title: Rpb3 in Q HHF2 Rep2 Input

source_name: Q cells

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

value: Rpb3 (Biolegend #665003)


title: Rpb3 in Q 5toA + Phenanthroline Rep2 IP

status: Public on Nov 04 2021

type: SRA

city: Seattle

first: Sarah

middle: G.

last: Swygert

state: WA

address: 1100 Fairview Avenue North MS A1-162

department: Basic Sciences Division

country: USA

institute: Fred Hutchinson Cancer Research Center

description: PolII_Q_5toA_Phenanthroline_merged_replicates_input_normalized.bw

library_source: genomic

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.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Q cells treated with phenanthroline

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-K16A,R17A,H18A,R19A,K20A

tag: strain

tag: chip antibody


title: Control Mint-ChIP-seq from mesothelial cell of epicardium (ENCLB986XYR)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR268SLH/
***************
biological replicate number: 1
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: ENCLB986XYR

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

organism: Homo sapiens

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

value: mesothelial cell of epicardium

value: in vitro differentiated cells

tag: description

value: WA09 derived epicardium (mesothelium)

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: healthy

tag: dev stage

value: embryonic

tag: age

value: 5 day

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: SESCC

tag: link

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

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB531UMR)

description:
https://www.encodeproject.org/experiments/ENCSR267CTW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (83 years).
experiment encode accession: ENCSR267CTW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR058XPK
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB531UMR
size range: 200-600

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

tag: antibody

value: middle frontal area 46

value: tissue

value: male

value: adult

value: 83 year

value: Rush University

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

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


title: Rpb3 in Q HHF2 Rep1 Input

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

value: Rpb3 (Biolegend #665003)


title: Histone ChIP-seq from middle frontal area 46 (ENCLB183SLF)

description:
https://www.encodeproject.org/experiments/ENCSR267CTW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (83 years).
experiment encode accession: ENCSR267CTW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR058XPK
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB183SLF
size range: 200-600


title: Histone ChIP-seq from middle frontal area 46 (ENCLB724SNM)

description:
https://www.encodeproject.org/experiments/ENCSR181OHF/
***************
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 Alzheimer's disease.
experiment encode accession: ENCSR181OHF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968MKZ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB724SNM
size range: 200-600

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

value: female

value: 90 or above year

value: ENCBS788LTG at ENCODE; https://www.encodeproject.org/ENCBS788LTG/

value: Derived from ENCODE donor ENCDO865EMM; https://www.encodeproject.org/ENCDO865EMM/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB774DFZ)

description:
https://www.encodeproject.org/experiments/ENCSR181OHF/
***************
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 Alzheimer's disease.
experiment encode accession: ENCSR181OHF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968MKZ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB774DFZ
size range: 200-600

value: Bradley Bernstein, Broad


title: Rpb3 in Q 5toA + Phenanthroline Rep1 IP

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB775FDJ)

description:
https://www.encodeproject.org/experiments/ENCSR346PKZ/
***************
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 mild cognitive impairment.
experiment encode accession: ENCSR346PKZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583BXC
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB775FDJ
size range: 200-600

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

value: ENCBS791EVU at ENCODE; https://www.encodeproject.org/ENCBS791EVU/

value: Derived from ENCODE donor ENCDO471EKG; https://www.encodeproject.org/ENCDO471EKG/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB957MUQ)

description:
https://www.encodeproject.org/experiments/ENCSR346PKZ/
***************
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 mild cognitive impairment.
experiment encode accession: ENCSR346PKZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583BXC
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB957MUQ
size range: 200-600

value: middle frontal area 46

value: tissue


title: Rpb3 in Q 5toA + Phenanthroline Rep1 Input


title: Histone ChIP-seq from middle frontal area 46 (ENCLB327ERJ)

description:
https://www.encodeproject.org/experiments/ENCSR060MAU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment.
experiment encode accession: ENCSR060MAU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583BXC
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB327ERJ
size range: 200-600

value: adult


title: Rpb3 in Q 5toA Rep2 IP

description: PolII_Q_5toA_merged_replicates_input_normalized.bw


title: Histone ChIP-seq from middle frontal area 46 (ENCLB302PJQ)

description:
https://www.encodeproject.org/experiments/ENCSR060MAU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment.
experiment encode accession: ENCSR060MAU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583BXC
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB302PJQ
size range: 200-600


title: Rpb3 in Q 5toA Rep1 IP


title: TF ChIP-seq from spleen (ENCLB046XYQ)

description:
https://www.encodeproject.org/experiments/ENCSR266CJT/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on spleen tissue female adult (59 years)
experiment encode accession: ENCSR266CJT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR955OYW
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB046XYQ
size range: 200-600

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

value: CTCF

value: spleen

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS297MNR at ENCODE; https://www.encodeproject.org/ENCBS297MNR/

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


title: TF ChIP-seq from middle frontal area 46 (ENCLB028SPN)

description:
https://www.encodeproject.org/experiments/ENCSR059KXR/
***************
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: ENCSR059KXR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR376YUP
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB028SPN
size range: 200-600

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

value: female

value: 87 year

value: Rush University

value: ENCBS592YXK at ENCODE; https://www.encodeproject.org/ENCBS592YXK/

value: Derived from ENCODE donor ENCDO940VNT; https://www.encodeproject.org/ENCDO940VNT/


title: TF ChIP-seq from spleen (ENCLB861HEW)

description:
https://www.encodeproject.org/experiments/ENCSR266CJT/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on spleen tissue female adult (59 years)
experiment encode accession: ENCSR266CJT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR955OYW
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB861HEW
size range: 200-600


title: Rpb3 in Q 5toA Rep2 Input

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

value: Rpb3 (Biolegend #665003)


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB781HMG)

description:
https://www.encodeproject.org/experiments/ENCSR060NQN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..
experiment encode accession: ENCSR060NQN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR299YBY
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB781HMG

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

value: primary cell

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS521XUI at ENCODE; https://www.encodeproject.org/ENCBS521XUI/

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


title: Rpb3 in Q 5toA Rep1 Input


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB895TYP)

description:
https://www.encodeproject.org/experiments/ENCSR260TLP/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (30 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR260TLP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR803FCO
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB895TYP

source_name: Homo sapiens male adult (30 years) activated CD8-positive, naive alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS777LNY at ENCODE; https://www.encodeproject.org/ENCBS777LNY/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: Histone ChIP-seq from heart right ventricle (ENCLB997VBP)

description:
https://www.encodeproject.org/experiments/ENCSR342KXD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on heart right ventricle tissue male adult (43 years).
experiment encode accession: ENCSR342KXD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481QDJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB997VBP
size range: 200-600

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

value: heart right ventricle

value: tissue

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: Control ChIP-seq from heart left ventricle (ENCLB080CIM)

description:
https://www.encodeproject.org/experiments/ENCSR261PLD/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on heart left ventricle tissue female adult (56 years).
experiment encode accession: ENCSR261PLD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB080CIM
size range: 200-600

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

value: heart left ventricle

value: female

value: PGD

value: 56 year

value: Bradley Bernstein, Broad

value: ENCBS906ICM at ENCODE; https://www.encodeproject.org/ENCBS906ICM/

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


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB343YLM)

description:
https://www.encodeproject.org/experiments/ENCSR260TLP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (30 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR260TLP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR803FCO
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB343YLM

value: primary cell

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;


title: Rpb3 in Log R17R19A Rep2 IP

description: PolII_Log_R17R19A_merged_replicates_input_normalized.bw

source_name: Log cells

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

value: Rpb3 (Biolegend #665003)


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB910YXQ)

description:
https://www.encodeproject.org/experiments/ENCSR060NQN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..
experiment encode accession: ENCSR060NQN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR299YBY
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB910YXQ

value: not collected

value: unknown

value: John Stamatoyannopoulos

value: ENCBS521XUI at ENCODE; https://www.encodeproject.org/ENCBS521XUI/

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


title: Rpb3 in Q 5toA + Phenanthroline Rep2 Input

description: PolII_Q_5toA_Phenanthroline_merged_replicates_input_normalized.bw

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB790JIP)

description:
https://www.encodeproject.org/experiments/ENCSR340FUG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (87 years)
experiment encode accession: ENCSR340FUG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR770XRC
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB790JIP
size range: 200-600

source_name: Homo sapiens female adult (87 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 87 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS892ROQ at ENCODE; https://www.encodeproject.org/ENCBS892ROQ/

value: Derived from ENCODE donor ENCDO423GGP; https://www.encodeproject.org/ENCDO423GGP/


title: TF ChIP-seq from adrenal gland (ENCLB370DBG)

description:
https://www.encodeproject.org/experiments/ENCSR188XCX/
***************
biological replicate number: 1
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: ENCLB370DBG
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: adult

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: Rpb3 in Log R17R19A Rep1 Input

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

value: Rpb3 (Biolegend #665003)


title: Control ChIP-seq from heart left ventricle (ENCLB616WVQ)

description:
https://www.encodeproject.org/experiments/ENCSR261PLD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on heart left ventricle tissue female adult (56 years).
experiment encode accession: ENCSR261PLD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB616WVQ
size range: 200-600

value: heart left ventricle

value: tissue

value: female

value: PGD

value: 56 year

value: Shin Lin

value: ENCBS906ICM at ENCODE; https://www.encodeproject.org/ENCBS906ICM/

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


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB413VEH)

description:
https://www.encodeproject.org/experiments/ENCSR178NOK/
***************
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: ENCSR178NOK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR404BIJ
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB413VEH

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

value: primary cell

value: male

value: adult

value: 42 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS591TQB at ENCODE; https://www.encodeproject.org/ENCBS591TQB/

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


title: Rpb3 in Log R17R19A Rep1 IP

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

value: Rpb3 (Biolegend #665003)


title: Control ChIP-seq from middle frontal area 46 (ENCLB276SMD)

description:
https://www.encodeproject.org/experiments/ENCSR058XPK/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on middle frontal area 46 tissue male adult (83 years).
experiment encode accession: ENCSR058XPK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB276SMD
size range: 200-600

value: middle frontal area 46

value: tissue

value: 83 year

value: Rush University

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

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


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB669RPY)

description:
https://www.encodeproject.org/experiments/ENCSR178NOK/
***************
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: ENCSR178NOK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR404BIJ
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB669RPY


title: Rpb3 in Log K16Q Rep2 IP

description: PolII_Log_K16Q_merged_replicates_input_normalized.bw

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


title: TF ChIP-seq from middle frontal area 46 (ENCLB297PCX)

description:
https://www.encodeproject.org/experiments/ENCSR059KXR/
***************
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: ENCSR059KXR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR376YUP
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB297PCX
size range: 200-600

value: CTCF

value: female

value: 87 year

value: ENCBS592YXK at ENCODE; https://www.encodeproject.org/ENCBS592YXK/

value: Derived from ENCODE donor ENCDO940VNT; https://www.encodeproject.org/ENCDO940VNT/


title: Control ChIP-seq from middle frontal area 46 (ENCLB721FSD)

description:
https://www.encodeproject.org/experiments/ENCSR058XPK/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on middle frontal area 46 tissue male adult (83 years).
experiment encode accession: ENCSR058XPK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB721FSD
size range: 200-600

value: male

value: adult

value: Bradley Bernstein, Broad


title: Histone ChIP-seq from heart right ventricle (ENCLB569DAP)

description:
https://www.encodeproject.org/experiments/ENCSR056GGE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on heart right ventricle tissue male adult (69 years).
experiment encode accession: ENCSR056GGE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481SJM
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB569DAP
size range: 200-600

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

value: heart right ventricle

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

value: 69 year

value: Shin Lin

value: ENCBS926ALQ at ENCODE; https://www.encodeproject.org/ENCBS926ALQ/

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


title: Histone ChIP-seq from heart right ventricle (ENCLB139LSZ)

description:
https://www.encodeproject.org/experiments/ENCSR056GGE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on heart right ventricle tissue male adult (69 years).
experiment encode accession: ENCSR056GGE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481SJM
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB139LSZ
size range: 200-600

value: tissue


title: Histone ChIP-seq from heart right ventricle (ENCLB152HSO)

description:
https://www.encodeproject.org/experiments/ENCSR178KWE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on heart right ventricle tissue male adult (43 years).
experiment encode accession: ENCSR178KWE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481QDJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152HSO
size range: 200-600

value: 43 year

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: Histone ChIP-seq from heart right ventricle (ENCLB279VJM)

description:
https://www.encodeproject.org/experiments/ENCSR342KXD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on heart right ventricle tissue male adult (43 years).
experiment encode accession: ENCSR342KXD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481QDJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB279VJM
size range: 200-600


title: Histone ChIP-seq from colonic mucosa (ENCLB486XPC)

description:
https://www.encodeproject.org/experiments/ENCSR340ARM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on colonic mucosa tissue female adult (41 years)
experiment encode accession: ENCSR340ARM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR557RJE
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB486XPC
size range: 200-600

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

value: colonic mucosa

value: female

value: 41 year

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: Histone ChIP-seq from heart right ventricle (ENCLB566REU)

description:
https://www.encodeproject.org/experiments/ENCSR178KWE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on heart right ventricle tissue male adult (43 years).
experiment encode accession: ENCSR178KWE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481QDJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB566REU
size range: 200-600

value: heart right ventricle

value: male

value: adult

value: Bradley Bernstein, Broad


title: Rpb3 in Log K16Q Rep1 Input

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

value: Rpb3 (Biolegend #665003)


title: Rpb3 in Log K16Q Rep2 Input


title: Histone ChIP-seq from middle frontal area 46 (ENCLB951JCZ)

description:
https://www.encodeproject.org/experiments/ENCSR340FUG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (87 years)
experiment encode accession: ENCSR340FUG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR770XRC
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB951JCZ
size range: 200-600

value: middle frontal area 46

value: tissue

value: 87 year

value: Rush University

value: ENCBS892ROQ at ENCODE; https://www.encodeproject.org/ENCBS892ROQ/

value: Derived from ENCODE donor ENCDO423GGP; https://www.encodeproject.org/ENCDO423GGP/


title: Histone ChIP-seq from colonic mucosa (ENCLB362ZIZ)

description:
https://www.encodeproject.org/experiments/ENCSR340ARM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on colonic mucosa tissue female adult (41 years)
experiment encode accession: ENCSR340ARM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR557RJE
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB362ZIZ
size range: 200-600

value: colonic mucosa

value: female

value: Shin Lin


title: TF ChIP-seq from middle frontal area 46 (ENCLB700JQW)

description:
https://www.encodeproject.org/experiments/ENCSR259PNW/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (88 years) with Alzheimer's disease.
experiment encode accession: ENCSR259PNW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR534WQA
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB700JQW
size range: 200-600

source_name: Homo sapiens female adult (88 years) with Alzheimer's disease; middle frontal area 46 tissue

value: CTCF

value: 88 year

value: ENCBS995IIS at ENCODE; https://www.encodeproject.org/ENCBS995IIS/

value: Derived from ENCODE donor ENCDO070VNS; https://www.encodeproject.org/ENCDO070VNS/


title: TF ChIP-seq from middle frontal area 46 (ENCLB859IHS)

description:
https://www.encodeproject.org/experiments/ENCSR259PNW/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (88 years) with Alzheimer's disease.
experiment encode accession: ENCSR259PNW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR534WQA
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB859IHS
size range: 200-600

value: adult


title: Histone ChIP-seq from middle frontal area 46 (ENCLB353ENZ)

description:
https://www.encodeproject.org/experiments/ENCSR339TAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue male adult (87 years) with Alzheimer's disease, Cognitive impairment
experiment encode accession: ENCSR339TAQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR534KYQ
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB353ENZ
size range: 200-600

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

value: male

value: Bradley Bernstein, Broad

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

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB210EWV)

description:
https://www.encodeproject.org/experiments/ENCSR339TAQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue male adult (87 years) with Alzheimer's disease, Cognitive impairment
experiment encode accession: ENCSR339TAQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR534KYQ
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB210EWV
size range: 200-600

value: middle frontal area 46

value: tissue


title: Rpb3 in Log HHF2 Rep2 IP

description: PolII_Log_HHF2_merged_replicates_input_normalized.bw

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

value: Rpb3 (Biolegend #665003)


title: Histone ChIP-seq from heart right ventricle (ENCLB974HAP)

description:
https://www.encodeproject.org/experiments/ENCSR259KUF/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on heart right ventricle tissue male adult (73 years).
experiment encode accession: ENCSR259KUF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR145RXI
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB974HAP
size range: 200-600

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

value: heart right ventricle

value: 73 year

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: Rpb3 in Log HHF2 Rep2 Input


title: Histone ChIP-seq from heart right ventricle (ENCLB484ZVZ)

description:
https://www.encodeproject.org/experiments/ENCSR259KUF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on heart right ventricle tissue male adult (73 years).
experiment encode accession: ENCSR259KUF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR145RXI
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB484ZVZ
size range: 200-600

value: Shin Lin


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB993BUI)

description:
https://www.encodeproject.org/experiments/ENCSR053BET/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR053BET
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR070IHF
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB993BUI

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

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: Rpb3 in Log HHF2 Rep1 Input


title: Rpb3 in Log 5toA Rep2 IP

description: PolII_Log_5toA_merged_replicates_input_normalized.bw

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB198GXK)

description:
https://www.encodeproject.org/experiments/ENCSR257VEO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue male adult (82 years).
experiment encode accession: ENCSR257VEO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR745AVM
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB198GXK
size range: 200-600

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

value: male

value: adult

value: 82 year

value: Bradley Bernstein, Broad

value: Rush University

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 (ENCLB956JPJ)

description:
https://www.encodeproject.org/experiments/ENCSR257VEO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue male adult (82 years).
experiment encode accession: ENCSR257VEO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR745AVM
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB956JPJ
size range: 200-600

value: middle frontal area 46

value: tissue


title: Histone ChIP-seq from middle frontal area 46 (ENCLB397KII)

description:
https://www.encodeproject.org/experiments/ENCSR052ETC/
***************
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 mild cognitive impairment.
experiment encode accession: ENCSR052ETC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR417AQU
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB397KII
size range: 200-600

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

value: female

value: 90 or above year

value: ENCBS173HMY at ENCODE; https://www.encodeproject.org/ENCBS173HMY/

value: Derived from ENCODE donor ENCDO739EFE; https://www.encodeproject.org/ENCDO739EFE/


title: Rpb3 in Log K16Q Rep1 IP

description: PolII_Log_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: Rpb3 in Log 5toA Rep1 IP


title: Histone ChIP-seq from middle frontal area 46 (ENCLB800KJG)

description:
https://www.encodeproject.org/experiments/ENCSR052ETC/
***************
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 mild cognitive impairment.
experiment encode accession: ENCSR052ETC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR417AQU
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB800KJG
size range: 200-600


title: Histone ChIP-seq from heart right ventricle (ENCLB613AMB)

description:
https://www.encodeproject.org/experiments/ENCSR174GMQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on heart right ventricle tissue male adult (69 years).
experiment encode accession: ENCSR174GMQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481SJM
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB613AMB
size range: 200-600

value: heart right ventricle

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

value: 69 year

value: Shin Lin

value: ENCBS926ALQ at ENCODE; https://www.encodeproject.org/ENCBS926ALQ/

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


title: Rpb3 in Log HHF2 Rep1 IP

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


title: Rpb3 in Log 5toA Rep2 Input

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


title: Rpb3 in Log 5toA Rep1 Input


title: Hho1 in Q Rep2 IP

description: Hho1_Q_merged_replicates_input_normalized.bw

source_name: Q cells

value: MATa RAD5+ prototroph HHO1-2L-3FLAG::KanMX

value: FLAG M2 (Sigma-Aldrich #F1804)


title: Histone ChIP-seq from middle frontal area 46 (ENCLB084IOB)

description:
https://www.encodeproject.org/experiments/ENCSR051QLZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (81 years) with Cognitive impairment
experiment encode accession: ENCSR051QLZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR646FGM
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB084IOB
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: adult

value: 81 year

value: Bradley Bernstein, Broad

value: Rush University

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

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB722QFW)

description:
https://www.encodeproject.org/experiments/ENCSR250CLO/
***************
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.
experiment encode accession: ENCSR250CLO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR237ZMF
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB722QFW
size range: 200-600

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

value: female

value: 90 or above year

value: ENCBS547CKT at ENCODE; https://www.encodeproject.org/ENCBS547CKT/

value: Derived from ENCODE donor ENCDO637GUS; https://www.encodeproject.org/ENCDO637GUS/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB433QSY)

description:
https://www.encodeproject.org/experiments/ENCSR051QLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (81 years) with Cognitive impairment
experiment encode accession: ENCSR051QLZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR646FGM
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB433QSY
size range: 200-600


title: Histone ChIP-seq from middle frontal area 46 (ENCLB876NZW)

description:
https://www.encodeproject.org/experiments/ENCSR250CLO/
***************
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.
experiment encode accession: ENCSR250CLO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR237ZMF
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB876NZW
size range: 200-600


title: Histone ChIP-seq from middle frontal area 46 (ENCLB785EQH)

description:
https://www.encodeproject.org/experiments/ENCSR049KUR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment.
experiment encode accession: ENCSR049KUR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR417AQU
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB785EQH
size range: 200-600

value: ENCBS173HMY at ENCODE; https://www.encodeproject.org/ENCBS173HMY/

value: Derived from ENCODE donor ENCDO739EFE; https://www.encodeproject.org/ENCDO739EFE/


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB913XRG)

description:
https://www.encodeproject.org/experiments/ENCSR171BDF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell
experiment encode accession: ENCSR171BDF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR810LRH
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB913XRG

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

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: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB077LGO)

description:
https://www.encodeproject.org/experiments/ENCSR171BDF/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell
experiment encode accession: ENCSR171BDF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR810LRH
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB077LGO


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB428WMA)

description:
https://www.encodeproject.org/experiments/ENCSR053BET/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR053BET
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR070IHF
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB428WMA

value: male

value: adult

value: 42 year

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

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


title: Control ChIP-seq from heart right ventricle (ENCLB075VQE)

description:
https://www.encodeproject.org/experiments/ENCSR049JKQ/
***************
biological replicate number: 1
technical replicate number: 3
description: Control ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR049JKQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB075VQE
size range: 200-600

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

value: heart right ventricle

value: tissue

value: female

value: 59 year

value: Bradley Bernstein, Broad

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: Hho1 in Q Rep1 Input

value: MATa RAD5+ prototroph HHO1-2L-3FLAG::KanMX

value: FLAG M2 (Sigma-Aldrich #F1804)


title: Hho1 in Q Rep2 Input


title: Histone ChIP-seq from middle frontal area 46 (ENCLB024BDN)

description:
https://www.encodeproject.org/experiments/ENCSR049KUR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment.
experiment encode accession: ENCSR049KUR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR417AQU
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB024BDN
size range: 200-600

value: middle frontal area 46

value: 90 or above year

value: Rush University

value: ENCBS173HMY at ENCODE; https://www.encodeproject.org/ENCBS173HMY/

value: Derived from ENCODE donor ENCDO739EFE; https://www.encodeproject.org/ENCDO739EFE/


title: Control ChIP-seq from heart right ventricle (ENCLB929DKN)

description:
https://www.encodeproject.org/experiments/ENCSR049JKQ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR049JKQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB929DKN
size range: 200-600

value: adult


title: Control ChIP-seq from heart left ventricle (ENCLB096RQL)

description:
https://www.encodeproject.org/experiments/ENCSR170MJE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on heart left ventricle tissue male adult (73 years).
experiment encode accession: ENCSR170MJE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB096RQL
size range: 200-600

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

value: heart left ventricle

value: male

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

value: 73 year

value: ENCBS919GVI at ENCODE; https://www.encodeproject.org/ENCBS919GVI/

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


title: Hho1 in Log Rep1 IP

description: Hho1_Log_merged_replicates_input_normalized.bw

source_name: Log cells


title: Control ChIP-seq from heart left ventricle (ENCLB210VVZ)

description:
https://www.encodeproject.org/experiments/ENCSR170MJE/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on heart left ventricle tissue male adult (73 years).
experiment encode accession: ENCSR170MJE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB210VVZ
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad

value: Shin Lin


title: Histone ChIP-seq from heart left ventricle (ENCLB060UIL)

description:
https://www.encodeproject.org/experiments/ENCSR048OAV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR048OAV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB060UIL
size range: 200-600

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

value: 54 year

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: Histone ChIP-seq from heart left ventricle (ENCLB607EHO)

description:
https://www.encodeproject.org/experiments/ENCSR048OAV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR048OAV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB607EHO
size range: 200-600


title: Hho1 in Log Rep2 IP

value: MATa RAD5+ prototroph HHO1-2L-3FLAG::KanMX

value: FLAG M2 (Sigma-Aldrich #F1804)


title: Histone ChIP-seq from middle frontal area 46 (ENCLB481KZQ)

description:
https://www.encodeproject.org/experiments/ENCSR169CRN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease, Cognitive impairment.
experiment encode accession: ENCSR169CRN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR732BRB
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB481KZQ
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: 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 heart right ventricle (ENCLB483WDJ)

description:
https://www.encodeproject.org/experiments/ENCSR174GMQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on heart right ventricle tissue male adult (69 years).
experiment encode accession: ENCSR174GMQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR481SJM
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB483WDJ
size range: 200-600

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

value: heart right ventricle

value: male

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

value: adult

value: 69 year

value: ENCBS926ALQ at ENCODE; https://www.encodeproject.org/ENCBS926ALQ/

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


title: Hho1 in Log Rep1 Input


title: Hho1 in Log Rep2 Input


title: Histone ChIP-seq from middle frontal area 46 (ENCLB710UGI)

description:
https://www.encodeproject.org/experiments/ENCSR169CRN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease, Cognitive impairment.
experiment encode accession: ENCSR169CRN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR732BRB
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB710UGI
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad


title: Hho1 in Q Rep1 IP

description: Hho1_Q_merged_replicates_input_normalized.bw

value: MATa RAD5+ prototroph HHO1-2L-3FLAG::KanMX


title: H4Ac in Q +TSA Rep2 IP

description: H4Ac_Q_TSA_merged_replicates_input_normalized.bw

source_name: Q cells treated with TSA

value: MATa RAD5+ prototroph

value: H4 penta-acetyl (Sigma Millipore #06-946)


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB951WBW)

description:
https://www.encodeproject.org/experiments/ENCSR168LSG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell.
experiment encode accession: ENCSR168LSG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR688UBO
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB951WBW
fragmentation methods: none

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell, preserved by cryopreservation

value: primary cell

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS677DRS at ENCODE; https://www.encodeproject.org/ENCBS677DRS/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB010JMA)

description:
https://www.encodeproject.org/experiments/ENCSR168WMQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..
experiment encode accession: ENCSR168WMQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR299YBY
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB010JMA

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

value: John Stamatoyannopoulos

value: ENCBS521XUI at ENCODE; https://www.encodeproject.org/ENCBS521XUI/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB895LZR)

description:
https://www.encodeproject.org/experiments/ENCSR168LSG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell.
experiment encode accession: ENCSR168LSG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR688UBO
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB895LZR
fragmentation methods: none


title: Giardia lamblia WB: 15279

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

description: stable cell lines

library_source: transcriptomic

data_processing:
Initially, the sequences generated went through a filtering process to obtain qualified reads. ConDeTri(1) was implemented to trim or remove the reads according to the quality score. Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks(2) for gene expression estimation.
Supplementary_files_format_and_content: The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles. The reference genome and gene annotations were retrieved from Ensembl database.

molecule: total RNA

organism: Giardia duodenalis

source_name: 15279 also know as pPSpo11

growth_protocol: PCR amplification and standard cloning techniques were used to insert 15279 gene from genomic DNA and then cloned into the pPop2NHA vector, resulting in plasmid 15279. (15279 also known as pPSpo11)

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).
All procedures were carried out according to the manufacture’s protocol from Illumina. Library construction of all samples were used by TruSeq RNA Sample Prep Kits v2 for   50SE    bp (Single-End or Paired-End) sequencing on Solexa platform. The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit. Raw sequences were obtained from the Illumina GA Pipeline software CASAVA v1.8 and expected to generate   10M    (million reads or Gb) per sample.

treatment_protocol: Giardia  cells were transfected with the 15279 or 5pac_5n plasmid containing the pac gene were selected and maintained with 54 ug/ml puromycin.

value: WB

tag: genotype/variation

value: 15279 (also know as pPSpo11)


title: Control Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB876UBT)

description:
https://www.encodeproject.org/experiments/ENCSR248FZA/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR248FZA
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB876UBT

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

value: male

value: adult

value: 42 year

value: Bradley Bernstein, Broad

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

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


title: Control Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB474VHO)

description:
https://www.encodeproject.org/experiments/ENCSR248FZA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR248FZA
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB474VHO

value: primary cell


title: H4Ac in Q + TSA Rep2 Input

value: MATa RAD5+ prototroph

value: H4 penta-acetyl (Sigma Millipore #06-946)


title: TF ChIP-seq from middle frontal area 46 (ENCLB975UHV)

description:
https://www.encodeproject.org/experiments/ENCSR244KEW/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (88 years) with mild cognitive impairment
experiment encode accession: ENCSR244KEW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR708TMV
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB975UHV
size range: 200-600

source_name: Homo sapiens female adult (88 years) with mild cognitive impairment; middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: tissue

value: female

value: 88 year

value: Rush University

value: ENCBS682YFH at ENCODE; https://www.encodeproject.org/ENCBS682YFH/

value: Derived from ENCODE donor ENCDO151OJB; https://www.encodeproject.org/ENCDO151OJB/


title: TF ChIP-seq from middle frontal area 46 (ENCLB644ORI)

description:
https://www.encodeproject.org/experiments/ENCSR244KEW/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (88 years) with mild cognitive impairment
experiment encode accession: ENCSR244KEW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR708TMV
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB644ORI
size range: 200-600


title: Giardia lamblia WB: 5pac_5n control

institute: College of Medicine, National Taiwan University

description: stable cell lines

source_name: 5pac_5n also know as 5'5n pac

value: WB

value: 5pac_5n (also know as 5'5n pac)


title: Control ChIP-seq from heart right ventricle (ENCLB068LZZ)

description:
https://www.encodeproject.org/experiments/ENCSR049JKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR049JKQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB068LZZ
size range: 200-600

value: heart right ventricle

value: adult

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: H4Ac in Q +TSA Rep1 IP

value: MATa RAD5+ prototroph

value: H4 penta-acetyl (Sigma Millipore #06-946)


title: H4Ac in Q + TSA Rep1 Input


title: PECs 80dynes/cm2_3

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: Sscrofa11.1.96
Supplementary_files_format_and_content: Raw counts measurements

organism: Sus scrofa

source_name: PecD_4 80dy

growth_protocol: Primary porcine aortic ECs used in this study were cultured in DMEM medium supplemented with 10% fetal calf serum and 100 g/mL heparin. Cells were grown in dishes coated with 1% gelatin (Sigma-Aldrich) at 37◦C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA II (Macherey-Nagel) according to the manufacturers’ instructions. The Quality of the all samples per condition was verified using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit (Agilent Technologies).
cDNA libraries were constructed by the Genomic platform of the University of Geneva using the Illumina TruSeq RNA sample Preparation Kit according to the manufacturers’ protocol.
Libraries were sequenced using single-end (100nt-long) on Illumina HiSeq2000. FastQ reads were mapped to the ENSEMBL reference genome (Sscrofa11.1.96) using STAR version 2.4.0j with standard settings, except that any reads mapping to more than one location of the genome (ambiguous reads) were discarded (m=1).

treatment_protocol: Exposure of 48 hours to 2, 30 or 80 dynes/cm2.

tag: cell type

value: endothelial cells

tag: shear stress


title: H4Ac in Q Rep2 IP

description: H4Ac_Q_merged_replicates_input_normalized.bw

source_name: Q cells

tag: genotype


title: PECs 80dynes/cm2_1

source_name: PecA_4 80dy


title: PECs 80dynes/cm2_2

source_name: PecC_4 80dy


title: Control ChIP-seq from heart left ventricle (ENCLB586NNE)

description:
https://www.encodeproject.org/experiments/ENCSR040TRJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR040TRJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB586NNE
size range: 200-600

value: heart left ventricle

value: tissue

value: male

value: 54 year

value: Bradley Bernstein, Broad

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 ChIP-seq from heart left ventricle (ENCLB754KHR)

description:
https://www.encodeproject.org/experiments/ENCSR040TRJ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR040TRJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB754KHR
size range: 200-600

value: adult


title: TF ChIP-seq from middle frontal area 46 (ENCLB309ORP)

description:
https://www.encodeproject.org/experiments/ENCSR168KQC/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR168KQC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR258GSA
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB309ORP
size range: 200-600

source_name: Homo sapiens female adult (84 years) middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: female

value: 84 year

value: Rush University

value: ENCBS224FBK at ENCODE; https://www.encodeproject.org/ENCBS224FBK/

value: Derived from ENCODE donor ENCDO461DJY; https://www.encodeproject.org/ENCDO461DJY/


title: Rpb3 in Log R17R19A Rep2 Input

description: PolII_Log_R17R19A_merged_replicates_input_normalized.bw

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

tag: strain

value: Rpb3 (Biolegend #665003)


title: TF ChIP-seq from middle frontal area 46 (ENCLB796DGN)

description:
https://www.encodeproject.org/experiments/ENCSR168KQC/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR168KQC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR258GSA
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB796DGN
size range: 200-600

value: tissue


title: PECs 30.2dynes/cm2_3

source_name: PecD_3 30dy

value: endothelial cells


title: H4Ac in Q Rep2 Input

value: MATa RAD5+ prototroph

tag: chip antibody

value: H4 penta-acetyl (Sigma Millipore #06-946)


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB916XPE)

description:
https://www.encodeproject.org/experiments/ENCSR168WMQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..
experiment encode accession: ENCSR168WMQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR299YBY
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB916XPE

value: primary cell

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS521XUI at ENCODE; https://www.encodeproject.org/ENCBS521XUI/

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


title: Histone ChIP-seq from heart left ventricle (ENCLB884JZR)

description:
https://www.encodeproject.org/experiments/ENCSR165LOY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on heart left ventricle tissue male adult (73 years).
experiment encode accession: ENCSR165LOY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR170MJE
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB884JZR
size range: 200-600

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

value: heart left ventricle

value: male

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

value: adult

value: 73 year

value: Shin Lin

value: ENCBS919GVI at ENCODE; https://www.encodeproject.org/ENCBS919GVI/

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


title: Histone ChIP-seq from heart left ventricle (ENCLB518RDU)

description:
https://www.encodeproject.org/experiments/ENCSR165LOY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on heart left ventricle tissue male adult (73 years).
experiment encode accession: ENCSR165LOY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR170MJE
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB518RDU
size range: 200-600

value: tissue


title: Control ChIP-seq from middle frontal area 46 (ENCLB335XPN)

description:
https://www.encodeproject.org/experiments/ENCSR237ZMF/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.
experiment encode accession: ENCSR237ZMF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB335XPN
size range: 200-600

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

value: middle frontal area 46

value: female

value: 90 or above year

value: Rush University

value: ENCBS547CKT at ENCODE; https://www.encodeproject.org/ENCBS547CKT/

value: Derived from ENCODE donor ENCDO637GUS; https://www.encodeproject.org/ENCDO637GUS/


title: PECs 30.2dynes/cm2_2

source_name: PecC_3 30dy

value: endothelial cells


title: Control ChIP-seq from middle frontal area 46 (ENCLB865ODD)

description:
https://www.encodeproject.org/experiments/ENCSR237ZMF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.
experiment encode accession: ENCSR237ZMF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB865ODD
size range: 200-600

value: Bradley Bernstein, Broad


title: TF ChIP-seq from middle frontal area 46 (ENCLB586GQC)

description:
https://www.encodeproject.org/experiments/ENCSR237BTA/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR237BTA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR617ONQ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB586GQC
size range: 200-600

source_name: Homo sapiens female adult (81 years) middle frontal area 46 tissue with Alzheimer's disease

value: CTCF

value: 81 year

value: ENCBS554ZGD at ENCODE; https://www.encodeproject.org/ENCBS554ZGD/

value: Derived from ENCODE donor ENCDO097MEH; https://www.encodeproject.org/ENCDO097MEH/


title: H4Ac in Log Rep1 IP

description: H4Ac_Log_merged_replicates_input_normalized.bw

source_name: Log cells

value: MATa RAD5+ prototroph

value: H4 penta-acetyl (Sigma Millipore #06-946)


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB216TEH)

description:
https://www.encodeproject.org/experiments/ENCSR236OFL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR236OFL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR186VDY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB216TEH

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

value: primary cell

value: male

value: adult

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: PECs 30.2dynes/cm2_1

source_name: PecA_3 30dy


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB289MUH)

description:
https://www.encodeproject.org/experiments/ENCSR236OFL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR236OFL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR186VDY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB289MUH


title: TF ChIP-seq from middle frontal area 46 (ENCLB701QQB)

description:
https://www.encodeproject.org/experiments/ENCSR237BTA/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR237BTA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR617ONQ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB701QQB
size range: 200-600

value: middle frontal area 46

value: tissue

value: female

value: Rush University


title: H4Ac in Log Rep2 IP


title: PECs 30.1dynes/cm2_3

source_name: PecD_1 30dy

value: endothelial cells


title: H4Ac in Log Rep2 Input


title: PECs 30.1dynes/cm2_2

source_name: PecC_1 30dy


title: Histone ChIP-seq from middle frontal area 46 (ENCLB935USM)

description:
https://www.encodeproject.org/experiments/ENCSR235BES/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (88 years) with Alzheimer's disease.
experiment encode accession: ENCSR235BES
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR534WQA
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB935USM
size range: 200-600

source_name: Homo sapiens female adult (88 years) with Alzheimer's disease; middle frontal area 46 tissue

value: 88 year

value: Bradley Bernstein, Broad

value: ENCBS995IIS at ENCODE; https://www.encodeproject.org/ENCBS995IIS/

value: Derived from ENCODE donor ENCDO070VNS; https://www.encodeproject.org/ENCDO070VNS/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB327FYJ)

description:
https://www.encodeproject.org/experiments/ENCSR235BES/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (88 years) with Alzheimer's disease.
experiment encode accession: ENCSR235BES
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR534WQA
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB327FYJ
size range: 200-600


title: H4Ac in Q Rep1 IP

description: H4Ac_Q_merged_replicates_input_normalized.bw

value: MATa RAD5+ prototroph

value: H4 penta-acetyl (Sigma Millipore #06-946)


title: Histone ChIP-seq from heart left ventricle (ENCLB412IDO)

description:
https://www.encodeproject.org/experiments/ENCSR165BJO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on heart left ventricle tissue male adult (43 years).
experiment encode accession: ENCSR165BJO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR109IWL
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB412IDO
size range: 200-600

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

value: heart left ventricle

value: male

value: 43 year

value: Shin Lin

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: H4Ac in Log Rep1 Input


title: H3 in Q Rep2 IP

description: H3_Q_merged_replicates_input_normalized.bw


title: H4Ac in Q Rep1 Input


title: Histone ChIP-seq from heart left ventricle (ENCLB478FDI)

description:
https://www.encodeproject.org/experiments/ENCSR165BJO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on heart left ventricle tissue male adult (43 years).
experiment encode accession: ENCSR165BJO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR109IWL
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB478FDI
size range: 200-600

value: tissue

value: adult


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB474IIN)

description:
https://www.encodeproject.org/experiments/ENCSR032XLY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..
experiment encode accession: ENCSR032XLY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR299YBY
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB474IIN

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

value: primary cell

value: not collected

value: unknown

value: John Stamatoyannopoulos

value: ENCBS521XUI at ENCODE; https://www.encodeproject.org/ENCBS521XUI/

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


title: PECs 2dynes/cm2_2

source_name: PecC_2 2dy

value: endothelial cells


title: PECs 2dynes/cm2_1

source_name: PecA_2 2dy


title: H3 in Q Rep1 IP

source_name: Q cells

value: MATa RAD5+ prototroph


title: H3 in Q Rep2 Input


title: Mint-ChIP-seq from activated T-cell (ENCLB882FUM)

description:
https://www.encodeproject.org/experiments/ENCSR163WUL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on activated T-cell male adult (42 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours..
experiment encode accession: ENCSR163WUL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR975DSD
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB882FUM

source_name: Homo sapiens male adult (42 years) activated T-cell primary cell

value: activated T-cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS351GLT at ENCODE; https://www.encodeproject.org/ENCBS351GLT/

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


title: Mint-ChIP-seq from activated T-cell (ENCLB819UIT)

description:
https://www.encodeproject.org/experiments/ENCSR163WUL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on activated T-cell male adult (42 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours..
experiment encode accession: ENCSR163WUL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR975DSD
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB819UIT

value: male


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB358MGM)

description:
https://www.encodeproject.org/experiments/ENCSR030MGY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR030MGY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR186VDY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB358MGM

value: Bradley Bernstein, Broad

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


title: PECs 2dynes/cm2_3

source_name: PecD_2 2dy


title: H3 in Q Rep1 Input


title: Histone ChIP-seq from heart right ventricle (ENCLB203RYS)

description:
https://www.encodeproject.org/experiments/ENCSR159RNX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR159RNX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR049JKQ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB203RYS
size range: 200-600

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

value: heart right ventricle

value: tissue

value: female

value: adult

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 heart right ventricle (ENCLB528OWK)

description:
https://www.encodeproject.org/experiments/ENCSR159RNX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR159RNX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR049JKQ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB528OWK
size range: 200-600


title: PECs 30.1dynes/cm2_1

source_name: PecA_1 30dy

value: endothelial cells


title: H3 in Log Rep2 IP

description: H3_Log_merged_replicates_input_normalized.bw

value: MATa RAD5+ prototroph


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB163JXL)

description:
https://www.encodeproject.org/experiments/ENCSR032XLY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..
experiment encode accession: ENCSR032XLY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR299YBY
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB163JXL

value: primary cell

value: not collected

value: unknown

value: John Stamatoyannopoulos

value: ENCBS521XUI at ENCODE; https://www.encodeproject.org/ENCBS521XUI/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB827XAF)

description:
https://www.encodeproject.org/experiments/ENCSR152MAZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (86 years) with Alzheimer's disease.
experiment encode accession: ENCSR152MAZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR564VBC
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB827XAF
size range: 200-600

source_name: Homo sapiens female adult (86 years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: 86 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS797LUE at ENCODE; https://www.encodeproject.org/ENCBS797LUE/

value: Derived from ENCODE donor ENCDO997SGX; https://www.encodeproject.org/ENCDO997SGX/


title: DNase-seq from kidney (ENCLB501URJ)

description:
https://www.encodeproject.org/experiments/ENCSR956RAI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR956RAI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB501URJ

organism: Mus musculus

source_name: Mus musculus strain B6CASTF1/J female (10 days) kidney tissue

value: kidney

value: tissue

tag: description

value: B6Cast F1 PND10 3x Females 05 kidney for Altius Stam core

value: female

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS140YRJ at ENCODE; https://www.encodeproject.org/ENCBS140YRJ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: TF ChIP-seq from middle frontal area 46 (ENCLB601VZP)

description:
https://www.encodeproject.org/experiments/ENCSR230RQK/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.
experiment encode accession: ENCSR230RQK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR237ZMF
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB601VZP
size range: 200-600

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

value: CTCF

tag: biosample encode accession

value: adult

value: 90 or above year

value: ENCBS547CKT at ENCODE; https://www.encodeproject.org/ENCBS547CKT/

value: Derived from ENCODE donor ENCDO637GUS; https://www.encodeproject.org/ENCDO637GUS/


title: TF ChIP-seq from middle frontal area 46 (ENCLB674EBG)

description:
https://www.encodeproject.org/experiments/ENCSR230RQK/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.
experiment encode accession: ENCSR230RQK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR237ZMF
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB674EBG
size range: 200-600

value: middle frontal area 46

tag: Sex

value: Bradley Bernstein, Broad

value: Rush University


title: Histone ChIP-seq from middle frontal area 46 (ENCLB415ADX)

description:
https://www.encodeproject.org/experiments/ENCSR016JFP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (88 years) with Alzheimer's disease.
experiment encode accession: ENCSR016JFP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR534WQA
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB415ADX
size range: 200-600

value: 88 year

value: ENCBS995IIS at ENCODE; https://www.encodeproject.org/ENCBS995IIS/

value: Derived from ENCODE donor ENCDO070VNS; https://www.encodeproject.org/ENCDO070VNS/


title: H3 in Log Rep2 Input

source_name: Log cells

value: MATa RAD5+ prototroph


title: Histone ChIP-seq from middle frontal area 46 (ENCLB653XTT)

description:
https://www.encodeproject.org/experiments/ENCSR016JFP/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (88 years) with Alzheimer's disease.
experiment encode accession: ENCSR016JFP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR534WQA
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB653XTT
size range: 200-600

value: tissue

value: female


title: Mint-ChIP-seq from WTC11 (ENCLB872KBT)

description:
https://www.encodeproject.org/experiments/ENCSR146DPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR146DPQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB872KBT

source_name: Homo sapiens WTC11 cell line

tag: line

value: cell line

value: male

value: 30 year

value: Yin Shen

tag: passage number

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

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


title: H3 in Log Rep1 IP


title: Mint-ChIP-seq from WTC11 (ENCLB300MON)

description:
https://www.encodeproject.org/experiments/ENCSR146DPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR146DPQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB300MON

tag: dev stage

value: adult

tag: age

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


title: DNase-seq from kidney (ENCLB591GYO)

description:
https://www.encodeproject.org/experiments/ENCSR692ASO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR692ASO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB591GYO

source_name: Mus musculus strain B6CASTF1/J male (4 days) kidney tissue

value: kidney

value: B6Cast F1 PND4 3x Males 05 kidney for Altius Stam core

value: unknown

value: 4 day

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

value: ENCBS209QZR at ENCODE; https://www.encodeproject.org/ENCBS209QZR/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Mint-ChIP-seq from WTC11 (ENCLB937TAM)

description:
https://www.encodeproject.org/experiments/ENCSR146DPQ/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR146DPQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB937TAM

tag: antibody

value: Bradley Bernstein, Broad

tag: link


title: H3 in Log Rep1 Input

value: MATa RAD5+ prototroph


title: Mint-ChIP-seq from WTC11 (ENCLB647YEP)

description:
https://www.encodeproject.org/experiments/ENCSR146DPQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR146DPQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB647YEP

value: cell line

value: male


title: DNase-seq from kidney (ENCLB184XAY)

description:
https://www.encodeproject.org/experiments/ENCSR956RAI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR956RAI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB184XAY

value: tissue

value: B6Cast F1 PND10 3x Females 06 kidney for Altius Stam core

value: female

value: 10 day

value: ENCBS363EKC at ENCODE; https://www.encodeproject.org/ENCBS363EKC/


title: Mint-ChIP-seq from neural crest cell (ENCLB732HGK)

description:
https://www.encodeproject.org/experiments/ENCSR012MIG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on neural crest cell
experiment encode accession: ENCSR012MIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR713YQD
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB732HGK
fragmentation methods: none

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

value: neural crest cell

value: in vitro differentiated cells

value: WA09 derived neural crest cells

tag: health state

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS200JOD at ENCODE; https://www.encodeproject.org/ENCBS200JOD/

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


title: DNase-seq from kidney (ENCLB242DDY)

description:
https://www.encodeproject.org/experiments/ENCSR939NQH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR939NQH
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB242DDY
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Mus musculus strain B6CASTF1/J female (25 days) kidney tissue

value: kidney

value: B6Cast F1 PND25 Female 06 kidney for Altius Stam core

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS664APR at ENCODE; https://www.encodeproject.org/ENCBS664APR/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: DNase-seq from layer of hippocampus (ENCLB854VCZ)

description:
https://www.encodeproject.org/experiments/ENCSR688XLI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR688XLI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB854VCZ

source_name: Mus musculus strain B6CASTF1/J male (10 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: B6Cast F1 PND10 3x male Hippocampus

value: male

value: 10 day

value: ENCBS592TLQ at ENCODE; https://www.encodeproject.org/ENCBS592TLQ/


title: DNase-seq from layer of hippocampus (ENCLB314POF)

description:
https://www.encodeproject.org/experiments/ENCSR688XLI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR688XLI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB314POF

value: ENCBS688WYJ at ENCODE; https://www.encodeproject.org/ENCBS688WYJ/


title: Mint-ChIP-seq from neural crest cell (ENCLB631QWV)

description:
https://www.encodeproject.org/experiments/ENCSR012MIG/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on neural crest cell
experiment encode accession: ENCSR012MIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR713YQD
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB631QWV

value: neural crest cell

value: in vitro differentiated cells

value: WA09 derived neural crest cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS417JEU at ENCODE; https://www.encodeproject.org/ENCBS417JEU/


title: Brn1 in Q R17R19A Rep1 IP

description: Brn1_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 Brn1-2L-3FLAG::KanMX

value: FLAG M2 (Sigma-Aldrich #F1804)


title: Brn1 in Q R17R19A Rep2 Input


title: Mint-ChIP-seq from neural crest cell (ENCLB340QAM)

description:
https://www.encodeproject.org/experiments/ENCSR012MIG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on neural crest cell
experiment encode accession: ENCSR012MIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR713YQD
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB340QAM
fragmentation methods: none

value: ENCBS200JOD at ENCODE; https://www.encodeproject.org/ENCBS200JOD/

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


title: Brn1 in Q R17R19A Rep2 IP


title: Brn1 in Q R17R19A Rep1 Input