title: ProE, SRS, replicate 1

value: Proerythroblast

tag: day of differentiation


title: Control#2

status: Public on Jul 25 2023

type: SRA

city: Bunkyo-ku

first: Yuya

last: Nagaoka

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
To process Hi-C data, we used Juicer version 1.6 and Juicer tools version 2.13.07.
Sequenced reads were aligned to the reference mouse genome (mm10) by BWA version 0.7.17.
25-kbp resolution contact matrix with SCALE normalization was generated.
TADs (25-kbp resolution) and loops (5-kbp, 10-kbp and 25-kbp resolutions) were called by ArrowHead and HiCCUPS,  respectively.
Log-scaled relative contact frequency and insulation score (500-kbp distance) were calculated by CustardPy.
Assembly: mm10
Supplementary files format and content: .hic files were generated by juicertools with default parameters.
Supplementary files format and content: Control.hic, NUP98-HOXA9.hic and AG_mutant.hic were generated by merging fastq files from Arima-HiC-mouse-01 and Arima-HiC-mouse-02, Arima-HiC-mouse-03 and Arima-HiC-mouse-04 or Arima-HiC-mouse-05 and Arima-HiC-mouse-06.

molecule: genomic DNA

organism: Mus musculus

source_name: EB3-derived control stable cell line (Empty vector)

extract_protocol:
Cells were collected and crosslinked with 37% formaldehyde solution. DNA isolated from the crosslinked cells was digested with two restriction enzymes (^GATC and G^ANTC).
After incorporating biotinylated nucleotides into the digested DNA ends, both ends were ligated to spatially proximal ends. The ligated DNA was mechanically sheared into an average size of 400-500 bp and the ligation junctions were enriched with streptavidin magnetic beads. The sequencing libraries were prepared from enriched DNA fragments with a TruSeq DNA PCR-Free Library Prep Kit (Illumina) and amplified for 4 PCR cycles.

tag: cell line

tag: cell type

value: Mouse embryonic stem cells (mESCs)


title: ProE, SRS, replicate 3

city: Palo Alto

first: Tamar

middle: P

last: Feldman

state: CA

address: 240 Pasteur Dr

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Data were assessed for quality with FastQC. Adapters were trimmed using TrimGalore. BBTools suite was used to remove human and parasite rRNA reads.
Reads were aligned to a concatenation of the human (GRCh38) and Plasmodium (ASM276v2) genomes using STAR with default settings. Gene counts were generated by the -quantMode flag in STAR.
Assembly: GRCh38, ASM276v2
Supplementary files format and content: tab-delimited text file contains raw gene counts for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Proerythroblast

extract_protocol:
Cells were sorted directly into Buffer RLT (Qiagen) for total RNA extraction with the Rneasy Micro kit (Qiagen).
Paired-end libraries were prepared using the Tecan Trio RNA-seq for low-input samples on the Agilent BRAVO. Custom AnyDeplete probes (Tecan) were added against the human mitochondrial genome, HBB, EEFA1, MALAT1, and HSP90aa1.

value: Day 7

tag: treatment

value: SRS


title: 92_6LM_distant_2_weeks

type: RNA

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

hyb_protocol: Labelled RNA (300 ng) was then hybridized to SurePrint G3 Hmn GE 8x60K Microarrays (Cat. #: G4851A, Agilent Technologies) 60K whole mouse genome microarray gene expression chips (Agilent Technologies) in a rotating hybridization oven for 17 hours at 65°C.

scan_protocol: Microarray chips were washed, dried and scanned (Agilent Technologies, model G2505B) according to the manufacturer’s protocol (manual ID #G4140-90050).

data_processing: Microarray data were extracted using Feature Extraction Software v.9.5.3.1 (Agilent Technologies). Processing of the output files was done with the R Bioconductor package LIMMA. (Linear Models for Microarray Data), version 3.14.4. The raw data were normalized using half background correction (offset of 50), LOESS within array and quantile between array normalization

source_name: 4T1-2792, liver met, distant, 2 weeks

label_protocol: Extracted RNA (5 ng) or universal mouse reference RNA (Cat. #: 740100, Stratagene) was linearly amplified using the RiboAmp HS PLUS RNA Amplification Kit (Cat. #: KIT0525, Applied Biosystems) and profiles of amplified RNA (aRNA) were assessed using the 2100 Bioanalyzer platform (Agilent). Microdissected aRNA (5 μg) was then labelled with Cy3dye (Cat. #: KIT0609, Applied Biosystems) while universal mouse reference aRNA was labelled with Cy5dye (Cat. #: KIT0610, Applied Biosystems).

growth_protocol: All cell lines were grown in DMEM supplemented with 10% fetal bovine serum, 10 mmol/L HEPES, 1 mmol/L sodium pyruvate, 1.5 g/L sodium bicarbonate, penicillin/streptomycin, and fungizone.

extract_protocol: RNA was extracted from microdissected material  using a PicoPure RNA Isolation Kit  (Cat. #: KIT0204, Applied Biosystems).

treatment_protocol: 4T1-2776 and 4T1-2792 cells were inejcted into the mammary fat pad of Balb/c mice and grown as priamry tumors or were grown as metastasis in the liver after splenic injection. Tumor samples were harvested and processed for laser-capture microdissection.

tag: tissue

value: liver tissue

tag: gender

value: female


title: 92_4LM_margin_3_weeks

source_name: 4T1-2792, liver met, margin, 3 weeks

value: liver metastasis


title: ProE, Media, replicate 6

value: Media


title: Sorted Tcon cells Green_B1

city: La Jolla

first: Klaus

last: Ley

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Sorted Tcon cells

data_processing:
Illumina DRAGEN to convert BCL to fastq files and trime for adapters
Read count extraction and normalization were performed using STAR v.2.7.1 and DESeq2 v1.34
Assembly: GENCODE GRCh38.p13 and GENCODE GRCm39 respectively
Supplementary files format and content: Tab-delimited text files include count values for each sample and decoder included information on the sample

source_name: Tcons

extract_protocol:
Mouse Tregs, exTregs, Tcons, human Tregs, Tnaive and Th1 were directly sorted in 750uL of TRIzol LS (ThermoFisher). Next, RNA was extracted using the miRNeasy micro kit (Qiagen). RNA quality was measured by using 2100 TapeStation (Agilent  Technologies). Samples with high quality RNA (RNA integrity number >8.0) were used for the  next steps. Low-input human exTregs were sorted in duplicate (1,000 cells twice) in 20uL of  lysis buffer as described previously 25 .
For both TRIzol LS and low-input samples, double-  stranded (ds)-cDNA was prepared using the SuperScript II reverse transcriptase  (ThermoFisher) according to the manufacturer’s instructions. cDNA was amplified using 15  cycles and eluted in 24 μl. 100ng of resulting cDNA was processed using the Illumina DNA Prep  Kit (Cat#20018704, Illumina) following manufacturer’s instructions. Samples were pooled and  loaded onto an Illumina NovaSeq6000, and sequenced with 50 base pair paired-end reads  (PR50).

tag: tissue type

value: Lymph

value: Tcons


title: Sorted Tcon cells Green_B2

description: Sorted Tcon cells


title: ProE, Media, replicate 5


title: Sorted Tcon cells Green_B3

description: Sorted Tcon cells


title: 92_3LM_margin_3_weeks


title: ProE, SRS, replicate 4


title: ProE, Media, replicate 4


title: Sorted Tcon cells Green_B4

description: Sorted Tcon cells


title: 92_3LM_margin_2_weeks

source_name: 4T1-2792, liver met, margin, 2 weeks


title: ProE, Media, replicate 3


title: Sorted Tcon cells Green_A5

description: Sorted Tcon cells

value: Spleen


title: Sorted Tcon cells Green_B5

description: Sorted Tcon cells


title: 92_3LM_distant_2_weeks


title: 92_3LM_core_2_weeks

source_name: 4T1-2792, liver met, core, 2 weeks


title: Sorted Treg cells Green_C2

description: Sorted Treg cells

source_name: Tregs

value: Tregs


title: 92_3LM_core_3_weeks

source_name: 4T1-2792, liver met, core, 3 weeks


title: ProE, Media, replicate 1


title: ProE, Media, replicate 2


title: Sorted Treg cells Green_C1

description: Sorted Treg cells


title: Sorted Treg cells Green_C3

description: Sorted Treg cells


title: WSB_Tau-1

city: Indianapolis

first: Dominic

middle: James

last: Acri

state: Indiana

address: 320 W 15 St, NB Room 107

department: Stark Neurosciences Research Institute

institute: Indiana University School of Medicine

hyb_protocol: 75 ng of total RNA was hybridized for 16 hrs with capture probes and reporter probes from the neuroinflammation 757 standardized genes-targeted nCounter Gene Expression code set

scan_protocol: . After hybridization, the probe-target complexes were scanned by a fluorescence microscope and labeled barcodes were counted. Gene expression analysis was performed using the nCounter system (NanoString Technologies) according to the manufacturer's instructions

data_processing: Data were analyzed using nSolver Advanced analysis software (NanoString Technologies) with built-in quality control, normalization, and statistical analyses. First analysis was performed in nSolver for the effect of hTauP301L versus eGFP in each genetic background separately. Second analysis was performed for each genetic background versus B6 within hTauP301L injected mice only.

label: NanoString

source_name: cortex

label_protocol: standard NanoString protocol

extract_protocol: TRI-reagent

tag: Sex

value: Female

tag: injection

tag: genetic background

value: WSB


title: WSB_Tau-2


title: NCI-H1975 cells, shRB 3

city: Guangzhou

first: Ying

last: Zhang

address: No. 613, Huangpu Avenue West

country: China

institute: Jinan University First Affiliated Hospital

description:
Knockdown of RB1
shRB_3

data_processing:
The RNA concentration was measured using Thermo Scientific NanoDrop.
mRNA with polyA tails was selected and enriched using Oligo(dT) magnetic beads.
The mRNA was randomly fragmented using NEB Fragmentation Buffer, and NEBNext® UltraTM RNA Library Prep Kit was used for RNA library construction.
The library was preliminarily quantified using Qubit2.0 Fluorometer and the size of the insert fragment of the library was detected using Agilent 2100 bioanalyzer to ensure its quality.
Illumina sequencing was performed after the quality inspection of the library was completed.
Raw data were filtered, and sequence alignment was performed using HISAT2v2.0.5. The number of gene reads was calculated using featureCounts (version 1.5.0-p3)
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

growth_protocol: NCI-H1975 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent. ≥1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

value: Lung

value: lung adenocarcinoma cells

tag: genotype

value: RB1 knockdown

value: Knockdown of RB1


title: 92_4LM_core_3_weeks


title: 92_3LM_adjacent_2_weeks

source_name: 4T1-2792, liver met, adjacent, 2 weeks


title: WSB_Tau-3


title: WSB_GFP-3

value: eGFP


title: NCI-H1975 cells, shRB 2

description:
Knockdown of RB1
shRB_2


title: WSB_GFP-2


title: WSB_GFP-1


title: Sorted Treg cells Green_C4

description: Sorted Treg cells


title: CAST_Tau-3

value: CAST


title: NCI-H1975 cells, shRB 1

description:
Knockdown of RB1
shRB_1


title: CAST_Tau-2


title: Sorted Treg cells Green_C5

description: Sorted Treg cells


title: CAST_Tau-1


title: 92_10LM_distant_10_days

source_name: 4T1-2792, liver met, distant, 10 days


title: Sorted Treg cells Green_D1

description: Sorted Treg cells


title: NCI-H1975 cells, shControl 2

description:
Control
shNC_2

value: WT

value: Control


title: Sorted Treg cells Green_D2

description: Sorted Treg cells


title: 92_10LM_core_10_days

source_name: 4T1-2792, liver met, core, 10 days

value: female


title: Sorted Treg cells Green_D3

description: Sorted Treg cells


title: CAST_GFP-3


title: NCI-H1975 cells, shControl 1

description:
Control
shNC_1


title: CAST_GFP-1


title: CAST_GFP-2


title: Sorted Treg cells AF_TR5

description: Sorted Treg cells


title: PWK_Tau-3

value: PWK


title: PWK_Tau-2


title: 76_5LM_distant_2_weeks

source_name: 4T1-2776, liver met, distant, 2 weeks

value: liver tissue


title: 92_10LM_margin_2_weeks

value: liver metastasis


title: 92_10LM_adjacent_2_weeks


title: 76_5LM_distant_10_days

source_name: 4T1-2776, liver met, distant, 10 days


title: Sorted Treg cells AF_TR3

description: Sorted Treg cells


title: Sorted exTreg cells Red_A1

description: Sorted exTreg cells

source_name: exTregs

value: Lymph

value: exTregs


title: Sorted Treg cells AF_TR7

description: Sorted Treg cells

value: Tregs


title: 92_10LM_adjacent_10_days

source_name: 4T1-2792, liver met, adjacent, 10 days


title: 76_5LM_margin_2_weeks

source_name: 4T1-2776, liver met, margin, 2 weeks


title: 76_5LM_adjacent_2_weeks


title: Sorted exTreg cells Red_A3

description: Sorted exTreg cells


title: Sorted Treg cells AF_TR1

description: Sorted Treg cells


title: PWK_Tau-1

value: Female


title: NCI-H1975 cells, shControl 3

description:
Control
shNC_3


title: 92_10LM_core_2_weeks


title: Sorted Treg cells AF_TR4

description: Sorted Treg cells


title: 76_5LM_adjacent_10_days

source_name: 4T1-2776, liver met, adjacent, 10 days


title: 76_5LM_core_10_days

source_name: 4T1-2776, liver met, core, 10 days


title: Sorted exTreg cells Red_B3

description: Sorted exTreg cells

value: Spleen


title: Sorted exTreg cells Red_A4

description: Sorted exTreg cells


title: 76_4LM_margin_3_weeks

source_name: 4T1-2776, liver met, margin, 3 weeks


title: Sorted Treg cells AF_TR2

description: Sorted Treg cells


title: PWK_GFP-2


title: Sorted Treg cells AF_TR6

description: Sorted Treg cells


title: Sorted exTreg cells Red_A2

description: Sorted exTreg cells


title: Sorted exTreg cells Red_B1

description: Sorted exTreg cells


title: 76_4LM_margin_2_weeks


title: PWK_GFP-1


title: B6_Tau-3


title: B6_GFP-3


title: Sorted exTreg cells Red_B5

description: Sorted exTreg cells


title: Sorted exTreg cells Red_B2

description: Sorted exTreg cells


title: Sorted Naive cells AF_TN6

description: Sorted Naive cells

source_name: naive

value: naive


title: B6_Tau-2


title: Sorted Naive cells AF_TN5

description: Sorted Naive cells


title: 76_4LM_distant_2_weeks


title: Sorted Naive cells AF_TN7

description: Sorted Naive cells


title: PWK_GFP-3


title: Sorted Naive cells AF_TN4

description: Sorted Naive cells


title: 76_4LM_core_3_weeks

source_name: 4T1-2776, liver met, core, 3 weeks


title: Bulk RNAseq AKT+NICD ICC rep5

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Bulk RNAseq AKT+NICD ICC rep5

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference mm10 by STAR aligner (version 2.6.1a)
Gene count quantification by STAR aligner (option: --quantMode GeneCounts) (version 2.6.1a)
Assembly: mm10

source_name: liver

growth_protocol: Regular chow diet

extract_protocol:
Trizol protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: University of Pittsburgh animal protocol

tag: strain

value: Male

tag: age

value: 2 months

tag: model

value: human AKT+NICD ICC


title: Sorted exTreg cells Red_A5

description: Sorted exTreg cells


title: B6_Tau-1


title: 76_4LM_core_2_weeks

source_name: 4T1-2776, liver met, core, 2 weeks


title: Sorted Naive cells AF_TN3

description: Sorted Naive cells


title: Sorted exTreg cells Red_B4

description: Sorted exTreg cells


title: Bulk RNAseq AKT+NICD ICC rep4

description: Bulk RNAseq AKT+NICD ICC rep4


title: Bulk RNAseq AKT+NICD ICC rep3

description: Bulk RNAseq AKT+NICD ICC rep3


title: Sorted Naive cells AF_TN2

description: Sorted Naive cells


title: 76_4LM_adjacent_2_weeks

source_name: 4T1-2776, liver met, adjacent, 2 weeks


title: B6_GFP-2

source_name: cortex

value: eGFP


title: Sorted Naive cells AF_TN1

description: Sorted Naive cells


title: Sorted Th1 cells AF_TH7

description: Sorted Th1 cells


title: MH3 (muscle hypoxic quiet3)

city: Jinan

first: Qinglu

last: Wang

state: Shandong

address: 10600 Century Avenue

institute: Shandong Sport University

description: Musculature

data_processing:
Raw data for sequencing were assessed for quality by FastQC. Mass shearing by Trimmomatic yielded relatively accurate and valid data. Alignment of the sample valid data to the reference genome, the software was used to perform gene structure, expression levels, expression differences, gene enrichment analysis and so on.
Assembly: not provided
Supplementary files format and content: gene_expression.xlsx: Excel file includes raw counts, FPKM values, and TPM values for each Sample.

organism: Rattus norvegicus

source_name: gastrocnemius muscle

growth_protocol: Gastrocnemal muscle and epididymal adipose tissue were isolated from trophic obese rats.

extract_protocol:
Total RNA was harvested from gastrocnemius muscle and epididymal adipose tissue in obese rats using Trizol reagent. Following the assessment of the quality of the RNA and then analyzed on sequencing system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Rats were randomly divided into four groups after exercise training, such as normoxia quiet group, normoxia exercise group, hypoxic quiet group and hypoxia exercise group.

value: Sprague Dawley

tag: condition

value: Trophic obesity

value: gastrocnemius muscle

value: hypoxic quiet training


title: MH1 (muscle hypoxic quiet1)

description: Musculature


title: MH2 (muscle hypoxic quiet2)

description: Musculature


title: 76_3LM_distant_10_days

value: female


title: Bulk RNAseq AKT+NICD ICC rep1

description: Bulk RNAseq AKT+NICD ICC rep1


title: 76_3LM_core_10_days


title: Sorted Th1 cells AF_TH6

description: Sorted Th1 cells


title: Bulk RNAseq WT rep3

description: Bulk RNAseq WT rep3

value: WT


title: Sorted Th1 cells AF_TH4

description: Sorted Th1 cells


title: Bulk RNAseq WT rep1

description: Bulk RNAseq WT rep1


title: MC3 (muscle normoxia quiet3)

description: Musculature

value: normoxia quiet training


title: VavCre+Jag1 f/f, 2

city: Chicago

first: Kostandin

middle: V

last: Pajcini

state: IL

address: 909 S Wolcott Ave.

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
NovaSeq optical duplicates were removed using the Clumpify.sh dedupe optical tool from the BBmap suite
Reads were aligned using STAR (version 2.7.6a)
Count tables were generated using featureCounts (Subread release 2.0.1)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Count

source_name: E14.5 Fetal Liver

extract_protocol:
2000 Fetal liver HSCs from E14.5 Jag1f/f, VavCre- and Jag1f/f, VavCre+ were sorted into RNA lysis buffer (Invitrogen) and stored at -80ºC until RNA extraction. Total RNA was extracted using PicoPure™ RNA Isolation Kit (ThemoFisher Scientific, USA) with inclusion of DNase treatment step.
RNA sequencing libraries for Illumina sequencing were prepared in one batch using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) along with negative and positive controls.

value: Mutant

tag: sorting gate


title: VavCre+Jag1 f/f, 3


title: MC2 (muscle normoxia quiet2)

description: Musculature


title: Bulk RNAseq WT rep2

description: Bulk RNAseq WT rep2


title: 76_1LM_margin_2_weeks

value: liver metastasis


title: MHE3 (muscle hypoxia exercise3)

description: Musculature

value: hypoxia exercise training


title: 76_3LM_core_3_weeks


title: Sorted Th1 cells AF_TH2

description: Sorted Th1 cells


title: Sorted Th1 cells AF_TH1

description: Sorted Th1 cells


title: MHE2 (muscle hypoxia exercise2)

description: Musculature


title: VavCre+Jag1 f/f, 1


title: Sorted Th1 cells AF_TH3

description: Sorted Th1 cells


title: MHE1 (muscle hypoxia exercise1)

description: Musculature


title: MC1 (muscle normoxia quiet1)

description: Musculature


title: Sorted Th1 cells AF_TH5

description: Sorted Th1 cells


title: Sorted exTreg cells AF_EXT7

description: Sorted exTreg cells

value: exTregs


title: 76_1LM_distant_2_weeks

value: liver tissue


title: VavCre-Jag1 f/f, 3


title: 76_3LM_margin_3_weeks


title: Bulk RNAseq AKT+NICD ICC rep2

description: Bulk RNAseq AKT+NICD ICC rep2


title: B6_GFP-1

value: Female


title: 76_3LM_adjacent_10_days


title: 76_1LM_margin_3_weeks


title: 76_1LM_distant_10_days


title: Sorted exTreg cells AF_EXT6

description: Sorted exTreg cells


title: VavCre-Jag1 f/f, 2


title: 76_1LM_core_3_weeks


title: MCE2 (muscle normoxia exercise2)

description: Musculature

value: Male

value: normoxia exercise training


title: MCE1 (muscle normoxia exercise1)

description: Musculature


title: 76_1LM_core_2_weeks


title: Sorted exTreg cells AF_EXT5

description: Sorted exTreg cells


title: MCE3 (muscle normoxia exercise3)

description: Musculature


title: FH3 (fat hypoxic quiet3)

source_name: epididymal adipose tissue

value: epididymal adipose tissue


title: Sorted exTreg cells AF_EXT4

description: Sorted exTreg cells


title: VavCre-Jag1 f/f, 1


title: 76_1LM_core_10_days


title: 76_1LM_adjacent_2_weeks


title: FH1 (fat hypoxic quiet1)


title: Sorted exTreg cells AF_EXT2

description: Sorted exTreg cells


title: Sorted exTreg cells AF_EXT1

description: Sorted exTreg cells


title: 76_1LM_adjacent_10_days


title: Sorted exTreg cells AF_EXT3

description: Sorted exTreg cells


title: RL2178_NeuN_invitro_RNAseq_rep2

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
mapping RNA reads to mm10 genome using HISAT2 v 2.1.0
sorting and indexing RNA bam files using SAMtools v 1.9
BPM normalization of RNA bam files with deepTools v 3.3.1 bamCoverage function
generating GTF files for TPM values using stringtie v 1.3.3.3b
Genome_build: mm10
Supplementary_files_format_and_content: GTF files containing normalized expression values for all genes covered by RNA-seq data

molecule: nuclear RNA

source_name: mESC-derived NeuN positive neurons day 38

growth_protocol: mESC cells lines R1 and G4 were maintained on gamma-irradiated mouse embryonic fibroblasts in mESC medium with LIF. Cells were fed daily and split based on confluency. Neural differentiation was initiated by dissociating the mESC colonies using Accutase and excess feeder cells were removed from the cell suspensions by panning on gelatin-coated plates. Dissociated cells were counted and transferred to ultra-low attachment cell culture plates at a dilution of 220,000 cells/ml, in differentiation medium. Neural induction was continued for 8 days, medium was changed every two days, and supplemented with 5 µM retinoic acid for the final 4 days. Cell aggregates were dissociated using Accutase, single cell selected through a 40 µm cell strainer, and plated onto poly-ornithine / laminin-coated plates in N2 medium. After 2 days, cells were changed into N2B27 which was changed every 4 days for 12 days, following which 50% media changes were performed for the remaining culture time.

extract_protocol:
Genomic DNA: Quiagen Blood and Tissue DNA Extraction kit with extended Proteinase K and RNAsA treatment steps. Total RNA: hot trizol RNA extraction on NeuN-sorted nuclei and DNAse I treatment.
Lucigen Nxseq Ampfree Low DNA Library Kit and Zymo EZ DNA Methylation Direct Kit for MethylC libraries. TruSeq stranded mRNA library prep kit with TruSeq unique dual index adapters for RNA-seq libraries.

treatment_protocol: High potassium-mediated depolarisation was performed by washing cells with low K+ buffer, transferring to high K+ buffer for 5 min, washed again in low K+ buffer and either harvested directly for RNA, immediately fixed for ICC, or chased in growth medium for the appropriate times prior to fixation or RNA extraction.

tag: cell culture

value: in vitro

value: 38 days


title: 1043_tumor_margin

source_name: 4T1-2776, primary tumor, margin

value: mammary fat pad tumor


title: FC1 (fat normoxia quiet1)

value: Sprague Dawley

value: Trophic obesity


title: FC3 (fat normoxia quiet3)


title: RL2177_NeuN_invitro_RNAseq_rep1

value: mESC-derived NeuN positive neurons day 38


title: FC2 (fat normoxia quiet2)


title: RL2143_NeuN_invitro_methylC_rep3

description: ESCs sorted for Nanog positive

data_processing:
Library strategy: Methyl-C-Seq
MethylC adapter trimming using Methpipe pipeline as described in Lister et al Science 2013
mapping MethylC reads to mm10 genome using Bowtie  as described in Lister et al Science 2013
merging mapped runs, convert to .slam, sort, collapse, trim reads using Methpipe pipeline as described in Lister et al Science 2013
stack creation and hammer correction using Methpipe pipeline as described in Lister et al Science 2013
make allC tables and count global statistics using Methpipe pipeline as described in Lister et al Science 2013
convert stacks to bedgraph files using simple awk script
generate bigwigs using bedgraphtobigwig v4
calling differentially methylated regions between in vitro and in vivo MethylC datasets using HOME v. 1.0
Genome_build: mm10
Supplementary_files_format_and_content: stacks.txt files containing all mapped methylated and total cytosines, bigWigs for coverage containing all mapped cytosines, bigWigs for mC containing percentage of methylated cytosines for contexts CG and CH
Supplementary_files_format_and_content: DMRs.txt files contain location of DMRs and confidence scores with positive values indicating higher methylation in vitro and negative values indicating higher methylation in vivo.


title: RL2142_NeuN_invitro_methylC_rep2

description: ESC-derived wild type neural differentiation, sorted NeuN negative fraction


title: 1043_tumor_core

source_name: 4T1-2776, primary tumor, core

value: female


title: ATAC-seq on MDA-MB-231 cells transfected with siRNA against Fra-1 rep3

city: Montpellier

first: Isabelle

last: Jariel-Encontre

state: Montpellier Cedex5

address: 208 Avenue des Apothicaires

country: France

institute: IRCM-U1194- INSERM

data_processing:
Reads were aligned to hg19 genome using Bowtie2 allowing no more than 2 mismatches and no multiple alignment sites.
Aligned reads were processed with R package PASHA (Fenouil et al., 2013; doi: 10.1093/bioinformatics/btw206) to eliminate PCR artefacts, extend reads to an estimated fragment length and generate WIG files.
R Package PASHA was used to normalize the WIG files to calculate the scores per million reads sequenced and Input DNA signal was subtracted from normalized WIG files.
The three biological replicates were then merged using UCSC bigWigMerge tool.
Assembly: Hg19
Supplementary files format and content: bigwig files of the 3 independent replicates for each conditoin (siCTL or siFra-1)
Supplementary files format and content: bigwig files of the merge of the 3 replicates for each condition

growth_protocol: MDA-MB-231 cells (ATCC, Rockville, MD, USA) were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each) in a humidified 5% CO2 atmosphere at 37°C. Cells freshly amplified and frozen after obtention from the ATCC were used every 3months and were routinely tested for the absence of mycoplasma contamination

extract_protocol:
Cells harvested and washed in PBS were resuspended in 100 µl of cold Cell Lysis Buffer (Tris-HCl pH 7.5 10 mM, NaCl 10 mM, MgCl2 3 mM and Igepal CA-630 0.1%). Lysed cells were centrifuged at 500 g at 4°C for 10 min and the pellets were then resuspended in 100 µl of the Transposase reaction mix (50 µl of 2X TD Buffer from Illumina, cat. n° 15027866) to which 5 µl Tn5 transposase (Illumina, cat. n° 15027865) and 45 µl of Nuclease-free water were added before an incubation of 30 minutes at 37°C. DNA was then purified using MinElute Qiagen columns (Qiagen cat. n° 28004) according to the manufacturer’s instructions
libraries were indexed using the Phusion® High-Fidelity DNA Polymerase (NEB cat. n° M0530)
Sequencing was performed using NovaSeq 6000 (Illumina) in paired-end (50 nt)

treatment_protocol: MDA-MB-231 cells were transfected with 4.5 nM of a control siRNA (Silencer® Negative Control N°1 siRNA, Ambion # AM4611) or 4.5 nM of a mix of 3 siRNA directed against Fra-1 (Tolza et al. 2019, Mol Cancer Research, DOI:10.1158/1541-7786.MCR-19-0036) for 72h before cells were haversted and ATAC seq performed as decribed in Buenrostro et al (2013) Nat. Methods 10, 1213, DOI10.1038/nmeth.2688, PMID 24097267

value: triple negative breast cancer


title: RL2179_NeuN_invitro_RNAseq_rep3


title: ATAC-seq on MDA-MB-231 cells transfected with siRNA against Fra-1 rep1


title: 1036_tumor_margin


title: FHE2 (fat hypoxia exercise2)


title: 1036_tumor_core


title: FHE3 (fat hypoxia exercise3)


title: RL383_NeuN_invitro_methylC_rep1

description: ESC-derived wild type neural differentiation, sorted NeuN positive fraction


title: 1034_tumor_margin


title: FCE2 (fat normoxia exercise2)


title: ATAC-seq on MDA-MB-231 cells  transfected with a control siRNA rep3

value: siCTL


title: 1034_tumor_core


title: FCE3 (fat normoxia exercise3)


title: 156OE, rep1

city: Piracicaba

first: Guilherme

middle: Bovi

last: Ambrosano

address: Av. Pádua Dias, 11

country: Brazil

institute: ESALQ

data_processing:
Trimming for adaptor sequence/low-quality sequence using Trimmomatic
rRNA removal using bbduk
Alignment to the tomato genome SL4.0 using hisat2
Duplicate removal using picard and samtools
Quantification using Salmon
Assembly: SL4.0 (SOLGENOMICS)
Supplementary files format and content: Quantification file output from Salmon (*.sf)
Supplementary files format and content: DGEList object with the data above (edgeRData.Rdata)

organism: Solanum lycopersicum

source_name: Floral apices and closed flower buds

extract_protocol:
Total RNA was treated with DNAse and reverse-transcribed to generate first-strand cDNA
Two total RNA replicates from each genotype were sent to construct RNA sequencing libraries

value: Floral apices and closed flower buds

value: MT overexpressing the miR156 (156OE)


title: 156OE, rep2


title: MT, rep1

value: MT


title: MT, rep2


title: ATAC-seq on MDA-MB-231 cells  transfected with a control siRNA rep1


title: ATAC-seq on MDA-MB-231 cells  transfected with a control siRNA rep2


title: intact Hi-C from right cardiac atrium (ENCLB488RDW)

status: Public on Jul 24 2023

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR994DPD/
***************
biological replicate number: 1
technical replicate number: 2
description: w76 right cardiac atrium intact dnase hic
experiment encode accession: ENCSR994DPD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB488RDW
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

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

source_name: Homo sapiens male adult (40 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

value: tissue

tag: biosample encode accession

tag: encode accession

value: male

tag: health state

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

tag: dev stage

value: adult

value: 40 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS620SDC at ENCODE; https://www.encodeproject.org/ENCBS620SDC/

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


title: intact Hi-C from heart left ventricle (ENCLB490MUV)

description:
https://www.encodeproject.org/experiments/ENCSR998LLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: uw67-heart-left-ventricle intact HiC
experiment encode accession: ENCSR998LLZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB490MUV
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 (66 years) heart left ventricle tissue

value: heart left ventricle

tag: Sex

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

value: 66 year

value: Shin Lin

value: ENCBS061ZSP at ENCODE; https://www.encodeproject.org/ENCBS061ZSP/

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


title: intact Hi-C from right cardiac atrium (ENCLB490WYI)

description:
https://www.encodeproject.org/experiments/ENCSR994DPD/
***************
biological replicate number: 1
technical replicate number: 1
description: w76 right cardiac atrium intact dnase hic
experiment encode accession: ENCSR994DPD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB490WYI
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 left cardiac atrium (ENCLB045WZF)

description:
https://www.encodeproject.org/experiments/ENCSR975NRV/
***************
biological replicate number: 1
technical replicate number: 2
description: w78 left cardiac atrium
experiment encode accession: ENCSR975NRV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB045WZF
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) left cardiac atrium tissue, preserved by flash-freezing

value: left cardiac atrium

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

value: 60 year

value: ENCBS791HHK at ENCODE; https://www.encodeproject.org/ENCBS791HHK/

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


title: intact Hi-C from heart left ventricle (ENCLB485EQD)

description:
https://www.encodeproject.org/experiments/ENCSR998LLZ/
***************
biological replicate number: 1
technical replicate number: 2
description: uw67-heart-left-ventricle intact HiC
experiment encode accession: ENCSR998LLZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB485EQD
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: male

value: adult


title: intact Hi-C from left colon (ENCLB490DAY)

description:
https://www.encodeproject.org/experiments/ENCSR972FIP/
***************
biological replicate number: 1
technical replicate number: 1
description: w72 left colon intact dnase hic
experiment encode accession: ENCSR972FIP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB490DAY
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 (46 years) left colon tissue, preserved by flash-freezing

value: left colon

value: female

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

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS812UUB at ENCODE; https://www.encodeproject.org/ENCBS812UUB/

value: derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: intact Hi-C from natural killer cell (ENCLB484DVD)

description:
https://www.encodeproject.org/experiments/ENCSR971CJS/
***************
biological replicate number: 1
technical replicate number: 1
description: NK intact Hi-C
experiment encode accession: ENCSR971CJS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB484DVD
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 (33 years) natural killer primary cell

value: natural killer cell

value: primary cell

value: 33 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS208JXH at ENCODE; https://www.encodeproject.org/ENCBS208JXH/

value: derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: intact Hi-C from left colon (ENCLB022XVC)

description:
https://www.encodeproject.org/experiments/ENCSR972FIP/
***************
biological replicate number: 1
technical replicate number: 2
description: w72 left colon intact dnase hic
experiment encode accession: ENCSR972FIP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB022XVC
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue


title: intact Hi-C from left cardiac atrium (ENCLB863PVH)

description:
https://www.encodeproject.org/experiments/ENCSR975NRV/
***************
biological replicate number: 1
technical replicate number: 1
description: w78 left cardiac atrium
experiment encode accession: ENCSR975NRV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB863PVH
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 cardiac atrium

value: male

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

value: adult

value: 60 year

value: ENCBS791HHK at ENCODE; https://www.encodeproject.org/ENCBS791HHK/

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


title: ATAC-seq on MDA-MB-231 cells transfected with siRNA against Fra-1 rep2

tag: cell line

tag: cell type

value: triple negative breast cancer

tag: treatment


title: intact Hi-C from natural killer cell (ENCLB839INL)

description:
https://www.encodeproject.org/experiments/ENCSR971CJS/
***************
biological replicate number: 1
technical replicate number: 3
description: NK intact Hi-C
experiment encode accession: ENCSR971CJS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB839INL
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 natural killer cell (ENCLB610PYK)

description:
https://www.encodeproject.org/experiments/ENCSR971CJS/
***************
biological replicate number: 1
technical replicate number: 2
description: NK intact Hi-C
experiment encode accession: ENCSR971CJS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB610PYK
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 mucosa of descending colon (ENCLB488CWU)

description:
https://www.encodeproject.org/experiments/ENCSR595UCM/
***************
biological replicate number: 1
technical replicate number: 2
description: W76 mucosa of descending colon
experiment encode accession: ENCSR595UCM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB488CWU
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (40 years) mucosa of descending colon tissue, preserved by flash-freezing

value: mucosa of descending colon

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

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS995QYA at ENCODE; https://www.encodeproject.org/ENCBS995QYA/

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


title: intact Hi-C from mucosa of descending colon (ENCLB398AEX)

description:
https://www.encodeproject.org/experiments/ENCSR595UCM/
***************
biological replicate number: 1
technical replicate number: 3
description: W76 mucosa of descending colon
experiment encode accession: ENCSR595UCM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB398AEX
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from prostate gland (ENCLB939GAM)

description:
https://www.encodeproject.org/experiments/ENCSR557QRO/
***************
biological replicate number: 1
technical replicate number: 2
description: entex prostate intact dnase hic
experiment encode accession: ENCSR557QRO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB939GAM
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) prostate gland tissue

value: prostate gland

value: 54 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS492XAH at ENCODE; https://www.encodeproject.org/ENCBS492XAH/

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


title: intact Hi-C from prostate gland (ENCLB952GQP)

description:
https://www.encodeproject.org/experiments/ENCSR557QRO/
***************
biological replicate number: 1
technical replicate number: 1
description: entex prostate intact dnase hic
experiment encode accession: ENCSR557QRO
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB952GQP
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: male

value: adult


title: intact Hi-C from mucosa of descending colon (ENCLB300KZJ)

description:
https://www.encodeproject.org/experiments/ENCSR595UCM/
***************
biological replicate number: 1
technical replicate number: 1
description: W76 mucosa of descending colon
experiment encode accession: ENCSR595UCM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB300KZJ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from posterior cingulate gyrus (ENCLB572HOZ)

description:
https://www.encodeproject.org/experiments/ENCSR968JCS/
***************
biological replicate number: 1
technical replicate number: 1
description: rush brain posterior cingulate gyrus healthy dnase hic
experiment encode accession: ENCSR968JCS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB572HOZ
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 (89 years) posterior cingulate gyrus tissue

value: posterior cingulate gyrus

value: female

value: 89 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS538BDR at ENCODE; https://www.encodeproject.org/ENCBS538BDR/

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


title: intact Hi-C from posterior cingulate gyrus (ENCLB973CUA)

description:
https://www.encodeproject.org/experiments/ENCSR968JCS/
***************
biological replicate number: 1
technical replicate number: 2
description: rush brain posterior cingulate gyrus healthy dnase hic
experiment encode accession: ENCSR968JCS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-03-15
lab: Erez Aiden, Baylor
library encode accession: ENCLB973CUA
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 heart left ventricle (ENCLB964ANM)

description:
https://www.encodeproject.org/experiments/ENCSR967VFA/
***************
biological replicate number: 1
technical replicate number: 1
description: uw076-heart-left-ventricle intact HiC
experiment encode accession: ENCSR967VFA
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB964ANM
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 (43 years) heart left ventricle tissue

value: heart left ventricle

value: nonischemic (EF 23%, LVEDD 6.1; RV moderate dilation, normal function)

value: 43 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS129GXC at ENCODE; https://www.encodeproject.org/ENCBS129GXC/

value: derived from ENCODE donor ENCDO967KID; https://www.encodeproject.org/ENCDO967KID/


title: intact Hi-C from heart left ventricle (ENCLB555TEV)

description:
https://www.encodeproject.org/experiments/ENCSR967VFA/
***************
biological replicate number: 1
technical replicate number: 2
description: uw076-heart-left-ventricle intact HiC
experiment encode accession: ENCSR967VFA
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB555TEV
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue


title: FCE1 (fat normoxia exercise1)

tag: strain

value: Sprague Dawley

value: Male

value: Trophic obesity

tag: tissue

value: epididymal adipose tissue

value: normoxia exercise training


title: intact Hi-C from cardiac septum (ENCLB593ZGN)

description:
https://www.encodeproject.org/experiments/ENCSR556QHB/
***************
biological replicate number: 1
technical replicate number: 2
description: w61 cardiac septum intact dnase hic
experiment encode accession: ENCSR556QHB
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB593ZGN
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) cardiac septum tissue

value: cardiac septum

value: female

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

value: adult

tag: age

value: 41 year

value: Yiing Lin, MD, PhD

value: ENCBS564WXW at ENCODE; https://www.encodeproject.org/ENCBS564WXW/

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


title: intact Hi-C from ovary (ENCLB693ODD)

description:
https://www.encodeproject.org/experiments/ENCSR872ZCP/
***************
biological replicate number: 1
technical replicate number: 1
description: w80-ovary intact HiC
experiment encode accession: ENCSR872ZCP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB693ODD
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) ovary tissue, preserved by flash-freezing

value: ovary

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

value: 61 year

value: Michael Snyder, Stanford

value: ENCBS959QTM at ENCODE; https://www.encodeproject.org/ENCBS959QTM/

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


title: intact Hi-C from ovary (ENCLB540PUJ)

description:
https://www.encodeproject.org/experiments/ENCSR872ZCP/
***************
biological replicate number: 1
technical replicate number: 2
description: w80-ovary intact HiC
experiment encode accession: ENCSR872ZCP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB540PUJ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue


title: intact Hi-C from cardiac septum (ENCLB767URQ)

description:
https://www.encodeproject.org/experiments/ENCSR556QHB/
***************
biological replicate number: 1
technical replicate number: 1
description: w61 cardiac septum intact dnase hic
experiment encode accession: ENCSR556QHB
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB767URQ
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 testis (ENCLB573ZJT)

description:
https://www.encodeproject.org/experiments/ENCSR870SXX/
***************
biological replicate number: 1
technical replicate number: 1
description: entex testis intact dnase hic
experiment encode accession: ENCSR870SXX
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB573ZJT
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) testis tissue

value: testis

value: male

value: 54 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS110JMD at ENCODE; https://www.encodeproject.org/ENCBS110JMD/

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


title: intact Hi-C from heart left ventricle (ENCLB901SQK)

description:
https://www.encodeproject.org/experiments/ENCSR942NSE/
***************
biological replicate number: 1
technical replicate number: 1
description: uw036-heart-left-ventricle intact HiC
experiment encode accession: ENCSR942NSE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB901SQK
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 (61 years) heart left ventricle tissue

value: heart left ventricle

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

value: adult

value: Shin Lin

value: ENCBS622IQQ at ENCODE; https://www.encodeproject.org/ENCBS622IQQ/

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


title: intact Hi-C from aorta (ENCLB750GTC)

description:
https://www.encodeproject.org/experiments/ENCSR554SLA/
***************
biological replicate number: 1
technical replicate number: 1
description: w73-aorta intact HiC
experiment encode accession: ENCSR554SLA
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB750GTC
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) aorta tissue, preserved by flash-freezing

value: aorta

value: female

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS872KJN at ENCODE; https://www.encodeproject.org/ENCBS872KJN/

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


title: intact Hi-C from heart left ventricle (ENCLB283YWT)

description:
https://www.encodeproject.org/experiments/ENCSR942NSE/
***************
biological replicate number: 1
technical replicate number: 2
description: uw036-heart-left-ventricle intact HiC
experiment encode accession: ENCSR942NSE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB283YWT
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: male

value: 61 year


title: intact Hi-C from PC-9 (ENCLB761PSX)

description:
https://www.encodeproject.org/experiments/ENCSR859DRK/
***************
biological replicate number: 1
technical replicate number: 5
description: PC9 intact Hi-C
experiment encode accession: ENCSR859DRK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB761PSX
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 PC-9 cell line

tag: line

value: cell line

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS829YOF at ENCODE; https://www.encodeproject.org/ENCBS829YOF/

value: derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: intact Hi-C from PC-9 (ENCLB707BJL)

description:
https://www.encodeproject.org/experiments/ENCSR859DRK/
***************
biological replicate number: 1
technical replicate number: 4
description: PC9 intact Hi-C
experiment encode accession: ENCSR859DRK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB707BJL
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: intact Hi-C from PC-9 (ENCLB750IEX)

description:
https://www.encodeproject.org/experiments/ENCSR859DRK/
***************
biological replicate number: 1
technical replicate number: 2
description: PC9 intact Hi-C
experiment encode accession: ENCSR859DRK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB750IEX
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: intact Hi-C from PC-9 (ENCLB037ELF)

description:
https://www.encodeproject.org/experiments/ENCSR859DRK/
***************
biological replicate number: 1
technical replicate number: 3
description: PC9 intact Hi-C
experiment encode accession: ENCSR859DRK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB037ELF
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: intact Hi-C from B cell (ENCLB082NLX)

description:
https://www.encodeproject.org/experiments/ENCSR847RHU/
***************
biological replicate number: 1
technical replicate number: 3
description: Bcell intact Hi-C
experiment encode accession: ENCSR847RHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB082NLX
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 (22 years) B primary cell

value: B cell

value: primary cell

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS570COZ at ENCODE; https://www.encodeproject.org/ENCBS570COZ/

value: derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: intact Hi-C from heart right ventricle (ENCLB984NXD)

description:
https://www.encodeproject.org/experiments/ENCSR941KKW/
***************
biological replicate number: 1
technical replicate number: 1
description: uw68 heart right ventricle
experiment encode accession: ENCSR941KKW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB984NXD
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 (56 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: female

value: PGD

value: 56 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS279NRP at ENCODE; https://www.encodeproject.org/ENCBS279NRP/

value: derived from ENCODE donor ENCDO907YUG; https://www.encodeproject.org/ENCDO907YUG/


title: intact Hi-C from PC-9 (ENCLB874ICT)

description:
https://www.encodeproject.org/experiments/ENCSR859DRK/
***************
biological replicate number: 1
technical replicate number: 1
description: PC9 intact Hi-C
experiment encode accession: ENCSR859DRK
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB874ICT
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: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS829YOF at ENCODE; https://www.encodeproject.org/ENCBS829YOF/

value: derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: intact Hi-C from B cell (ENCLB668APC)

description:
https://www.encodeproject.org/experiments/ENCSR847RHU/
***************
biological replicate number: 1
technical replicate number: 1
description: Bcell intact Hi-C
experiment encode accession: ENCSR847RHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB668APC
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: B cell

value: primary cell

value: male

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS570COZ at ENCODE; https://www.encodeproject.org/ENCBS570COZ/


title: intact Hi-C from B cell (ENCLB777ACA)

description:
https://www.encodeproject.org/experiments/ENCSR847RHU/
***************
biological replicate number: 1
technical replicate number: 6
description: Bcell intact Hi-C
experiment encode accession: ENCSR847RHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB777ACA
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 ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: intact Hi-C from aorta (ENCLB898FXW)

description:
https://www.encodeproject.org/experiments/ENCSR554SLA/
***************
biological replicate number: 1
technical replicate number: 2
description: w73-aorta intact HiC
experiment encode accession: ENCSR554SLA
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB898FXW
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: aorta

value: tissue

value: female

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS872KJN at ENCODE; https://www.encodeproject.org/ENCBS872KJN/

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


title: intact Hi-C from B cell (ENCLB815XUB)

description:
https://www.encodeproject.org/experiments/ENCSR847RHU/
***************
biological replicate number: 1
technical replicate number: 2
description: Bcell intact Hi-C
experiment encode accession: ENCSR847RHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB815XUB
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: B cell

value: primary cell


title: intact Hi-C from B cell (ENCLB021XIE)

description:
https://www.encodeproject.org/experiments/ENCSR847RHU/
***************
biological replicate number: 1
technical replicate number: 5
description: Bcell intact Hi-C
experiment encode accession: ENCSR847RHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB021XIE
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: adult


title: intact Hi-C from psoas muscle (ENCLB149TLS)

description:
https://www.encodeproject.org/experiments/ENCSR538PNC/
***************
biological replicate number: 1
technical replicate number: 2
description: W80 psoas muscle intact dnase hic
experiment encode accession: ENCSR538PNC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB149TLS
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) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

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

value: 61 year

value: ENCBS567WBB at ENCODE; https://www.encodeproject.org/ENCBS567WBB/

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


title: intact Hi-C from posterior vena cava (ENCLB927DHX)

description:
https://www.encodeproject.org/experiments/ENCSR941AMF/
***************
biological replicate number: 1
technical replicate number: 3
description: w73 posterior vena cava
experiment encode accession: ENCSR941AMF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB927DHX
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) posterior vena cava tissue, preserved by flash-freezing

value: posterior vena cava

value: tissue

value: ENCBS193ENT at ENCODE; https://www.encodeproject.org/ENCBS193ENT/


title: intact Hi-C from B cell (ENCLB151BYS)

description:
https://www.encodeproject.org/experiments/ENCSR847RHU/
***************
biological replicate number: 1
technical replicate number: 4
description: Bcell intact Hi-C
experiment encode accession: ENCSR847RHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB151BYS
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: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS570COZ at ENCODE; https://www.encodeproject.org/ENCBS570COZ/

value: derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: intact Hi-C from posterior vena cava (ENCLB832ENR)

description:
https://www.encodeproject.org/experiments/ENCSR941AMF/
***************
biological replicate number: 1
technical replicate number: 2
description: w73 posterior vena cava
experiment encode accession: ENCSR941AMF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB832ENR
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: female

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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


title: intact Hi-C from testis (ENCLB834QSS)

description:
https://www.encodeproject.org/experiments/ENCSR870SXX/
***************
biological replicate number: 1
technical replicate number: 2
description: entex testis intact dnase hic
experiment encode accession: ENCSR870SXX
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB834QSS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: testis

value: male

value: adult

value: 54 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS110JMD at ENCODE; https://www.encodeproject.org/ENCBS110JMD/

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


title: intact Hi-C from posterior vena cava (ENCLB399TFP)

description:
https://www.encodeproject.org/experiments/ENCSR941AMF/
***************
biological replicate number: 1
technical replicate number: 1
description: w73 posterior vena cava
experiment encode accession: ENCSR941AMF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB399TFP
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: posterior vena cava

value: tissue

value: ENCBS193ENT at ENCODE; https://www.encodeproject.org/ENCBS193ENT/


title: intact Hi-C from aorta (ENCLB078QSY)

description:
https://www.encodeproject.org/experiments/ENCSR797MWY/
***************
biological replicate number: 1
technical replicate number: 1
description: w61-aorta intact dnase HIC
experiment encode accession: ENCSR797MWY
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB078QSY
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) aorta tissue, preserved by flash-freezing

value: aorta

value: female

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

value: 41 year

value: ENCBS068FKD at ENCODE; https://www.encodeproject.org/ENCBS068FKD/

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


title: intact Hi-C from HCT116 (ENCLB059CBC)

description:
https://www.encodeproject.org/experiments/ENCSR533VUS/
***************
biological replicate number: 1
technical replicate number: 6
description: HCT116 Pol2RA auxin untreated degron intact mnase hic
experiment encode accession: ENCSR533VUS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB059CBC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A

value: cell line

value: colorectal carcinoma

value: 48 year

value: Dr. Masato Kanemaki

value: ENCBS455QGB at ENCODE; https://www.encodeproject.org/ENCBS455QGB/

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


title: intact Hi-C from HCT116 (ENCLB846YWS)

description:
https://www.encodeproject.org/experiments/ENCSR533VUS/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 Pol2RA auxin untreated degron intact mnase hic
experiment encode accession: ENCSR533VUS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB846YWS
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: adult

value: Erez Aiden, Baylor


title: intact Hi-C from HCT116 (ENCLB968KPN)

description:
https://www.encodeproject.org/experiments/ENCSR533VUS/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 Pol2RA auxin untreated degron intact mnase hic
experiment encode accession: ENCSR533VUS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB968KPN
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 (ENCLB722AOH)

description:
https://www.encodeproject.org/experiments/ENCSR533VUS/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116 Pol2RA auxin untreated degron intact mnase hic
experiment encode accession: ENCSR533VUS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB722AOH
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 (ENCLB702FNE)

description:
https://www.encodeproject.org/experiments/ENCSR533VUS/
***************
biological replicate number: 1
technical replicate number: 5
description: HCT116 Pol2RA auxin untreated degron intact mnase hic
experiment encode accession: ENCSR533VUS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB702FNE
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 heart right ventricle (ENCLB449RSW)

description:
https://www.encodeproject.org/experiments/ENCSR941KKW/
***************
biological replicate number: 1
technical replicate number: 2
description: uw68 heart right ventricle
experiment encode accession: ENCSR941KKW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB449RSW
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: PGD

value: 56 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS279NRP at ENCODE; https://www.encodeproject.org/ENCBS279NRP/

value: derived from ENCODE donor ENCDO907YUG; https://www.encodeproject.org/ENCDO907YUG/


title: intact Hi-C from HCT116 (ENCLB747FOI)

description:
https://www.encodeproject.org/experiments/ENCSR533VUS/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116 Pol2RA auxin untreated degron intact mnase hic
experiment encode accession: ENCSR533VUS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-02-01
lab: Erez Aiden, Baylor
library encode accession: ENCLB747FOI
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 aorta (ENCLB947JPA)

description:
https://www.encodeproject.org/experiments/ENCSR797MWY/
***************
biological replicate number: 1
technical replicate number: 2
description: w61-aorta intact dnase HIC
experiment encode accession: ENCSR797MWY
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB947JPA
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: aorta

value: female

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

value: 41 year

value: Yiing Lin, MD, PhD

value: ENCBS068FKD at ENCODE; https://www.encodeproject.org/ENCBS068FKD/

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


title: intact Hi-C from activated CD4-positive, alpha-beta T cell (ENCLB096DFZ)

description:
https://www.encodeproject.org/experiments/ENCSR923PPH/
***************
biological replicate number: 1
technical replicate number: 2
description: naive CD4+ T cell Th0 effector _activated intact mnase
experiment encode accession: ENCSR923PPH
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB096DFZ
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 CD4-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 for 14 days, anti-CD3 and anti-CD28 coated beads for 24 hours, anti-CD3 and anti-CD28 coated beads for 14 days

value: primary cell

value: male

value: adult

value: 35 year

value: Charles Lee

value: AllCells

tag: treatments

value: 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:24; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day;

value: ENCBS226EME at ENCODE; https://www.encodeproject.org/ENCBS226EME/

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


title: intact Hi-C from heart right ventricle (ENCLB918XYB)

description:
https://www.encodeproject.org/experiments/ENCSR530DID/
***************
biological replicate number: 1
technical replicate number: 2
description: uw076-heart-right-ventricle intact HiC
experiment encode accession: ENCSR530DID
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB918XYB
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 (43 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: nonischemic (EF 23%, LVEDD 6.1; RV moderate dilation, normal function)

value: 43 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS332OOL at ENCODE; https://www.encodeproject.org/ENCBS332OOL/

value: derived from ENCODE donor ENCDO967KID; https://www.encodeproject.org/ENCDO967KID/


title: intact Hi-C from heart right ventricle (ENCLB507KFU)

description:
https://www.encodeproject.org/experiments/ENCSR530DID/
***************
biological replicate number: 1
technical replicate number: 1
description: uw076-heart-right-ventricle intact HiC
experiment encode accession: ENCSR530DID
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB507KFU
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 endothelial cell of umbilical vein (ENCLB862RLN)

description:
https://www.encodeproject.org/experiments/ENCSR788FBI/
***************
biological replicate number: 1
technical replicate number: 2
description: HUVEC intact Hi-C
experiment encode accession: ENCSR788FBI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB862RLN
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 male newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: primary cell

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS045DGX at ENCODE; https://www.encodeproject.org/ENCBS045DGX/

value: derived from ENCODE donor ENCDO628LXZ; https://www.encodeproject.org/ENCDO628LXZ/


title: intact Hi-C from endothelial cell of umbilical vein (ENCLB541QYB)

description:
https://www.encodeproject.org/experiments/ENCSR788FBI/
***************
biological replicate number: 1
technical replicate number: 1
description: HUVEC intact Hi-C
experiment encode accession: ENCSR788FBI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB541QYB
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: male


title: intact Hi-C from endothelial cell of umbilical vein (ENCLB775GMB)

description:
https://www.encodeproject.org/experiments/ENCSR788FBI/
***************
biological replicate number: 1
technical replicate number: 4
description: HUVEC intact Hi-C
experiment encode accession: ENCSR788FBI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB775GMB
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: intact Hi-C from endothelial cell of umbilical vein (ENCLB578RCE)

description:
https://www.encodeproject.org/experiments/ENCSR788FBI/
***************
biological replicate number: 1
technical replicate number: 3
description: HUVEC intact Hi-C
experiment encode accession: ENCSR788FBI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB578RCE
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: intact Hi-C from Right ventricle myocardium inferior (ENCLB414VAH)

description:
https://www.encodeproject.org/experiments/ENCSR921BHU/
***************
biological replicate number: 1
technical replicate number: 3
description: W78 right ventricle myocardium inferior intact HIC
experiment encode accession: ENCSR921BHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB414VAH
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 4
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

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

value: Right ventricle myocardium inferior

tag: note

value: Inferior wall of right ventricle.

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

value: adult

value: 60 year

value: Yiing Lin, MD, PhD

value: ENCBS853AXZ at ENCODE; https://www.encodeproject.org/ENCBS853AXZ/

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


title: intact Hi-C from Right ventricle myocardium inferior (ENCLB161WQI)

description:
https://www.encodeproject.org/experiments/ENCSR921BHU/
***************
biological replicate number: 1
technical replicate number: 1
description: W78 right ventricle myocardium inferior intact HIC
experiment encode accession: ENCSR921BHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB161WQI
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 7
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

tag: biosample encode accession

value: Michael Snyder, Stanford


title: intact Hi-C from psoas muscle (ENCLB139SBH)

description:
https://www.encodeproject.org/experiments/ENCSR538PNC/
***************
biological replicate number: 1
technical replicate number: 1
description: W80 psoas muscle intact dnase hic
experiment encode accession: ENCSR538PNC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB139SBH
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: psoas muscle

tag: encode accession

value: female

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

value: 61 year

value: ENCBS567WBB at ENCODE; https://www.encodeproject.org/ENCBS567WBB/

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


title: intact Hi-C from ovary (ENCLB828SVQ)

description:
https://www.encodeproject.org/experiments/ENCSR782YIX/
***************
biological replicate number: 1
technical replicate number: 3
description: w73 ovary intact dnase hi-c
experiment encode accession: ENCSR782YIX
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB828SVQ
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) ovary tissue, preserved by flash-freezing

value: ovary

tag: health state

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

value: 59 year

value: ENCBS760ECF at ENCODE; https://www.encodeproject.org/ENCBS760ECF/

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


title: intact Hi-C from ovary (ENCLB171KWY)

description:
https://www.encodeproject.org/experiments/ENCSR782YIX/
***************
biological replicate number: 1
technical replicate number: 2
description: w73 ovary intact dnase hi-c
experiment encode accession: ENCSR782YIX
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB171KWY
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

tag: dev stage

value: adult


title: intact Hi-C from ovary (ENCLB138YJI)

description:
https://www.encodeproject.org/experiments/ENCSR782YIX/
***************
biological replicate number: 1
technical replicate number: 1
description: w73 ovary intact dnase hi-c
experiment encode accession: ENCSR782YIX
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB138YJI
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

tag: lab

value: Yiing Lin, MD, PhD


title: intact Hi-C from heart left ventricle (ENCLB071DYC)

description:
https://www.encodeproject.org/experiments/ENCSR529BKV/
***************
biological replicate number: 1
technical replicate number: 1
description: w72 heart left ventricle intact dnase hic
experiment encode accession: ENCSR529BKV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB071DYC
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 (46 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

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

value: 46 year

tag: source

value: ENCBS307CIW at ENCODE; https://www.encodeproject.org/ENCBS307CIW/

value: derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: intact Hi-C from heart left ventricle (ENCLB064WIS)

description:
https://www.encodeproject.org/experiments/ENCSR529BKV/
***************
biological replicate number: 1
technical replicate number: 2
description: w72 heart left ventricle intact dnase hic
experiment encode accession: ENCSR529BKV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB064WIS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: female

value: Michael Snyder, Stanford

tag: link


title: intact Hi-C from GM12878 (ENCLB628HEW)

description:
https://www.encodeproject.org/experiments/ENCSR916MFV/
***************
biological replicate number: 1
technical replicate number: 6
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: ENCLB628HEW
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

value: cell line

tag: Sex

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: intact Hi-C from GM12878 (ENCLB321FJG)

description:
https://www.encodeproject.org/experiments/ENCSR916MFV/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB321FJG
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 GM12878 (ENCLB516AHP)

description:
https://www.encodeproject.org/experiments/ENCSR916MFV/
***************
biological replicate number: 1
technical replicate number: 1
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: ENCLB516AHP
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 GM12878 (ENCLB264WKT)

description:
https://www.encodeproject.org/experiments/ENCSR916MFV/
***************
biological replicate number: 1
technical replicate number: 4
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: ENCLB264WKT
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 GM12878 (ENCLB756EYE)

description:
https://www.encodeproject.org/experiments/ENCSR916MFV/
***************
biological replicate number: 1
technical replicate number: 5
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: ENCLB756EYE
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 (ENCLB670FJB)

description:
https://www.encodeproject.org/experiments/ENCSR777YML/
***************
biological replicate number: 1
technical replicate number: 3
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: ENCLB670FJB
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: 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: intact Hi-C from heart left ventricle (ENCLB816HIY)

description:
https://www.encodeproject.org/experiments/ENCSR518LPK/
***************
biological replicate number: 1
technical replicate number: 1
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: ENCLB816HIY
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: adult

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 activated CD4-positive, alpha-beta T cell (ENCLB256PTU)

description:
https://www.encodeproject.org/experiments/ENCSR923PPH/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD4+ T cell Th0 effector _activated intact mnase
experiment encode accession: ENCSR923PPH
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB256PTU
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: primary cell

value: 35 year

value: Charles Lee

value: AllCells

value: 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:24; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:14; duration_units:day;

value: ENCBS226EME at ENCODE; https://www.encodeproject.org/ENCBS226EME/

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


title: intact Hi-C from HCT116 (ENCLB220FER)

description:
https://www.encodeproject.org/experiments/ENCSR777YML/
***************
biological replicate number: 1
technical replicate number: 4
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: ENCLB220FER
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

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki


title: intact Hi-C from HCT116 (ENCLB391UGD)

description:
https://www.encodeproject.org/experiments/ENCSR777YML/
***************
biological replicate number: 1
technical replicate number: 5
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: ENCLB391UGD
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

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

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


title: intact Hi-C from Right ventricle myocardium inferior (ENCLB564WIE)

description:
https://www.encodeproject.org/experiments/ENCSR921BHU/
***************
biological replicate number: 1
technical replicate number: 2
description: W78 right ventricle myocardium inferior intact HIC
experiment encode accession: ENCSR921BHU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB564WIE
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 2
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: Right ventricle myocardium inferior

value: tissue

value: Inferior wall of right ventricle.

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

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS853AXZ at ENCODE; https://www.encodeproject.org/ENCBS853AXZ/

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


title: intact Hi-C from heart right ventricle (ENCLB299FSU)

description:
https://www.encodeproject.org/experiments/ENCSR771MVF/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB299FSU
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 (73 years) heart right ventricle tissue

value: heart right ventricle

value: male

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

value: 73 year

value: Shin Lin

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 HCT116 (ENCLB968QAI)

description:
https://www.encodeproject.org/experiments/ENCSR777YML/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB968QAI
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: ENCBS719AUN at ENCODE; https://www.encodeproject.org/ENCBS719AUN/

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