJC
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: activated T-helper 2 cell

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; duration:36; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:14; duration_units:day; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:36; duration_units:hour;

value: ENCBS408YDW at ENCODE; https://www.encodeproject.org/ENCBS408YDW/


title: intact Hi-C from ascending aorta (ENCLB511VID)

description:
https://www.encodeproject.org/experiments/ENCSR464RYO/
***************
biological replicate number: 1
technical replicate number: 1
description: entex aorta intact dnase hic
experiment encode accession: ENCSR464RYO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB511VID
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) ascending aorta tissue

value: ascending aorta

value: tissue

value: 53 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS492AJV at ENCODE; https://www.encodeproject.org/ENCBS492AJV/

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


title: endothelial_ATACseq_uninjured_rep3

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

tag: cell type

value: endothelial cells

value: uninjured


title: endothelial_ATACseq_uninjured_rep2


title: endothelial_ATACseq_3dpa_rep2

value: 3 day post vetricular apex amputation


title: intact Hi-C from ascending aorta (ENCLB509ZZP)

description:
https://www.encodeproject.org/experiments/ENCSR464RYO/
***************
biological replicate number: 1
technical replicate number: 2
description: entex aorta intact dnase hic
experiment encode accession: ENCSR464RYO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB509ZZP
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

value: adult


title: endothelial_ATACseq_uninjued_rep1


title: endothelial_ATACseq_3dpa_rep3


title: endothelial_ATACseq_1dpa_rep3

value: 1 day post vetricular apex amputation


title: endothelial_ATACseq_3dpa_rep1


title: intact Hi-C from Caco-2 (ENCLB554LEW)

description:
https://www.encodeproject.org/experiments/ENCSR820DYU/
***************
biological replicate number: 1
technical replicate number: 1
description: Caco-2 intact Hi-C
experiment encode accession: ENCSR820DYU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB554LEW
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens Caco-2 cell line

value: cell line

value: male

value: colorectal adenocarcinoma

value: 72 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS022WBK at ENCODE; https://www.encodeproject.org/ENCBS022WBK/

value: derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: intact Hi-C from Caco-2 (ENCLB173OXL)

description:
https://www.encodeproject.org/experiments/ENCSR820DYU/
***************
biological replicate number: 1
technical replicate number: 3
description: Caco-2 intact Hi-C
experiment encode accession: ENCSR820DYU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB173OXL
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: intact Hi-C from Caco-2 (ENCLB121SGK)

description:
https://www.encodeproject.org/experiments/ENCSR820DYU/
***************
biological replicate number: 1
technical replicate number: 4
description: Caco-2 intact Hi-C
experiment encode accession: ENCSR820DYU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB121SGK
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: intact Hi-C from stomach (ENCLB241ELN)

description:
https://www.encodeproject.org/experiments/ENCSR569OBN/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB241ELN
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: 53 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

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


title: endothelial_ATACseq_1dpa_rep2

value: Heart

value: endothelial cells


title: intact Hi-C from Caco-2 (ENCLB709IBO)

description:
https://www.encodeproject.org/experiments/ENCSR820DYU/
***************
biological replicate number: 1
technical replicate number: 2
description: Caco-2 intact Hi-C
experiment encode accession: ENCSR820DYU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB709IBO
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1900000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: adult