title: Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCLB060CZS)

description:
https://www.encodeproject.org/experiments/ENCSR291JVD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR291JVD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR398KXE
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB060CZS

source_name: Homo sapiens male adult (42 years) CD4-positive naive resting alpha-beta T primary cell

value: primary cell

value: 42 year

value: John Stamatoyannopoulos

value: ENCBS706CSJ at ENCODE; https://www.encodeproject.org/ENCBS706CSJ/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: Sample 34 DNB

status: Public on Nov 04 2021

type: SRA

city: Eastbourne

first: Guan

last: Wang

address: 30 Carlisle Rd

department: School of Sport and Health Sciences

country: United Kingdom

institute: University of Brighton

library_source: transcriptomic

data_processing:
Base call files were generated by base-calling software implemented on the RNA-seq instruments, generating raw sequences for subsequent analysis.
Raw sequences were examined by FastQC for basic quality checks (e.g. per base sequence quality, adaptor content, and per base N content), FastQ Screen for detecting sample swaps or sample contamination, HISAT2 for alignment to the reference genomeassembly (GRCh38.p12) using the Ensembl 94 annotation prior to RseQC for read distribution analysis.
Salmon selective alignment was performed for transcriptome mapping, over a k-mer length of 31, along with --SeqBias and --gcBias flags switched on. The bioconductor package “tximport” was used to summarise transcript-level estimates to genes. DESeq2 was used for paired sample DGE analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts matrix for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Three milliliters of whole blood was collected from an antecubital vein using the Tempus Blood RNA tubes (Thermo Fisher Scientific, Waltham, MA, USA). Total RNA was isolated from the whole blood according to the manufacturer’s instructions (Tempus Spin RNA Isolation Kit, Thermo Fisher Scientific, Waltham, MA, USA). The purified total RNA was eluted in 90 μL elution buffer and stored in three aliquots at −80°C until further analysis.
Five hundred nanograms of total RNA was used for sequencing according to the Illumina TruSeq Stranded mRNA sample prep guide - high sample protocol (Illumina, San Diego, CA, USA). Briefly, mRNA molecules were purified using the poly-T oligo attached magnetic beads following which the mRNA was fragmented and primed for cDNA synthesis. A single “A” base was subsequently added to the 3-prime end of the synthesised blunt-ended cDNA and ligated with index adapters for hybridisation onto a flow cell. The DNA fragments with adapters on both ends were amplified via polymerase chain reaction to generate the final double-stranded cDNA (ds-cDNA) library followed by library validation and normalisation and pooling of the samples. Samples were sequenced at 2x75 bp read length to a depth aimed at approximately 64 M reads per sample on the Illumina NextSeq 500 (Illumina, San Diego, CA, USA). Four hundred nanograms of total RNA was used for sequencing on the MGI DNBSEQ-G400RS instrument (MGI, Shenzhen, China). Total RNA was first treated with Globin-Zero Gold Kit (Illumina, San Diego, CA, USA) for rRNA depletion and globin mRNA reduction. The ds-cDNA library preparation is in line with the Illumina RNA-seq protocol described above. The ds-cDNAs were then heat denatured and circularised by the splint oligo sequence to generate the single strand circle DNA followed by rolling circle replication to create DNA nanoballs (DNB) for processing on the MGI DNBSEQ-G400RS.

tag: age (year)

tag: Sex

value: Male

tag: disease state

value: Healthy

tag: time (day)


title: Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCLB779OED)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR291JVD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR291JVD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR398KXE
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB779OED

library_source: genomic

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

molecule: genomic DNA

tag: antibody

tag: biosample encode accession

value: male

tag: dev stage

value: adult

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: link


title: TF ChIP-seq from middle frontal area 46 (ENCLB800YNM)

description:
https://www.encodeproject.org/experiments/ENCSR211AFA/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment
experiment encode accession: ENCSR211AFA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR295FXG
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB800YNM
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: Rush University

value: ENCBS034DIU at ENCODE; https://www.encodeproject.org/ENCBS034DIU/

value: Derived from ENCODE donor ENCDO915WZE; https://www.encodeproject.org/ENCDO915WZE/


title: TF ChIP-seq from middle frontal area 46 (ENCLB919TGA)

description:
https://www.encodeproject.org/experiments/ENCSR378KET/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF TF ChIP-seq on middle frontal area 46 tissue male adult (83 years).
experiment encode accession: ENCSR378KET
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR058XPK
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919TGA
size range: 200-600

source_name: Homo sapiens male adult (83 years) middle frontal area 46 tissue

value: 83 year

value: ENCBS959TDJ at ENCODE; https://www.encodeproject.org/ENCBS959TDJ/

value: Derived from ENCODE donor ENCDO592ZWW; https://www.encodeproject.org/ENCDO592ZWW/


title: Sample 33 DNB


title: Sample 32 DNB

value: Base2 (0)


title: Sample 31 DNB

value: Male


title: Histone ChIP-seq from heart left ventricle (ENCLB433DSO)

description:
https://www.encodeproject.org/experiments/ENCSR208XKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on heart left ventricle tissue male adult (55 years).
experiment encode accession: ENCSR208XKJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR979YKY
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB433DSO
size range: 200-600

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

value: heart left ventricle

value: 55 year

value: Shin Lin

tag: health state

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

value: ENCBS471DJO at ENCODE; https://www.encodeproject.org/ENCBS471DJO/

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


title: TF ChIP-seq from middle frontal area 46 (ENCLB990PPD)

description:
https://www.encodeproject.org/experiments/ENCSR211AFA/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment
experiment encode accession: ENCSR211AFA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR295FXG
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB990PPD
size range: 200-600

value: CTCF

value: middle frontal area 46

value: tissue

value: adult

value: Bradley Bernstein, Broad


title: Sample 30 DNB

value: Healthy


title: Control ChIP-seq from heart left ventricle (ENCLB435PCQ)

description:
https://www.encodeproject.org/experiments/ENCSR109IWL/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on heart left ventricle tissue male adult (43 years).
experiment encode accession: ENCSR109IWL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB435PCQ
size range: 200-600

source_name: Homo sapiens male adult (43 years) heart left ventricle tissue

value: male

value: 43 year

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

value: ENCBS552CFU at ENCODE; https://www.encodeproject.org/ENCBS552CFU/

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


title: Histone ChIP-seq from heart left ventricle (ENCLB829HKT)

description:
https://www.encodeproject.org/experiments/ENCSR288QJI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on heart left ventricle tissue male adult (55 years).
experiment encode accession: ENCSR288QJI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR979YKY
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB829HKT
size range: 200-600

value: heart left ventricle


title: Histone ChIP-seq from heart right ventricle (ENCLB421QSZ)

description:
https://www.encodeproject.org/experiments/ENCSR379SOG/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K4me1 ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR379SOG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR049JKQ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB421QSZ
size range: 200-600

source_name: Homo sapiens female adult (59 years) heart right ventricle tissue

value: heart right ventricle

value: female

value: 59 year

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

value: ENCBS637BEQ at ENCODE; https://www.encodeproject.org/ENCBS637BEQ/

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


title: Sample 29 DNB

value: Male


title: Histone ChIP-seq from heart left ventricle (ENCLB647LYJ)

description:
https://www.encodeproject.org/experiments/ENCSR288QJI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on heart left ventricle tissue male adult (55 years).
experiment encode accession: ENCSR288QJI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR979YKY
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB647LYJ
size range: 200-600

value: tissue

value: 55 year

value: Shin Lin

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

value: ENCBS471DJO at ENCODE; https://www.encodeproject.org/ENCBS471DJO/

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


title: Control ChIP-seq from heart left ventricle (ENCLB821HKF)

description:
https://www.encodeproject.org/experiments/ENCSR109IWL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on heart left ventricle tissue male adult (43 years).
experiment encode accession: ENCSR109IWL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB821HKF
size range: 200-600

value: male

value: adult

value: 43 year

value: Bradley Bernstein, Broad

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


title: TF ChIP-seq from middle frontal area 46 (ENCLB427XEX)

description:
https://www.encodeproject.org/experiments/ENCSR378BVM/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR378BVM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR394ZWY
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB427XEX
size range: 200-600

source_name: Homo sapiens female adult (87 years) middle frontal area 46 tissue with mild cognitive impairment

value: CTCF

value: middle frontal area 46

value: female

value: 87 year

value: Rush University

value: ENCBS401VAK at ENCODE; https://www.encodeproject.org/ENCBS401VAK/

value: Derived from ENCODE donor ENCDO354SJE; https://www.encodeproject.org/ENCDO354SJE/


title: Sample 28 DNB

value: Male

value: Healthy


title: TF ChIP-seq from middle frontal area 46 (ENCLB684DFS)

description:
https://www.encodeproject.org/experiments/ENCSR378BVM/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR378BVM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR394ZWY
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB684DFS
size range: 200-600

value: tissue


title: Sample 27 DNB

value: Base2 (0)


title: Histone ChIP-seq from middle frontal area 46 (ENCLB744YXU)

description:
https://www.encodeproject.org/experiments/ENCSR207FYD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment
experiment encode accession: ENCSR207FYD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR891ZHA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB744YXU
size range: 200-600

value: 90 or above year

value: ENCBS693PDQ at ENCODE; https://www.encodeproject.org/ENCBS693PDQ/

value: Derived from ENCODE donor ENCDO033BMB; https://www.encodeproject.org/ENCDO033BMB/


title: Histone ChIP-seq from heart right ventricle (ENCLB461GXC)

description:
https://www.encodeproject.org/experiments/ENCSR377RPJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on heart right ventricle tissue female adult (56 years).
experiment encode accession: ENCSR377RPJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR278ACD
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB461GXC
size range: 200-600

source_name: Homo sapiens female adult (56 years) heart right ventricle tissue

value: heart right ventricle

value: adult

value: 56 year

value: Shin Lin

value: PGD

value: ENCBS664CKV at ENCODE; https://www.encodeproject.org/ENCBS664CKV/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB204ZMK)

description:
https://www.encodeproject.org/experiments/ENCSR207FYD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment
experiment encode accession: ENCSR207FYD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR891ZHA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB204ZMK
size range: 200-600

value: middle frontal area 46

value: female

value: Bradley Bernstein, Broad

value: Rush University


title: Sample 26 DNB

value: Male

value: Healthy


title: Histone ChIP-seq from heart right ventricle (ENCLB879VCU)

description:
https://www.encodeproject.org/experiments/ENCSR377RPJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on heart right ventricle tissue female adult (56 years).
experiment encode accession: ENCSR377RPJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR278ACD
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB879VCU
size range: 200-600

value: tissue


title: Histone ChIP-seq from heart left ventricle (ENCLB440VKS)

description:
https://www.encodeproject.org/experiments/ENCSR208XKJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on heart left ventricle tissue male adult (55 years).
experiment encode accession: ENCSR208XKJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR979YKY
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB440VKS
size range: 200-600

value: heart left ventricle

value: male

value: 55 year

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

value: ENCBS471DJO at ENCODE; https://www.encodeproject.org/ENCBS471DJO/

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


title: Sample 23 DNB


title: TF ChIP-seq from heart right ventricle (ENCLB298JAF)

description:
https://www.encodeproject.org/experiments/ENCSR376EOW/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF TF ChIP-seq on heart right ventricle tissue male adult (66 years).
experiment encode accession: ENCSR376EOW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR898WPF
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB298JAF
size range: 200-600

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

value: CTCF

value: heart right ventricle

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

value: adult

value: 66 year

value: Shin Lin

value: ENCBS948AHG at ENCODE; https://www.encodeproject.org/ENCBS948AHG/

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


title: Sample 25 DNB

value: Male


title: Mint-ChIP-seq from activated T-helper 1 cell (ENCLB074FBO)

description:
https://www.encodeproject.org/experiments/ENCSR102SOR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on activated T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR102SOR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR188HBL
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB074FBO

source_name: Homo sapiens male adult (35 years) activated T-helper 1 primary cell treated with 1 μg/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads

value: activated T-helper 1 cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS279ECG at ENCODE; https://www.encodeproject.org/ENCBS279ECG/

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


title: Sample 22 DNB

value: Healthy


title: Sample 24 DNB


title: TF ChIP-seq from middle frontal area 46 (ENCLB698UBI)

description:
https://www.encodeproject.org/experiments/ENCSR372JWF/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR372JWF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR714GKF
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB698UBI
size range: 200-600

source_name: Homo sapiens male adult (71 years) middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: tissue

value: male

value: 71 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS552CLR at ENCODE; https://www.encodeproject.org/ENCBS552CLR/

value: Derived from ENCODE donor ENCDO570AKP; https://www.encodeproject.org/ENCDO570AKP/


title: TF ChIP-seq from middle frontal area 46 (ENCLB827PFO)

description:
https://www.encodeproject.org/experiments/ENCSR372JWF/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR372JWF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR714GKF
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB827PFO
size range: 200-600

value: adult


title: Sample 21 DNB

value: Male


title: Histone ChIP-seq from heart right ventricle (ENCLB961ALN)

description:
https://www.encodeproject.org/experiments/ENCSR370LLS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on heart right ventricle tissue male adult (43 years).
experiment encode accession: ENCSR370LLS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481QDJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB961ALN
size range: 200-600

source_name: Homo sapiens male adult (43 years) heart right ventricle tissue

value: heart right ventricle

value: 43 year

value: Shin Lin

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

value: ENCBS096INK at ENCODE; https://www.encodeproject.org/ENCBS096INK/

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


title: Sample 20 DNB

value: Healthy


title: TF ChIP-seq from middle frontal area 46 (ENCLB414UFR)

description:
https://www.encodeproject.org/experiments/ENCSR369RRE/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR369RRE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR698YQL
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB414UFR
size range: 200-600

source_name: Homo sapiens female adult (74 years) middle frontal area 46 tissue with Alzheimer's disease

value: CTCF

value: middle frontal area 46

value: female

value: 74 year

value: ENCBS242LMI at ENCODE; https://www.encodeproject.org/ENCBS242LMI/

value: Derived from ENCODE donor ENCDO907CMO; https://www.encodeproject.org/ENCDO907CMO/


title: TF ChIP-seq from middle frontal area 46 (ENCLB152SYF)

description:
https://www.encodeproject.org/experiments/ENCSR369RRE/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR369RRE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR698YQL
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152SYF
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad

value: Rush University


title: TF ChIP-seq from middle frontal area 46 (ENCLB002OCB)

description:
https://www.encodeproject.org/experiments/ENCSR094PSL/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (88 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR094PSL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR291VCJ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB002OCB
size range: 200-600

source_name: Homo sapiens female adult (88 years) middle frontal area 46 tissue

value: adult

value: 88 year

value: ENCBS844HXF at ENCODE; https://www.encodeproject.org/ENCBS844HXF/

value: Derived from ENCODE donor ENCDO669IVL; https://www.encodeproject.org/ENCDO669IVL/


title: Sample 19 DNB

value: Male


title: TF ChIP-seq from middle frontal area 46 (ENCLB248QLQ)

description:
https://www.encodeproject.org/experiments/ENCSR094PSL/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (88 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR094PSL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR291VCJ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB248QLQ
size range: 200-600


title: Sample 18 DNB


title: TF ChIP-seq from heart right ventricle (ENCLB268HBA)

description:
https://www.encodeproject.org/experiments/ENCSR376EOW/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF TF ChIP-seq on heart right ventricle tissue male adult (66 years).
experiment encode accession: ENCSR376EOW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR898WPF
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB268HBA
size range: 200-600

value: heart right ventricle

value: male

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

value: 66 year

value: Shin Lin

value: ENCBS948AHG at ENCODE; https://www.encodeproject.org/ENCBS948AHG/

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


title: Mint-ChIP-seq from activated T-helper 1 cell (ENCLB764TOS)

description:
https://www.encodeproject.org/experiments/ENCSR102SOR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on activated T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR102SOR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR188HBL
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB764TOS

value: activated T-helper 1 cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS279ECG at ENCODE; https://www.encodeproject.org/ENCBS279ECG/

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


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB089CRF)

description:
https://www.encodeproject.org/experiments/ENCSR368UYD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR368UYD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR070IHF
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB089CRF

source_name: Homo sapiens male adult (42 years) CD8-positive naive resting alpha-beta T primary cell

value: adult

value: 42 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS859TOE at ENCODE; https://www.encodeproject.org/ENCBS859TOE/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB877MDK)

description:
https://www.encodeproject.org/experiments/ENCSR194LMK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (81 years) with Cognitive impairment
experiment encode accession: ENCSR194LMK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR646FGM
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB877MDK
size range: 200-600

source_name: Homo sapiens female adult (81 years) with Cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 81 year

value: Rush University

value: ENCBS460QXN at ENCODE; https://www.encodeproject.org/ENCBS460QXN/

value: Derived from ENCODE donor ENCDO077CCP; https://www.encodeproject.org/ENCDO077CCP/


title: Sample 17 DNB

value: Male

value: Healthy


title: Histone ChIP-seq from heart right ventricle (ENCLB862SPE)

description:
https://www.encodeproject.org/experiments/ENCSR379SOG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR379SOG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR049JKQ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB862SPE
size range: 200-600

value: heart right ventricle

value: 59 year

value: Shin Lin

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

value: ENCBS637BEQ at ENCODE; https://www.encodeproject.org/ENCBS637BEQ/

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


title: Histone ChIP-seq from spleen (ENCLB820OMG)

description:
https://www.encodeproject.org/experiments/ENCSR205APY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on spleen tissue female adult (61 years)
experiment encode accession: ENCSR205APY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR119AVG
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB820OMG
size range: 200-600

source_name: Homo sapiens female adult (61 years) spleen tissue

value: spleen

value: adult

value: 61 year

value: Bradley Bernstein, Broad

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

value: ENCBS193VFU at ENCODE; https://www.encodeproject.org/ENCBS193VFU/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB205KMC)

description:
https://www.encodeproject.org/experiments/ENCSR194LMK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (81 years) with Cognitive impairment
experiment encode accession: ENCSR194LMK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR646FGM
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB205KMC
size range: 200-600

value: middle frontal area 46

value: tissue

value: female

value: 81 year

value: Rush University

value: ENCBS460QXN at ENCODE; https://www.encodeproject.org/ENCBS460QXN/


title: Sample 16 DNB

source_name: Whole blood

value: Male

value: Healthy


title: Histone ChIP-seq from spleen (ENCLB436CPR)

description:
https://www.encodeproject.org/experiments/ENCSR205APY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on spleen tissue female adult (61 years)
experiment encode accession: ENCSR205APY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR119AVG
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB436CPR
size range: 200-600

value: Shin Lin


title: Control ChIP-seq from heart right ventricle (ENCLB021POB)

description:
https://www.encodeproject.org/experiments/ENCSR278ACD/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on heart right ventricle tissue female adult (56 years).
experiment encode accession: ENCSR278ACD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB021POB
size range: 200-600

value: heart right ventricle

value: 56 year

value: PGD

value: ENCBS664CKV at ENCODE; https://www.encodeproject.org/ENCBS664CKV/

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


title: Histone ChIP-seq from heart right ventricle (ENCLB151XRA)

description:
https://www.encodeproject.org/experiments/ENCSR370LLS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on heart right ventricle tissue male adult (43 years).
experiment encode accession: ENCSR370LLS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481QDJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB151XRA
size range: 200-600

value: male

value: adult

value: 43 year

value: Bradley Bernstein, Broad

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

value: ENCBS096INK at ENCODE; https://www.encodeproject.org/ENCBS096INK/

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


title: Sample 14 DNB


title: Histone ChIP-seq from heart right ventricle (ENCLB343DJC)

description:
https://www.encodeproject.org/experiments/ENCSR368KWU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on heart right ventricle tissue male adult (66 years).
experiment encode accession: ENCSR368KWU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR898WPF
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB343DJC
size range: 200-600

value: tissue

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

value: 66 year

value: ENCBS948AHG at ENCODE; https://www.encodeproject.org/ENCBS948AHG/

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


title: Sample 15 DNB

value: Male

value: Healthy


title: TF ChIP-seq from middle frontal area 46 (ENCLB787DDD)

description:
https://www.encodeproject.org/experiments/ENCSR092VKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR092VKJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR917XOL
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB787DDD
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with Alzheimer's disease

value: CTCF

value: middle frontal area 46

value: female

value: 90 or above year

value: Rush University

value: ENCBS837PKE at ENCODE; https://www.encodeproject.org/ENCBS837PKE/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: TF ChIP-seq from heart right ventricle (ENCLB348JST)

description:
https://www.encodeproject.org/experiments/ENCSR089NBS/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF TF ChIP-seq on heart right ventricle tissue male adult (73 years).
experiment encode accession: ENCSR089NBS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR145RXI
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB348JST
size range: 200-600

source_name: Homo sapiens male adult (73 years) heart right ventricle tissue

value: heart right ventricle

value: male

value: adult

value: 73 year

value: Bradley Bernstein, Broad

value: Shin Lin

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

value: ENCBS237SHK at ENCODE; https://www.encodeproject.org/ENCBS237SHK/

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


title: Sample 13 DNB

value: Male

value: Healthy


title: Histone ChIP-seq from heart right ventricle (ENCLB013OUN)

description:
https://www.encodeproject.org/experiments/ENCSR368KWU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on heart right ventricle tissue male adult (66 years).
experiment encode accession: ENCSR368KWU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR898WPF
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB013OUN
size range: 200-600

value: tissue

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

value: 66 year

value: ENCBS948AHG at ENCODE; https://www.encodeproject.org/ENCBS948AHG/

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


title: Control ChIP-seq from heart right ventricle (ENCLB692GON)

description:
https://www.encodeproject.org/experiments/ENCSR278ACD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on heart right ventricle tissue female adult (56 years).
experiment encode accession: ENCSR278ACD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB692GON
size range: 200-600

value: female

value: 56 year

value: PGD

value: ENCBS664CKV at ENCODE; https://www.encodeproject.org/ENCBS664CKV/

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


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB388DPR)

description:
https://www.encodeproject.org/experiments/ENCSR368UYD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR368UYD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR070IHF
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB388DPR

value: primary cell

value: male

value: adult

value: 42 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS859TOE at ENCODE; https://www.encodeproject.org/ENCBS859TOE/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: TF ChIP-seq from heart right ventricle (ENCLB963GPC)

description:
https://www.encodeproject.org/experiments/ENCSR089NBS/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF TF ChIP-seq on heart right ventricle tissue male adult (73 years).
experiment encode accession: ENCSR089NBS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR145RXI
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB963GPC
size range: 200-600

value: CTCF

value: heart right ventricle

value: tissue

value: 73 year

value: Shin Lin

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

value: ENCBS237SHK at ENCODE; https://www.encodeproject.org/ENCBS237SHK/

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


title: Sample 12 DNB

value: Male

value: Healthy

value: Base2 (0)


title: Histone ChIP-seq from pancreas (ENCLB074IHD)

description:
https://www.encodeproject.org/experiments/ENCSR368EPJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on pancreas tissue female adult (59 years)
experiment encode accession: ENCSR368EPJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR490NCK
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB074IHD
size range: 200-600

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

value: pancreas

value: female

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

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS483KZB at ENCODE; https://www.encodeproject.org/ENCBS483KZB/

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


title: Histone ChIP-seq from pancreas (ENCLB249DWZ)

description:
https://www.encodeproject.org/experiments/ENCSR368EPJ/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K9me3 ChIP-seq on pancreas tissue female adult (59 years)
experiment encode accession: ENCSR368EPJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR490NCK
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB249DWZ
size range: 200-600

value: tissue


title: Histone ChIP-seq from pancreas (ENCLB155KSM)

description:
https://www.encodeproject.org/experiments/ENCSR368EPJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on pancreas tissue female adult (59 years)
experiment encode accession: ENCSR368EPJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR490NCK
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB155KSM
size range: 200-600


title: Histone ChIP-seq from lower lobe of left lung (ENCLB720JTL)

description:
https://www.encodeproject.org/experiments/ENCSR368APT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on lower lobe of left lung tissue female adult (59 years)
experiment encode accession: ENCSR368APT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR846VGG
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB720JTL
size range: 200-600

source_name: Homo sapiens female adult (59 years) lower lobe of left lung tissue, preserved by flash-freezing

value: lower lobe of left lung

value: ENCBS493HET at ENCODE; https://www.encodeproject.org/ENCBS493HET/


title: Sample 10 DNB


title: Histone ChIP-seq from colonic mucosa (ENCLB906RAX)

description:
https://www.encodeproject.org/experiments/ENCSR078LIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on colonic mucosa tissue female adult (41 years)
experiment encode accession: ENCSR078LIZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR557RJE
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB906RAX
size range: 200-600

source_name: Homo sapiens female adult (41 years) colonic mucosa tissue

value: colonic mucosa

value: 41 year

value: Bradley Bernstein, Broad

value: Shin Lin

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

value: ENCBS312CUX at ENCODE; https://www.encodeproject.org/ENCBS312CUX/

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


title: Sample 11 DNB

value: Male

value: Healthy


title: Histone ChIP-seq from colonic mucosa (ENCLB763UTB)

description:
https://www.encodeproject.org/experiments/ENCSR078LIZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on colonic mucosa tissue female adult (41 years)
experiment encode accession: ENCSR078LIZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR557RJE
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB763UTB
size range: 200-600

value: female

value: adult


title: TF ChIP-seq from middle frontal area 46 (ENCLB368EZB)

description:
https://www.encodeproject.org/experiments/ENCSR092VKJ/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR092VKJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR917XOL
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB368EZB
size range: 200-600

value: CTCF

value: middle frontal area 46

value: 90 or above year

value: Rush University

value: ENCBS837PKE at ENCODE; https://www.encodeproject.org/ENCBS837PKE/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: Histone ChIP-seq from lower lobe of left lung (ENCLB771IPW)

description:
https://www.encodeproject.org/experiments/ENCSR368APT/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on lower lobe of left lung tissue female adult (59 years)
experiment encode accession: ENCSR368APT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR846VGG
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB771IPW
size range: 200-600

value: lower lobe of left lung

value: tissue

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS493HET at ENCODE; https://www.encodeproject.org/ENCBS493HET/

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


title: Control Mint-ChIP-seq from activated T-helper 2 cell (ENCLB339OIM)

description:
https://www.encodeproject.org/experiments/ENCSR193QAG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on activated T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4 , anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR193QAG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB339OIM

source_name: Homo sapiens male adult (35 years) activated T-helper 2 primary cell treated with 5 μg/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4 , anti-CD3 and anti-CD28 coated beads

value: activated T-helper 2 cell

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS271FSH at ENCODE; https://www.encodeproject.org/ENCBS271FSH/

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


title: Sample 08 DNB

value: Male

value: Healthy


title: Mint-ChIP-seq from mesothelial cell of epicardium (ENCLB323KRA)

description:
https://www.encodeproject.org/experiments/ENCSR191AZW/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on mesothelial cell of epicardium
experiment encode accession: ENCSR191AZW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR268SLH
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB323KRA

source_name: Homo sapiens female embryo (5 days) mesothelial of epicardium in vitro differentiated cells

value: mesothelial cell of epicardium

value: in vitro differentiated cells

tag: description

value: WA09 derived epicardium (mesothelium)

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: healthy

value: ENCBS048EDA at ENCODE; https://www.encodeproject.org/ENCBS048EDA/

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


title: Mint-ChIP-seq from mesothelial cell of epicardium (ENCLB173OJL)

description:
https://www.encodeproject.org/experiments/ENCSR191AZW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on mesothelial cell of epicardium
experiment encode accession: ENCSR191AZW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR268SLH
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB173OJL


title: Mint-ChIP-seq from mesothelial cell of epicardium (ENCLB992PPS)

description:
https://www.encodeproject.org/experiments/ENCSR191AZW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on mesothelial cell of epicardium
experiment encode accession: ENCSR191AZW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR268SLH
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB992PPS

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

value: ENCBS924VAR at ENCODE; https://www.encodeproject.org/ENCBS924VAR/


title: Mint-ChIP-seq from mesothelial cell of epicardium (ENCLB817AGU)

description:
https://www.encodeproject.org/experiments/ENCSR191AZW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on mesothelial cell of epicardium
experiment encode accession: ENCSR191AZW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR268SLH
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB817AGU


title: Control Mint-ChIP-seq from activated T-helper 2 cell (ENCLB974PAO)

description:
https://www.encodeproject.org/experiments/ENCSR193QAG/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on activated T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4 , anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR193QAG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB974PAO

value: activated T-helper 2 cell

value: primary cell

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB904TMZ)

description:
https://www.encodeproject.org/experiments/ENCSR367RUF/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR367RUF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR248FZA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB904TMZ

source_name: Homo sapiens male adult (42 years) activated CD8-positive, naive alpha-beta T primary cell

value: 42 year

value: John Stamatoyannopoulos

value: ENCBS819MUY at ENCODE; https://www.encodeproject.org/ENCBS819MUY/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB342WXZ)

description:
https://www.encodeproject.org/experiments/ENCSR367RUF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR367RUF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR248FZA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB342WXZ

value: Bradley Bernstein, Broad


title: TF ChIP-seq from middle frontal area 46 (ENCLB102NCQ)

description:
https://www.encodeproject.org/experiments/ENCSR073BPG/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR073BPG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR799VTP
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB102NCQ
size range: 200-600

source_name: Homo sapiens female adult (83 years) middle frontal area 46 tissue with mild cognitive impairment

value: CTCF

value: middle frontal area 46

value: tissue

value: female

value: 83 year

value: Rush University

value: ENCBS104CPK at ENCODE; https://www.encodeproject.org/ENCBS104CPK/

value: Derived from ENCODE donor ENCDO832DBZ; https://www.encodeproject.org/ENCDO832DBZ/


title: Sample 06 DNB

value: Male

value: Healthy


title: Sample 07 DNB


title: TF ChIP-seq from middle frontal area 46 (ENCLB087NZJ)

description:
https://www.encodeproject.org/experiments/ENCSR073BPG/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR073BPG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR799VTP
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB087NZJ
size range: 200-600

value: adult


title: Histone ChIP-seq from middle frontal area 46 (ENCLB500DTH)

description:
https://www.encodeproject.org/experiments/ENCSR072GKC/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (82 years).
experiment encode accession: ENCSR072GKC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR745AVM
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB500DTH
size range: 200-600

source_name: Homo sapiens male adult (82 years) middle frontal area 46 tissue

value: male

value: 82 year

value: ENCBS145CHN at ENCODE; https://www.encodeproject.org/ENCBS145CHN/

value: Derived from ENCODE donor ENCDO407UTA; https://www.encodeproject.org/ENCDO407UTA/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB550MSM)

description:
https://www.encodeproject.org/experiments/ENCSR072GKC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (82 years).
experiment encode accession: ENCSR072GKC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR745AVM
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB550MSM
size range: 200-600


title: Control Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB761VBC)

description:
https://www.encodeproject.org/experiments/ENCSR070IHF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR070IHF
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB761VBC

value: primary cell

value: 42 year

value: John Stamatoyannopoulos

value: ENCBS859TOE at ENCODE; https://www.encodeproject.org/ENCBS859TOE/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: Control Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB120ANJ)

description:
https://www.encodeproject.org/experiments/ENCSR070IHF/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR070IHF
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB120ANJ

value: Bradley Bernstein, Broad


title: Sample 02 DNB


title: Sample 09 DNB


title: Control Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCLB942BIE)

description:
https://www.encodeproject.org/experiments/ENCSR069ZFG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (35 years)
experiment encode accession: ENCSR069ZFG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB942BIE

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

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS417NZZ at ENCODE; https://www.encodeproject.org/ENCBS417NZZ/

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


title: Sample 01 DNB

description: Illumina_RNAseq_raw_counts_EnsemblID.txt

value: Male

value: Healthy


title: TF ChIP-seq from left ventricle myocardium inferior (ENCLB951UFA)

description:
https://www.encodeproject.org/experiments/ENCSR068HEE/
***************
biological replicate number: 2
technical replicate number: 2
description: CTCF ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR068HEE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR608IVH
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB951UFA
size range: 200-600

source_name: Homo sapiens male adult (60 years) left ventricle myocardium inferior tissue

value: CTCF

value: left ventricle myocardium inferior

value: tissue

value: male

value: adult

value: 60 year

value: Shin Lin

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

value: ENCBS267RXN at ENCODE; https://www.encodeproject.org/ENCBS267RXN/

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


title: Control Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCLB063VTF)

description:
https://www.encodeproject.org/experiments/ENCSR069ZFG/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (35 years)
experiment encode accession: ENCSR069ZFG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB063VTF

value: primary cell

value: 35 year


title: Histone ChIP-seq from middle frontal area 46 (ENCLB526INP)

description:
https://www.encodeproject.org/experiments/ENCSR067BGS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on middle frontal area 46 tissue male adult (87 years) with Alzheimer's disease, Cognitive impairment
experiment encode accession: ENCSR067BGS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR534KYQ
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB526INP
size range: 200-600

source_name: Homo sapiens male adult (87 years) with Alzheimer's disease, Cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: 87 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS584OEO at ENCODE; https://www.encodeproject.org/ENCBS584OEO/

value: Derived from ENCODE donor ENCDO776JEI; https://www.encodeproject.org/ENCDO776JEI/


title: TF ChIP-seq from left ventricle myocardium inferior (ENCLB534KAZ)

description:
https://www.encodeproject.org/experiments/ENCSR068HEE/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR068HEE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR608IVH
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB534KAZ
size range: 200-600

value: CTCF

value: left ventricle myocardium inferior


title: TF ChIP-seq from left ventricle myocardium inferior (ENCLB386VDZ)

description:
https://www.encodeproject.org/experiments/ENCSR068HEE/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR068HEE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR608IVH
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB386VDZ
size range: 200-600

value: tissue

value: male

value: ENCBS672IKS at ENCODE; https://www.encodeproject.org/ENCBS672IKS/


title: TF ChIP-seq from left ventricle myocardium inferior (ENCLB191KSM)

description:
https://www.encodeproject.org/experiments/ENCSR068HEE/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR068HEE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR608IVH
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB191KSM
size range: 200-600

value: adult

value: 60 year

value: Shin Lin


title: Histone ChIP-seq from middle frontal area 46 (ENCLB504DZN)

description:
https://www.encodeproject.org/experiments/ENCSR067BGS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue male adult (87 years) with Alzheimer's disease, Cognitive impairment
experiment encode accession: ENCSR067BGS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR534KYQ
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB504DZN
size range: 200-600


title: Mint-ChIP-seq from T-helper 2 cell (ENCLB160SWJ)

description:
https://www.encodeproject.org/experiments/ENCSR066VKF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4
experiment encode accession: ENCSR066VKF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR635PGB
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB160SWJ

source_name: Homo sapiens male adult (35 years) T-helper 2 primary cell treated with 5 ug/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4

value: T-helper 2 cell

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein;

value: ENCBS965HLC at ENCODE; https://www.encodeproject.org/ENCBS965HLC/

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


title: Sample 05 DNB

value: Male

value: Healthy


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB297VAU)

description:
https://www.encodeproject.org/experiments/ENCSR065QAA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell
experiment encode accession: ENCSR065QAA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR810LRH
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB297VAU

source_name: Homo sapiens CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS749OUL at ENCODE; https://www.encodeproject.org/ENCBS749OUL/

value: Derived from ENCODE donor ENCDO930DIF; https://www.encodeproject.org/ENCDO930DIF/


title: Q + TSA

city: Seattle

first: Sarah

middle: G.

last: Swygert

state: WA

address: 1100 Fairview Avenue North MS A1-162

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

data_processing:
Reads were aligned to the sacCer3 reference genome using Bowtie2 in very sensitive mode.
All read pairs where either end received MAPQ score < 6 were removed. All the remaining in-facing read pairs were removed. The resulting read pairs were processed into the multiple-bin size contact matrix in the Cooler format (https://github.com/mirnylab/cooler).
Data from two independent biological replicates was compared using HiCRep (except for Q HHF2 which contains one replicate only). Agreement between replicates was determined to be 0.88 or greater. Data from agreeing replicates were then merged to maximize read depth.
Genome_build: sacCer3 reference genome (release R64-2-1)
Supplementary_files_format_and_content: Processed data files are suitable for viewing in Juicebox (https://aidenlab.org/juicebox/)

organism: Saccharomyces cerevisiae

source_name: Q cells treated with TSA

growth_protocol: All strains were generated in prototrophic W303 backgrounds.  200 mL cultures of log cells were grown to 0.55 OD.  Q cells were purified from 25 mL 7-day cultures via Percoll density gradient.

extract_protocol:
Spheroplasts were incubated with a concentration of micrococcal nuclease titrated to each experiment designed to retain ~90% mononucleosome sized fragments in the insoluble chromatin fraction for 20 min at 37 degrees. DNA ends were repaired and biotin labeled, fragments were proximity ligated, crosslinking was reversed, and DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Purified DNA ends were readied for ligation, A-tailed, and Illumina Truseq adapters were ligated.  Proximity ligated DNA was pulled down with streptavidin beads, and library was amplified with Illumina Truseq primers.
Micro-C XL

treatment_protocol: Cells were fixed in 3% formaldehyde at 30 degrees for 10 minutes, cell walls were permeabilized at 30 degrees in 250 ug/mL zymolyase for 30 min (log) or 1 mg/mL zymolyase for 1.5 hours (quiescent), then spheroplasts were crosslinked in 3mM disuccinimidyl glutarate for 40 min at 30 degrees (except "No DSG" samples).

tag: genotype

value: MATa RAD5+ prototroph

tag: strain

value: yTT5781 and yTT5783

tag: culture condition

value: grown to quiescence and purified, treated with TSA on day 6 during quiescence entry


title: Sample 04 DNB

source_name: Whole blood

tag: age (year)


title: Mint-ChIP-seq from T-helper 2 cell (ENCLB705GBH)

description:
https://www.encodeproject.org/experiments/ENCSR066VKF/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4
experiment encode accession: ENCSR066VKF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR635PGB
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB705GBH

value: T-helper 2 cell

tag: Sex

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX


title: Q

source_name: Q cells

value: grown to quiescence and purified


title: Q R17R19A

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-R17A,R19A

value: yTT7200 and yTT7207


title: Mint-ChIP-seq from WTC11 (ENCLB158GGQ)

description:
https://www.encodeproject.org/experiments/ENCSR356QPN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR356QPN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB158GGQ

source_name: Homo sapiens WTC11 cell line

tag: line

value: cell line

value: 30 year

tag: passage number

value: Yin Shen

value: ENCBS869UGY at ENCODE; https://www.encodeproject.org/ENCBS869UGY/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: Mint-ChIP-seq from WTC11 (ENCLB759VJX)

description:
https://www.encodeproject.org/experiments/ENCSR356QPN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR356QPN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB759VJX

tag: antibody

value: Bradley Bernstein, Broad

value: ENCBS532TBS at ENCODE; https://www.encodeproject.org/ENCBS532TBS/


title: Sample 03 DNB

value: Male

tag: disease state

value: Healthy

tag: time (day)


title: Q no DSG

value: MATa RAD5+ prototroph

value: yTT5781 and yTT5783


title: Mint-ChIP-seq from WTC11 (ENCLB309JOI)

description:
https://www.encodeproject.org/experiments/ENCSR356QPN/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR356QPN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB309JOI

tag: biosample encode accession

value: male

tag: dev stage

value: adult

tag: age


title: Mint-ChIP-seq from WTC11 (ENCLB777RUL)

description:
https://www.encodeproject.org/experiments/ENCSR356QPN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR356QPN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB777RUL

tag: lab

tag: source

tag: link


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB129BKO)

description:
https://www.encodeproject.org/experiments/ENCSR065QAA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell
experiment encode accession: ENCSR065QAA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR810LRH
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB129BKO

value: primary cell

value: not collected

value: unknown

value: John Stamatoyannopoulos

value: ENCBS749OUL at ENCODE; https://www.encodeproject.org/ENCBS749OUL/

value: Derived from ENCODE donor ENCDO930DIF; https://www.encodeproject.org/ENCDO930DIF/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB186GXK)

description:
https://www.encodeproject.org/experiments/ENCSR190FSS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease, Cognitive impairment.
experiment encode accession: ENCSR190FSS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR732BRB
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB186GXK
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) with Alzheimer's disease, Cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: Rush University

value: ENCBS587MGS at ENCODE; https://www.encodeproject.org/ENCBS587MGS/

value: Derived from ENCODE donor ENCDO754RFQ; https://www.encodeproject.org/ENCDO754RFQ/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB934BXA)

description:
https://www.encodeproject.org/experiments/ENCSR190FSS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease, Cognitive impairment.
experiment encode accession: ENCSR190FSS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR732BRB
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB934BXA
size range: 200-600

value: Bradley Bernstein, Broad


title: Q HHF2

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-HHF2

value: grown to quiescence and purified


title: Q 5toA

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-K16A,R17A,H18A,R19A,K20A

value: yTT7175 and yTT7208


title: TF ChIP-seq from adrenal gland (ENCLB611TLV)

description:
https://www.encodeproject.org/experiments/ENCSR188XCX/
***************
biological replicate number: 2
technical replicate number: 2
description: CTCF ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR188XCX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB611TLV
size range: 200-600

source_name: Homo sapiens female adult (41 years) adrenal gland tissue

value: CTCF

value: adrenal gland

value: adult

value: 41 year

value: Shin Lin

tag: health state

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

value: ENCBS648AMG at ENCODE; https://www.encodeproject.org/ENCBS648AMG/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB144QBM)

description:
https://www.encodeproject.org/experiments/ENCSR064PTX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease
experiment encode accession: ENCSR064PTX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR869KBA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB144QBM
size range: 200-600

source_name: Homo sapiens female adult (89 years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 89 year

value: ENCBS967JLM at ENCODE; https://www.encodeproject.org/ENCBS967JLM/

value: Derived from ENCODE donor ENCDO830KFO; https://www.encodeproject.org/ENCDO830KFO/


title: Rpb3 in Q R17R19A Rep2 IP

description: PolII_Q_R17R19A_merged_replicates_input_normalized.bw

data_processing:
Reads were aligned to the sacCer3 reference genome using Bowtie2 in very sensitive mode.
Aligned reads were filtered and indexed using SAMtools.
Bam files were converted to bigwig files and IP files were normalized to input
Genome_build: sacCer3 reference genome (release R64-2-1)
Supplementary_files_format_and_content: Processed files are files as they were used in the manuscript, and have IP from both replicates merged and normalized to the merged inputs. These can be viewed using the free software IGB or IGV, or further analysed using available methods.

growth_protocol: All strains were generated in prototrophic W303 backgrounds.  Log cells were grown to ~0.6-0.8 OD.  Q cells were purified from 7-day cultures via Percoll density gradient.

extract_protocol:
Approximately 300 OD units of cells were bead-beat until cell walls were disrupted.  Lysates were sonicated to shear chromatin to ~200-400 bp fragments and clarified.  Protein was immuniprecipitated using the indicated antibody.
Tecan Ovation Ultra-Low v2

treatment_protocol: Cells were fixed in formaldehyde for 20 minutes

tag: genotype

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-R17A,R19A

tag: chip antibody

value: Rpb3 (Biolegend #665003)


title: Log

source_name: Log cells

value: MATa RAD5+ prototroph

tag: strain

value: yTT5781 and yTT5783

tag: culture condition

value: log growth


title: Control Mint-ChIP-seq from activated T-helper 1 cell (ENCLB826NUJ)

description:
https://www.encodeproject.org/experiments/ENCSR188HBL/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on activated T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR188HBL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB826NUJ

source_name: Homo sapiens male adult (35 years) activated T-helper 1 primary cell treated with 1 μg/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads

value: activated T-helper 1 cell

value: primary cell

tag: Sex

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS279ECG at ENCODE; https://www.encodeproject.org/ENCBS279ECG/

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


title: Control Mint-ChIP-seq from activated T-helper 1 cell (ENCLB899LYZ)

description:
https://www.encodeproject.org/experiments/ENCSR188HBL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on activated T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR188HBL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB899LYZ


title: TF ChIP-seq from adrenal gland (ENCLB787VJZ)

description:
https://www.encodeproject.org/experiments/ENCSR188XCX/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR188XCX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB787VJZ
size range: 200-600

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

value: CTCF

value: adrenal gland

value: tissue

value: female

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS491ORA at ENCODE; https://www.encodeproject.org/ENCBS491ORA/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB620HAU)

description:
https://www.encodeproject.org/experiments/ENCSR274HDQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years)
experiment encode accession: ENCSR274HDQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR836KPL
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB620HAU
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: middle frontal area 46

value: adult

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS464LBN at ENCODE; https://www.encodeproject.org/ENCBS464LBN/

value: Derived from ENCODE donor ENCDO006DAA; https://www.encodeproject.org/ENCDO006DAA/


title: Log no DSG

value: MATa RAD5+ prototroph

value: yTT5781 and yTT5783

value: log growth


title: Histone ChIP-seq from middle frontal area 46 (ENCLB761MCL)

description:
https://www.encodeproject.org/experiments/ENCSR064PTX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease
experiment encode accession: ENCSR064PTX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR869KBA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB761MCL
size range: 200-600

value: tissue

value: female

value: 89 year

value: ENCBS967JLM at ENCODE; https://www.encodeproject.org/ENCBS967JLM/

value: Derived from ENCODE donor ENCDO830KFO; https://www.encodeproject.org/ENCDO830KFO/


title: Rpb3 in Q K16Q Rep2 IP

description: PolII_Q_K16Q_merged_replicates_input_normalized.bw

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-K16Q

value: Rpb3 (Biolegend #665003)


title: Control Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB182ETM)

description:
https://www.encodeproject.org/experiments/ENCSR186VDY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR186VDY
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182ETM

source_name: Homo sapiens male adult (42 years) activated CD4 positive, naive alpha-beta T primary cell

value: primary cell

value: male

value: 42 year

value: John Stamatoyannopoulos

value: ENCBS607NQI at ENCODE; https://www.encodeproject.org/ENCBS607NQI/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: Rpb3 in Q R17R19A Rep2 Input

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-R17A,R19A


title: Control Mint-ChIP-seq from T-helper 1 cell (ENCLB344PJP)

description:
https://www.encodeproject.org/experiments/ENCSR352UAU/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta
experiment encode accession: ENCSR352UAU
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB344PJP

source_name: Homo sapiens male adult (35 years) T-helper 1 primary cell treated with 1 μg/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta

value: T-helper 1 cell

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein;

value: ENCBS111UJE at ENCODE; https://www.encodeproject.org/ENCBS111UJE/

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


title: TF ChIP-seq from heart left ventricle (ENCLB736CJR)

description:
https://www.encodeproject.org/experiments/ENCSR350NBQ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF TF ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR350NBQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB736CJR
size range: 200-600

source_name: Homo sapiens male adult (54 years) heart left ventricle tissue

value: CTCF

value: heart left ventricle

value: tissue

value: 54 year

value: Bradley Bernstein, Broad

value: Shin Lin

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

value: ENCBS115UFJ at ENCODE; https://www.encodeproject.org/ENCBS115UFJ/

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


title: Rpb3 in Q K16Q Rep1 IP

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-K16Q

value: Rpb3 (Biolegend #665003)


title: Rpb3 in Q R17R19A Rep1 IP

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-R17A,R19A


title: Control Mint-ChIP-seq from T-helper 1 cell (ENCLB605PMA)

description:
https://www.encodeproject.org/experiments/ENCSR352UAU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta
experiment encode accession: ENCSR352UAU
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB605PMA

value: T-helper 1 cell

value: primary cell

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX


title: Control Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB618PHC)

description:
https://www.encodeproject.org/experiments/ENCSR186VDY/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR186VDY
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB618PHC

value: 42 year

value: John Stamatoyannopoulos

value: ENCBS607NQI at ENCODE; https://www.encodeproject.org/ENCBS607NQI/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB914BFJ)

description:
https://www.encodeproject.org/experiments/ENCSR274HDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years)
experiment encode accession: ENCSR274HDQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR836KPL
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB914BFJ
size range: 200-600

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS464LBN at ENCODE; https://www.encodeproject.org/ENCBS464LBN/

value: Derived from ENCODE donor ENCDO006DAA; https://www.encodeproject.org/ENCDO006DAA/


title: TF ChIP-seq from middle frontal area 46 (ENCLB458PDN)

description:
https://www.encodeproject.org/experiments/ENCSR062JAC/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR062JAC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR153LYY
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB458PDN
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with mild cognitive impairment

value: CTCF

value: ENCBS835TES at ENCODE; https://www.encodeproject.org/ENCBS835TES/

value: Derived from ENCODE donor ENCDO672KST; https://www.encodeproject.org/ENCDO672KST/


title: TF ChIP-seq from middle frontal area 46 (ENCLB753JWY)

description:
https://www.encodeproject.org/experiments/ENCSR062JAC/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR062JAC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR153LYY
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB753JWY
size range: 200-600

value: adult


title: Rpb3 in Q K16Q Rep2 Input

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-K16Q

value: Rpb3 (Biolegend #665003)


title: Mint-ChIP-seq from endodermal cell (ENCLB182NXJ)

description:
https://www.encodeproject.org/experiments/ENCSR349NAK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on endodermal cell originated from H1
experiment encode accession: ENCSR349NAK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR637MGY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182NXJ

source_name: Homo sapiens male embryo endodermal in vitro differentiated cells originated from H1, preserved by flash-freezing

value: endodermal cell

value: in vitro differentiated cells

value: male

value: embryonic

value: not collected

value: Job Dekker, UMass

value: René Maehr

value: healthy

value: ENCBS180HZM at ENCODE; https://www.encodeproject.org/ENCBS180HZM/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: Mint-ChIP-seq from endodermal cell (ENCLB273JAG)

description:
https://www.encodeproject.org/experiments/ENCSR349NAK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on endodermal cell originated from H1
experiment encode accession: ENCSR349NAK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR637MGY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB273JAG


title: Rpb3 in Q K16Q Rep1 Input


title: Rpb3 in Q R17R19A Rep1 Input

description: PolII_Q_R17R19A_merged_replicates_input_normalized.bw

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-hhf2-R17A,R19A


title: Rpb3 in Q HHF2 Rep1 IP

description: PolII_Q_HHF2_merged_replicates_input_normalized.bw

value: MATa RAD5+ ura3-1 hht1-hhf1::Nat hht2-hhf2::Hyg trp1-1::pRS404-HHT2-HHF2


title: Rpb3 in Q HHF2 Rep2 IP


title: TF ChIP-seq from middle frontal area 46 (ENCLB994WNC)

description:
https://www.encodeproject.org/experiments/ENCSR270KFY/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR270KFY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR096QCF
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB994WNC
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with Cognitive impairment

value: CTCF

value: middle frontal area 46

value: tissue

value: female

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS736CMF at ENCODE; https://www.encodeproject.org/ENCBS736CMF/

value: Derived from ENCODE donor ENCDO359XWR; https://www.encodeproject.org/ENCDO359XWR/


title: TF ChIP-seq from middle frontal area 46 (ENCLB249LFX)

description:
https://www.encodeproject.org/experiments/ENCSR270KFY/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR270KFY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR096QCF
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB249LFX
size range: 200-600

value: adult


title: Control ChIP-seq from heart left ventricle (ENCLB550KCT)

description:
https://www.encodeproject.org/experiments/ENCSR061EXX/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on heart left ventricle tissue male adult (66 years).
experiment encode accession: ENCSR061EXX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB550KCT
size range: 200-600

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

value: heart left ventricle

value: male

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

value: 66 year

value: Shin Lin

value: ENCBS966SZA at ENCODE; https://www.encodeproject.org/ENCBS966SZA/

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


title: Control ChIP-seq from heart left ventricle (ENCLB384KUS)

description:
https://www.encodeproject.org/experiments/ENCSR061EXX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on heart left ventricle tissue male adult (66 years).
experiment encode accession: ENCSR061EXX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB384KUS
size range: 200-600


title: TF ChIP-seq from adrenal gland (ENCLB909CKK)

description:
https://www.encodeproject.org/experiments/ENCSR188XCX/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR188XCX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB909CKK
size range: 200-600

value: CTCF

value: adrenal gland

value: 41 year

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

value: ENCBS648AMG at ENCODE; https://www.encodeproject.org/ENCBS648AMG/

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


title: Control Mint-ChIP-seq from mesothelial cell of epicardium (ENCLB303ALS)

description:
https://www.encodeproject.org/experiments/ENCSR268SLH/
***************
biological replicate number: 2
technical replicate number: 1
description: Control Mint-ChIP-seq on mesothelial cell of epicardium
experiment encode accession: ENCSR268SLH
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB303ALS

source_name: Homo sapiens female embryo (5 days) mesothelial of epicardium in vitro differentiated cells

value: mesothelial cell of epicardium

value: in vitro differentiated cells

tag: description

value: WA09 derived epicardium (mesothelium)

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: healthy

value: ENCBS048EDA at ENCODE; https://www.encodeproject.org/ENCBS048EDA/

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


title: TF ChIP-seq from heart left ventricle (ENCLB870YBH)

description:
https://www.encodeproject.org/experiments/ENCSR350NBQ/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF TF ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR350NBQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB870YBH
size range: 200-600

tag: antibody

value: CTCF

value: heart left ventricle

value: tissue

value: male

value: adult

value: 54 year

value: Shin Lin

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

value: ENCBS115UFJ at ENCODE; https://www.encodeproject.org/ENCBS115UFJ/

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


title: Control Mint-ChIP-seq from mesothelial cell of epicardium (ENCLB309MPD)

description:
https://www.encodeproject.org/experiments/ENCSR268SLH/
***************
biological replicate number: 2
technical replicate number: 2
description: Control Mint-ChIP-seq on mesothelial cell of epicardium
experiment encode accession: ENCSR268SLH
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB309MPD

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: female

value: embryonic


title: Control Mint-ChIP-seq from mesothelial cell of epicardium (ENCLB453CUI)

description:
https://www.encodeproject.org/experiments/ENCSR268SLH/
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biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on mesothelial cell of epicardium
experiment encode accession: ENCSR268SLH
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB453CUI

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

value: healthy

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS924VAR at ENCODE; https://www.encodeproject.org/ENCBS924VAR/