title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB202CVP)

description:
https://www.encodeproject.org/experiments/ENCSR789TBW/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR789TBW
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB202CVP
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: primary cell

value: male

value: adult

value: 6 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS548NEG at ENCODE; https://www.encodeproject.org/ENCBS548NEG/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: DNase-seq from heart (ENCLB460DVX)

status: Public on Nov 04 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR657WHR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR657WHR
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB460DVX

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: Mus musculus strain B6CASTF1/J male (14 days) heart tissue

value: heart

value: tissue

tag: description

value: B6Cast F1 PND14 Male 06 heart for Altius Stam biobank

tag: biosample encode accession

tag: Sex

tag: dev stage

value: unknown

tag: age

value: 14 day

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS032GQQ at ENCODE; https://www.encodeproject.org/ENCBS032GQQ/

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


title: Control ChIP-seq from spleen (ENCLB142HKG)

description:
https://www.encodeproject.org/experiments/ENCSR119AVG/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on spleen tissue female adult (61 years)
experiment encode accession: ENCSR119AVG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-06-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB142HKG
size range: 200-600

organism: Homo sapiens

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

value: spleen

value: female

value: 61 year

value: Bradley Bernstein, Broad

value: Shin Lin

tag: health state

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

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

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


title: Mint-ChIP-seq from endodermal cell (ENCLB469KJK)

description:
https://www.encodeproject.org/experiments/ENCSR121HJH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on endodermal cell originated from H1
experiment encode accession: ENCSR121HJH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR637MGY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB469KJK

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

tag: antibody

value: endodermal cell

value: in vitro differentiated cells

value: male

value: embryonic

value: not collected

value: Job Dekker, UMass

value: René Maehr

value: healthy

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

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


title: Mint-ChIP-seq from endodermal cell (ENCLB729SDV)

description:
https://www.encodeproject.org/experiments/ENCSR121HJH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on endodermal cell originated from H1
experiment encode accession: ENCSR121HJH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR637MGY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB729SDV


title: Control ChIP-seq from spleen (ENCLB632OFH)

description:
https://www.encodeproject.org/experiments/ENCSR119AVG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on spleen tissue female adult (61 years)
experiment encode accession: ENCSR119AVG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-06-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB632OFH
size range: 200-600

value: spleen

value: tissue

value: female

value: adult


title: DNase-seq from urinary bladder (ENCLB182GGC)

description:
https://www.encodeproject.org/experiments/ENCSR863SWY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR863SWY
assay title: DNase-seq
assembly: mm10
encode release date: 2021-07-15
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB182GGC

source_name: Mus musculus strain B6CASTF1/J female (4 days) urinary bladder tissue

value: urinary bladder

value: B6Cast F1 PND4 Female 05 urinary bladder for Altius Stam biobank

value: unknown

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS089CNP at ENCODE; https://www.encodeproject.org/ENCBS089CNP/

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


title: Mint-ChIP-seq from chondrocyte (ENCLB971RAP)

description:
https://www.encodeproject.org/experiments/ENCSR117SLI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on chondrocyte.
experiment encode accession: ENCSR117SLI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466ZEA
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB971RAP

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

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS497BNU at ENCODE; https://www.encodeproject.org/ENCBS497BNU/

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


title: DNase-seq from urinary bladder (ENCLB342MBE)

description:
https://www.encodeproject.org/experiments/ENCSR863SWY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR863SWY
assay title: DNase-seq
assembly: mm10
encode release date: 2021-07-15
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB342MBE

value: urinary bladder

value: tissue

value: B6Cast F1 PND4 Female 06 urinary bladder for Altius Stam biobank

value: female

value: ENCBS780FEQ at ENCODE; https://www.encodeproject.org/ENCBS780FEQ/


title: Mint-ChIP-seq from chondrocyte (ENCLB251BIA)

description:
https://www.encodeproject.org/experiments/ENCSR117SLI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on chondrocyte.
experiment encode accession: ENCSR117SLI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466ZEA
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251BIA

value: healthy


title: Mint-ChIP-seq from chondrocyte (ENCLB049BXV)

description:
https://www.encodeproject.org/experiments/ENCSR117SLI/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on chondrocyte.
experiment encode accession: ENCSR117SLI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466ZEA
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB049BXV

value: ENCBS434TAN at ENCODE; https://www.encodeproject.org/ENCBS434TAN/


title: Histone ChIP-seq from heart left ventricle (ENCLB557IDE)

description:
https://www.encodeproject.org/experiments/ENCSR123OMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on heart left ventricle tissue male adult (66 years).
experiment encode accession: ENCSR123OMJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR061EXX
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB557IDE
size range: 200-600

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

value: heart left ventricle

value: male

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

value: adult

value: 66 year

value: Shin Lin

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

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


title: polyA plus RNA-seq from regulatory T cell (ENCLB710RZU)

description:
https://www.encodeproject.org/experiments/ENCSR486LMB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR486LMB
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB710RZU
fragmentation methods: shearing (Covaris generic)
size range: 100-300

library_source: transcriptomic

molecule: total RNA

source_name: Mus musculus male (9 weeks) regulatory T primary cell originated from whole organism

value: regulatory T cell

value: primary cell

value: unknown

value: 9 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS882ARJ at ENCODE; https://www.encodeproject.org/ENCBS882ARJ/

value: Derived from ENCODE donor ENCDO200AUG; https://www.encodeproject.org/ENCDO200AUG/


title: TF ChIP-seq from middle frontal area 46 (ENCLB258LMD)

description:
https://www.encodeproject.org/experiments/ENCSR329KRE/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (89 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR329KRE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR151NEZ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB258LMD
size range: 200-600

source_name: Homo sapiens female adult (89 years) middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: tissue

value: female

value: 89 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS738TIQ at ENCODE; https://www.encodeproject.org/ENCBS738TIQ/

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


title: DNase-seq from heart (ENCLB317WUS)

description:
https://www.encodeproject.org/experiments/ENCSR961EFP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR961EFP
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB317WUS

source_name: Mus musculus strain B6CASTF1/J female (4 days) heart tissue

value: heart

value: B6Cast F1 PND4 Female 05 heart for Altius Stam biobank

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS567MZA at ENCODE; https://www.encodeproject.org/ENCBS567MZA/

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


title: polyA plus RNA-seq from regulatory T cell (ENCLB413QXA)

description:
https://www.encodeproject.org/experiments/ENCSR480XMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR480XMW
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB413QXA
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (4 months) regulatory T primary cell originated from bone marrow hematopoietic cell

value: regulatory T cell

value: primary cell

value: male

value: adult

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS521XWU at ENCODE; https://www.encodeproject.org/ENCBS521XWU/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: DNase-seq from heart (ENCLB290GOS)

description:
https://www.encodeproject.org/experiments/ENCSR961EFP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961EFP
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB290GOS

value: tissue

value: B6Cast F1 PND4 Female 06 heart for Altius Stam biobank

value: female

value: unknown

value: ENCBS486UHR at ENCODE; https://www.encodeproject.org/ENCBS486UHR/


title: DNase-seq from kidney (ENCLB065UFL)

description:
https://www.encodeproject.org/experiments/ENCSR706HQD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR706HQD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB065UFL

source_name: Mus musculus strain B6CASTF1/J female adult (18-20 months) kidney tissue

value: kidney

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS730KPY at ENCODE; https://www.encodeproject.org/ENCBS730KPY/


title: polyA plus RNA-seq from regulatory T cell (ENCLB803YPV)

description:
https://www.encodeproject.org/experiments/ENCSR479UTA/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR479UTA
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB803YPV
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus adult (4 months) regulatory T primary cell originated from bone marrow hematopoietic cell

value: regulatory T cell

value: primary cell

value: not collected

value: adult

value: ENCBS340LXJ at ENCODE; https://www.encodeproject.org/ENCBS340LXJ/


title: polyA plus RNA-seq from regulatory T cell (ENCLB697GWY)

description:
https://www.encodeproject.org/experiments/ENCSR486LMB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR486LMB
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB697GWY
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: male

value: 9 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS882ARJ at ENCODE; https://www.encodeproject.org/ENCBS882ARJ/

value: Derived from ENCODE donor ENCDO200AUG; https://www.encodeproject.org/ENCDO200AUG/


title: DNase-seq from kidney (ENCLB195WJI)

description:
https://www.encodeproject.org/experiments/ENCSR706HQD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR706HQD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB195WJI

value: kidney

value: tissue

value: female

value: ENCBS382LCV at ENCODE; https://www.encodeproject.org/ENCBS382LCV/

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


title: DNase-seq from testis (ENCLB587ESA)

description:
https://www.encodeproject.org/experiments/ENCSR443DSO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR443DSO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB587ESA

source_name: Mus musculus strain B6CASTF1/J male (14 days) testis tissue

value: testis

value: B6Cast F1 PND14 Male 06 testis for Altius Stam biobank

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS799DEP at ENCODE; https://www.encodeproject.org/ENCBS799DEP/


title: polyA plus RNA-seq from regulatory T cell (ENCLB338QFX)

description:
https://www.encodeproject.org/experiments/ENCSR479UTA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR479UTA
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB338QFX
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: regulatory T cell

value: primary cell

value: not collected

value: adult

value: 4 month

value: ENCBS340LXJ at ENCODE; https://www.encodeproject.org/ENCBS340LXJ/


title: Histone ChIP-seq from regulatory T cell (ENCLB750DQB)

description:
https://www.encodeproject.org/experiments/ENCSR896QWJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR896QWJ
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB750DQB

value: male

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS044PBX at ENCODE; https://www.encodeproject.org/ENCBS044PBX/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB337TMV)

description:
https://www.encodeproject.org/experiments/ENCSR116MKX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (88 years) with mild cognitive impairment
experiment encode accession: ENCSR116MKX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR708TMV
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB337TMV
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: female

value: 88 year

value: Bradley Bernstein, Broad

value: Rush University

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

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


title: Mint-ChIP-seq from T-helper 2 cell (ENCLB826LKX)

description:
https://www.encodeproject.org/experiments/ENCSR327ZJA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4
experiment encode accession: ENCSR327ZJA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR635PGB
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB826LKX

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

value: T-helper 2 cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

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

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

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


title: Mint-ChIP-seq from T-helper 2 cell (ENCLB012JQM)

description:
https://www.encodeproject.org/experiments/ENCSR327ZJA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4
experiment encode accession: ENCSR327ZJA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR635PGB
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB012JQM

value: male

value: adult


title: Histone ChIP-seq from middle frontal area 46 (ENCLB093DUP)

description:
https://www.encodeproject.org/experiments/ENCSR326YRW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment.
experiment encode accession: ENCSR326YRW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583BXC
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB093DUP
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 90 or above year

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

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


title: Mint-ChIP-seq from chondrocyte (ENCLB252AZX)

description:
https://www.encodeproject.org/experiments/ENCSR115EBL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on chondrocyte
experiment encode accession: ENCSR115EBL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466ZEA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB252AZX
fragmentation methods: none

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS434TAN at ENCODE; https://www.encodeproject.org/ENCBS434TAN/

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


title: Mint-ChIP-seq from chondrocyte (ENCLB017PNE)

description:
https://www.encodeproject.org/experiments/ENCSR117SLI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on chondrocyte.
experiment encode accession: ENCSR117SLI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466ZEA
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB017PNE


title: Mint-ChIP-seq from chondrocyte (ENCLB168LGW)

description:
https://www.encodeproject.org/experiments/ENCSR115EBL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on chondrocyte
experiment encode accession: ENCSR115EBL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466ZEA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB168LGW
fragmentation methods: none


title: Histone ChIP-seq from middle frontal area 46 (ENCLB542WZZ)

description:
https://www.encodeproject.org/experiments/ENCSR326YRW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment.
experiment encode accession: ENCSR326YRW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583BXC
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB542WZZ
size range: 200-600

value: adult

value: Rush University


title: Mint-ChIP-seq from chondrocyte (ENCLB056OZV)

description:
https://www.encodeproject.org/experiments/ENCSR115EBL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on chondrocyte
experiment encode accession: ENCSR115EBL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466ZEA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB056OZV

value: ENCBS497BNU at ENCODE; https://www.encodeproject.org/ENCBS497BNU/


title: Mint-ChIP-seq from chondrocyte (ENCLB110UFD)

description:
https://www.encodeproject.org/experiments/ENCSR115EBL/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on chondrocyte
experiment encode accession: ENCSR115EBL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466ZEA
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB110UFD


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB677CBJ)

description:
https://www.encodeproject.org/experiments/ENCSR889IRT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR889IRT
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB677CBJ
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus strain B6.SJL-Ptprca Pepcb/BoyJ male adult (5 months) naive thymus-derived CD4-positive, alpha-beta T primary cell originated from whole organism

value: primary cell

value: male

value: 5 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS761GOT at ENCODE; https://www.encodeproject.org/ENCBS761GOT/

value: Derived from ENCODE donor ENCDO620MAO; https://www.encodeproject.org/ENCDO620MAO/


title: DNase-seq from testis (ENCLB980AWC)

description:
https://www.encodeproject.org/experiments/ENCSR443DSO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR443DSO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB980AWC

value: testis

value: tissue

value: B6Cast F1 PND14 3x Males 05 testis for Altius Stam biobank

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS925TFJ at ENCODE; https://www.encodeproject.org/ENCBS925TFJ/

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


title: TF ChIP-seq from middle frontal area 46 (ENCLB378DRY)

description:
https://www.encodeproject.org/experiments/ENCSR329KRE/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (89 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR329KRE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR151NEZ
encode release date: 2021-07-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB378DRY
size range: 200-600

value: CTCF

value: middle frontal area 46

value: female

value: adult

value: 89 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS738TIQ at ENCODE; https://www.encodeproject.org/ENCBS738TIQ/

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


title: Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCLB158RRG)

description:
https://www.encodeproject.org/experiments/ENCSR324IEM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR324IEM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR398KXE
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB158RRG

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

value: primary cell

value: male

value: 42 year

value: John Stamatoyannopoulos

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

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


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB797DIP)

description:
https://www.encodeproject.org/experiments/ENCSR889IRT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR889IRT
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB797DIP
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: 5 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS761GOT at ENCODE; https://www.encodeproject.org/ENCBS761GOT/

value: Derived from ENCODE donor ENCDO620MAO; https://www.encodeproject.org/ENCDO620MAO/


title: Histone ChIP-seq from activated regulatory T cell (ENCLB438MYH)

description:
https://www.encodeproject.org/experiments/ENCSR969CUM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR969CUM
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB438MYH

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (4 months) activated regulatory T primary cell originated from bone marrow hematopoietic cell

value: activated regulatory T cell

value: adult

value: 4 month

value: ENCBS107SNL at ENCODE; https://www.encodeproject.org/ENCBS107SNL/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: DNase-seq from gastrocnemius (ENCLB080WQT)

description:
https://www.encodeproject.org/experiments/ENCSR639OQQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639OQQ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB080WQT

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

value: gastrocnemius

value: tissue

value: B6Cast F1 PND4 3x Males 06 gastrocnemius for Altius Stam core

value: unknown

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS709WWH at ENCODE; https://www.encodeproject.org/ENCBS709WWH/

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


title: polyA plus RNA-seq from regulatory T cell (ENCLB534WSH)

description:
https://www.encodeproject.org/experiments/ENCSR480XMW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR480XMW
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB534WSH
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: regulatory T cell

value: primary cell

value: male

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS521XWU at ENCODE; https://www.encodeproject.org/ENCBS521XWU/


title: Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCLB756NDA)

description:
https://www.encodeproject.org/experiments/ENCSR324IEM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (42 years)
experiment encode accession: ENCSR324IEM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR398KXE
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB756NDA

value: adult

value: 42 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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


title: DNase-seq from gastrocnemius (ENCLB304RBU)

description:
https://www.encodeproject.org/experiments/ENCSR701ODD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR701ODD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB304RBU

source_name: Mus musculus strain B6CASTF1/J male (10 days) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: B6Cast F1 PND10 3x Males 06 gastrocnemius for Altius Stam core

value: unknown

value: 10 day

value: ENCBS228CJW at ENCODE; https://www.encodeproject.org/ENCBS228CJW/


title: Histone ChIP-seq from heart right ventricle (ENCLB111GGE)

description:
https://www.encodeproject.org/experiments/ENCSR324APQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR324APQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR049JKQ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB111GGE
size range: 200-600

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

value: heart right ventricle

value: female

value: 59 year

value: 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 middle frontal area 46 (ENCLB665KFM)

description:
https://www.encodeproject.org/experiments/ENCSR116MKX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (88 years) with mild cognitive impairment
experiment encode accession: ENCSR116MKX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR708TMV
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB665KFM
size range: 200-600

value: middle frontal area 46

value: adult

value: 88 year

value: Bradley Bernstein, Broad

value: Rush University

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

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


title: Histone ChIP-seq from heart right ventricle (ENCLB251GKZ)

description:
https://www.encodeproject.org/experiments/ENCSR324APQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on heart right ventricle tissue female adult (59 years).
experiment encode accession: ENCSR324APQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR049JKQ
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251GKZ
size range: 200-600

value: tissue


title: polyA plus RNA-seq from regulatory T cell (ENCLB106LYV)

description:
https://www.encodeproject.org/experiments/ENCSR479UTA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR479UTA
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB106LYV
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: regulatory T cell

value: primary cell

value: not collected

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS340LXJ at ENCODE; https://www.encodeproject.org/ENCBS340LXJ/


title: TF ChIP-seq from heart right ventricle (ENCLB199TYD)

description:
https://www.encodeproject.org/experiments/ENCSR323ZAP/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF TF ChIP-seq on heart right ventricle tissue female adult (56 years).
experiment encode accession: ENCSR323ZAP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR278ACD
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB199TYD
size range: 200-600

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

value: CTCF

value: heart right ventricle

value: female

value: 56 year

value: Shin Lin

value: PGD

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

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


title: TF ChIP-seq from heart right ventricle (ENCLB497IQD)

description:
https://www.encodeproject.org/experiments/ENCSR323ZAP/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF TF ChIP-seq on heart right ventricle tissue female adult (56 years).
experiment encode accession: ENCSR323ZAP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR278ACD
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB497IQD
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB550GZI)

description:
https://www.encodeproject.org/experiments/ENCSR889IRT/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR889IRT
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB550GZI
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: male

value: 5 month

value: ENCBS761GOT at ENCODE; https://www.encodeproject.org/ENCBS761GOT/

value: Derived from ENCODE donor ENCDO620MAO; https://www.encodeproject.org/ENCDO620MAO/


title: DNase-seq from cerebellum (ENCLB466FWB)

description:
https://www.encodeproject.org/experiments/ENCSR641YOC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR641YOC
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB466FWB

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

value: cerebellum

value: tissue

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

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS266AID at ENCODE; https://www.encodeproject.org/ENCBS266AID/

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


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB447RLA)

description:
https://www.encodeproject.org/experiments/ENCSR726DNP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR726DNP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB447RLA
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus male (9 weeks) activated regulatory T primary cell originated from whole organism

value: activated regulatory T cell

value: primary cell

value: 9 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS284MHK at ENCODE; https://www.encodeproject.org/ENCBS284MHK/

value: Derived from ENCODE donor ENCDO200AUG; https://www.encodeproject.org/ENCDO200AUG/


title: DNase-seq from gastrocnemius (ENCLB442KFX)

description:
https://www.encodeproject.org/experiments/ENCSR566VOB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR566VOB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB442KFX

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

value: gastrocnemius

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

value: female

value: ENCBS279UZL at ENCODE; https://www.encodeproject.org/ENCBS279UZL/


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB948XKN)

description:
https://www.encodeproject.org/experiments/ENCSR726DNP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR726DNP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB948XKN
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: male

value: unknown


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB989XAG)

description:
https://www.encodeproject.org/experiments/ENCSR112DVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on progenitor cell of endocrine pancreas
experiment encode accession: ENCSR112DVZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546XZC
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB989XAG

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: healthy

value: ENCBS832MSN at ENCODE; https://www.encodeproject.org/ENCBS832MSN/

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


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB675WVA)

description:
https://www.encodeproject.org/experiments/ENCSR112DVZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on progenitor cell of endocrine pancreas
experiment encode accession: ENCSR112DVZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546XZC
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB675WVA


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB278HWL)

description:
https://www.encodeproject.org/experiments/ENCSR112DVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on progenitor cell of endocrine pancreas
experiment encode accession: ENCSR112DVZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546XZC
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB278HWL

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells originated from progenitor cell of endocrine pancreas

value: ENCBS825BIV at ENCODE; https://www.encodeproject.org/ENCBS825BIV/


title: Mint-ChIP-seq from endodermal cell (ENCLB275NSM)

description:
https://www.encodeproject.org/experiments/ENCSR322YYC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on endodermal cell originated from H1
experiment encode accession: ENCSR322YYC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR637MGY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB275NSM

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

value: endodermal cell

value: not collected

value: Job Dekker, UMass

value: René Maehr

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

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


title: DNase-seq from kidney (ENCLB019QBM)

description:
https://www.encodeproject.org/experiments/ENCSR634ZDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR634ZDI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB019QBM

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

value: kidney

value: tissue

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

value: female

value: unknown

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS054TXJ at ENCODE; https://www.encodeproject.org/ENCBS054TXJ/

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


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB849OFM)

description:
https://www.encodeproject.org/experiments/ENCSR726DNP/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR726DNP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB849OFM
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: activated regulatory T cell

value: primary cell

value: male

value: 9 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS284MHK at ENCODE; https://www.encodeproject.org/ENCBS284MHK/

value: Derived from ENCODE donor ENCDO200AUG; https://www.encodeproject.org/ENCDO200AUG/


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB203SPQ)

description:
https://www.encodeproject.org/experiments/ENCSR112DVZ/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on progenitor cell of endocrine pancreas
experiment encode accession: ENCSR112DVZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546XZC
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB203SPQ

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS825BIV at ENCODE; https://www.encodeproject.org/ENCBS825BIV/

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


title: DNase-seq from left cerebral cortex (ENCLB628CPQ)

description:
https://www.encodeproject.org/experiments/ENCSR552BOB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR552BOB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB628CPQ

source_name: Mus musculus strain B6CASTF1/J female (36 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND36 Female 05 left cerebral cortex for Altius Stam biobank

value: female

value: unknown

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS072HKQ at ENCODE; https://www.encodeproject.org/ENCBS072HKQ/

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


title: Histone ChIP-seq from regulatory T cell (ENCLB271QHY)

description:
https://www.encodeproject.org/experiments/ENCSR874WRY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR874WRY
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB271QHY

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (4 months) regulatory T primary cell originated from bone marrow hematopoietic cell

value: regulatory T cell

value: primary cell

value: male

value: adult

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS044PBX at ENCODE; https://www.encodeproject.org/ENCBS044PBX/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: DNase-seq from left cerebral cortex (ENCLB074SML)

description:
https://www.encodeproject.org/experiments/ENCSR552BOB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR552BOB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB074SML

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND36 Female 06 left cerebral cortex for Altius Stam biobank

value: ENCBS827WAS at ENCODE; https://www.encodeproject.org/ENCBS827WAS/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB007HES)

description:
https://www.encodeproject.org/experiments/ENCSR315UUP/
***************
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: ENCSR315UUP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR386UHY
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB007HES
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: Bradley Bernstein, Broad

value: Rush University

value: ENCBS145CCA at ENCODE; https://www.encodeproject.org/ENCBS145CCA/

value: Derived from ENCODE donor ENCDO847KYQ; https://www.encodeproject.org/ENCDO847KYQ/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB320RPL)

description:
https://www.encodeproject.org/experiments/ENCSR315UUP/
***************
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: ENCSR315UUP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR386UHY
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB320RPL
size range: 200-600

value: adult


title: Histone ChIP-seq from regulatory T cell (ENCLB769NHO)

description:
https://www.encodeproject.org/experiments/ENCSR874WRY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR874WRY
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB769NHO

value: regulatory T cell

value: primary cell

value: male

value: 4 month


title: DNase-seq from gastrocnemius (ENCLB024AWM)

description:
https://www.encodeproject.org/experiments/ENCSR618EUZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR618EUZ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB024AWM

source_name: Mus musculus strain B6CASTF1/J male adult (18-20 months) gastrocnemius tissue

value: gastrocnemius

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS251CPK at ENCODE; https://www.encodeproject.org/ENCBS251CPK/

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


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB582BLB)

description:
https://www.encodeproject.org/experiments/ENCSR711SJN/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR711SJN
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB582BLB
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: activated regulatory T cell

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS113IML at ENCODE; https://www.encodeproject.org/ENCBS113IML/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: Histone ChIP-seq from activated regulatory T cell (ENCLB673PPR)

description:
https://www.encodeproject.org/experiments/ENCSR969CUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR969CUM
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB673PPR

value: adult

value: ENCBS107SNL at ENCODE; https://www.encodeproject.org/ENCBS107SNL/


title: [RNA-Seq] Human brain pericytes_T50_replicate4

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

country: Australia

institute: University of Sydney

description:
RNA-seq profile
T0-50.csv

data_processing:
RNA-seq reads were aligned to Ensembl hg38 H. sapiens reference transcriptome using Hisat2.
StringTie was utilized to assemble and quantify expressed transcripts.
The transcript abundance and differential expression tables were generated using Ballgown.
Gene ontology (GO) enrichment analysis was done using the NetworkAnalyst platform and the Reactome database as reference for transcripts with p<0.001
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited csv files represent log2fold change and FDR

molecule: polyA RNA

source_name: Human brain pericytes

growth_protocol: Human neural pericytes were purchased from ScienCell (Carlsbad, CA; #1200). Human neural pericytes were cultured in Dulbecco's Modified Eagle Medium/F12 (DMEM/F12) supplemented with 10% fetal calf serum, recombinant human FGF‐2 20 ng/ml (R&D Systems, 233‐FB), and Antibiotic‐Antimycotic (100×, Life Technologies).

extract_protocol:
RNA was harvested using Bioline RNA isolation kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In order to simulate the combined effect of absence of mechanical cues and enhanced reductive stress on induction of pro-neural transcription factors, we cultured pericytes in serum-free neurobasal medium (Gibco) containing the reductive N2 supplement (0.25mM transferrin-bound Fe3+, redox potential of Fe3+/Fe2+: +0.77 volts, Gibco) and GlutaMAX (Gibco).

tag: group

value: Transdifferentiating

tag: time

value: 50 min

tag: treatment

value: N2 medium


title: Mint-ChIP-seq from endodermal cell (ENCLB837FCT)

description:
https://www.encodeproject.org/experiments/ENCSR322YYC/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on endodermal cell originated from H1
experiment encode accession: ENCSR322YYC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR637MGY
encode release date: 2021-06-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB837FCT

value: endodermal cell

value: in vitro differentiated cells

value: male

value: embryonic

value: not collected

value: Job Dekker, UMass

value: René Maehr

value: healthy

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

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


title: [RNA-Seq] Human brain pericytes_T50_replicate3

description:
RNA-seq profile
T0-50.csv


title: [RNA-Seq] Human brain pericytes_T50

description:
RNA-seq profile
T0-50.csv


title: [RNA-Seq] Human brain pericytes_T20_replicate4

description:
RNA-seq profile
T0-20.csv

value: 20 min


title: DNase-seq from kidney (ENCLB117MPB)

description:
https://www.encodeproject.org/experiments/ENCSR697ADE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR697ADE
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB117MPB

source_name: Mus musculus strain B6CASTF1/J male adult (18-20 months) kidney tissue

value: kidney

value: tissue

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS434SOA at ENCODE; https://www.encodeproject.org/ENCBS434SOA/

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


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB204CTK)

description:
https://www.encodeproject.org/experiments/ENCSR711SJN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR711SJN
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB204CTK
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (4 months) activated regulatory T primary cell originated from bone marrow hematopoietic cell

value: activated regulatory T cell

value: primary cell

value: male

value: adult

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS113IML at ENCODE; https://www.encodeproject.org/ENCBS113IML/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: [RNA-Seq] Human brain pericytes_T20_replicate3

description:
RNA-seq profile
T0-20.csv

value: Transdifferentiating

value: 20 min

value: N2 medium


title: DNase-seq from gastrocnemius (ENCLB903WCR)

description:
https://www.encodeproject.org/experiments/ENCSR618EUZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR618EUZ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB903WCR

value: gastrocnemius

value: tissue

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: ENCBS350SIV at ENCODE; https://www.encodeproject.org/ENCBS350SIV/


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB851MVO)

description:
https://www.encodeproject.org/experiments/ENCSR711SJN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR711SJN
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB851MVO
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: activated regulatory T cell


title: DNase-seq from kidney (ENCLB465GGM)

description:
https://www.encodeproject.org/experiments/ENCSR697ADE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR697ADE
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB465GGM

value: kidney

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS274TKP at ENCODE; https://www.encodeproject.org/ENCBS274TKP/

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


title: [RNA-Seq] Human brain pericytes_T15_replicate4

description:
RNA-seq profile
T0-15.csv

value: 15 min


title: [RNA-Seq] Human brain pericytes_T15_replicate3

description:
RNA-seq profile
T0-15.csv


title: [RNA-Seq] Human brain pericytes_T20

description:
RNA-seq profile
T0-20.csv


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB328MWQ)

description:
https://www.encodeproject.org/experiments/ENCSR757VAW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR757VAW
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB328MWQ
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus male (7 weeks) inflammation-experienced regulatory T-cells primary cell originated from activated regulatory T cell

value: primary cell

value: male

value: unknown

value: 7 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS578IJB at ENCODE; https://www.encodeproject.org/ENCBS578IJB/

value: Derived from ENCODE donor ENCDO405HZR; https://www.encodeproject.org/ENCDO405HZR/


title: DNase-seq from right cerebral cortex (ENCLB438UWC)

description:
https://www.encodeproject.org/experiments/ENCSR601CHF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR601CHF
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB438UWC

source_name: Mus musculus strain B6CASTF1/J male (2 months) right cerebral cortex tissue

value: right cerebral cortex

value: tissue

value: B6Cast F1 PND 2 months Male 05 right cerebral cortex for Altius Stam biobank

value: 2 month

value: ENCBS491MJL at ENCODE; https://www.encodeproject.org/ENCBS491MJL/


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB188OSV)

description:
https://www.encodeproject.org/experiments/ENCSR757VAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR757VAW
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB188OSV
fragmentation methods: shearing (Covaris generic)
size range: 100-300


title: DNase-seq from right cerebral cortex (ENCLB549JSE)

description:
https://www.encodeproject.org/experiments/ENCSR601CHF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR601CHF
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB549JSE

value: B6Cast F1 PND 2 months Male 06 right cerebral cortex for Altius Stam biobank

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS134NTH at ENCODE; https://www.encodeproject.org/ENCBS134NTH/


title: [RNA-Seq] Human brain pericytes_T15_replicate2

description:
RNA-seq profile
T0-15.csv

value: Transdifferentiating

value: 15 min

value: N2 medium


title: [RNA-Seq] Human brain pericytes_T15

description:
RNA-seq profile
T0-15.csv


title: [RNA-Seq] Human brain pericytes_T50_replicate2

description:
RNA-seq profile
T0-50.csv

value: 50 min


title: [RNA-Seq] Human brain pericytes_T10_replicate4

description:
RNA-seq profile
T0-10.csv

value: 10 min


title: polyA plus RNA-seq from regulatory T cell (ENCLB868IWE)

description:
https://www.encodeproject.org/experiments/ENCSR961TDP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR961TDP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB868IWE
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus strain Foxp3GFP-DTRCD4CreERT2R26tdTomato male adult (9 weeks) regulatory T primary cell originated from whole organism

value: regulatory T cell

value: primary cell

value: male

value: adult

value: 9 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS175VON at ENCODE; https://www.encodeproject.org/ENCBS175VON/

value: Derived from ENCODE donor ENCDO717MZS; https://www.encodeproject.org/ENCDO717MZS/


title: DNase-seq from cerebellum (ENCLB855UFL)

description:
https://www.encodeproject.org/experiments/ENCSR678NQS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR678NQS
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB855UFL

source_name: Mus musculus strain B6CASTF1/J male (25 days) cerebellum tissue

value: cerebellum

value: tissue

value: B6Cast F1 PND25 Male 05 cerebellum for Altius Stam core

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: ENCBS452UBM at ENCODE; https://www.encodeproject.org/ENCBS452UBM/

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


title: [RNA-Seq] Human brain pericytes_T10_replicate3

description:
RNA-seq profile
T0-10.csv

value: Transdifferentiating

value: 10 min

value: N2 medium


title: [RNA-Seq] Human brain pericytes_T10_replicate2

description:
RNA-seq profile
T0-10.csv


title: DNase-seq from cerebellum (ENCLB826EMJ)

description:
https://www.encodeproject.org/experiments/ENCSR678NQS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR678NQS
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB826EMJ

value: B6Cast F1 PND25 Male 06 cerebellum for Altius Stam core

value: male

value: The Jackson Laboratory

value: ENCBS187HXC at ENCODE; https://www.encodeproject.org/ENCBS187HXC/


title: DNase-seq from gastrocnemius (ENCLB623XVJ)

description:
https://www.encodeproject.org/experiments/ENCSR701ODD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR701ODD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB623XVJ

source_name: Mus musculus strain B6CASTF1/J male (10 days) gastrocnemius tissue

value: gastrocnemius

value: B6Cast F1 PND10 3x Males 05 gastrocnemius for Altius Stam core

value: 10 day

value: ENCBS955CKU at ENCODE; https://www.encodeproject.org/ENCBS955CKU/


title: polyA plus RNA-seq from regulatory T cell (ENCLB886DKT)

description:
https://www.encodeproject.org/experiments/ENCSR961TDP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961TDP
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB886DKT
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: regulatory T cell

value: primary cell

value: adult

value: 9 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS175VON at ENCODE; https://www.encodeproject.org/ENCBS175VON/

value: Derived from ENCODE donor ENCDO717MZS; https://www.encodeproject.org/ENCDO717MZS/


title: [RNA-Seq] Human brain pericytes_T10

description:
RNA-seq profile
T0-10.csv

value: Transdifferentiating

value: 10 min

value: N2 medium


title: [RNA-Seq] Human brain pericytes_T5_replicate4

description:
RNA-seq profile
T0-5.csv

value: 5 min


title: Histone ChIP-seq from macrophage (ENCLB930VXM)

description:
https://www.encodeproject.org/experiments/ENCSR570YMM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K79me2 ChIP-seq on fragement DNA which is part of BMDM cell with no stimulation
experiment encode accession: ENCSR570YMM
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR698GIN
encode release date: 2021-07-21
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB930VXM
size range: 350-480
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J macrophage primary cell

value: macrophage

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS032QUO at ENCODE; https://www.encodeproject.org/ENCBS032QUO/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: [RNA-Seq] Human brain pericytes_T5_replicate3

description:
RNA-seq profile
T0-5.csv


title: [RNA-Seq] Human brain pericytes_T5_replicate2

description:
RNA-seq profile
T0-5.csv


title: [RNA-Seq] Human brain pericytes_T20_replicate2

description:
RNA-seq profile
T0-20.csv

value: 20 min


title: Histone ChIP-seq from macrophage (ENCLB389JIV)

description:
https://www.encodeproject.org/experiments/ENCSR570YMM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K79me2 ChIP-seq on fragement DNA which is part of BMDM cell with no stimulation
experiment encode accession: ENCSR570YMM
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR698GIN
encode release date: 2021-07-21
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB389JIV
size range: 350-480
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: primary cell

value: ENCBS832PBE at ENCODE; https://www.encodeproject.org/ENCBS832PBE/


title: DNase-seq from cerebellum (ENCLB666SYY)

description:
https://www.encodeproject.org/experiments/ENCSR594HUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR594HUH
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB666SYY

source_name: Mus musculus strain B6CASTF1/J male (10 days) cerebellum tissue

value: cerebellum

value: tissue

value: B6Cast F1 PND10 3x Males 06 cerebellum for Altius Stam core

value: male

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS209WIA at ENCODE; https://www.encodeproject.org/ENCBS209WIA/

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


title: [RNA-Seq] Human brain pericytes_Ct_replicate4

description:
RNA-seq profile
T0-5.csv

value: Control

value: 0 min

value: Growth medium


title: [RNA-Seq] Human brain pericytes_T5

description:
RNA-seq profile
T0-5.csv

value: Transdifferentiating

value: 5 min

value: N2 medium


title: [RNA-Seq] Human brain pericytes_Ct_replicate3

description:
RNA-seq profile
T0-5.csv


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB392YYF)

description:
https://www.encodeproject.org/experiments/ENCSR646QSC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR646QSC
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB392YYF
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (6 months) inflammation-experienced regulatory T-cells primary cell originated from bone marrow hematopoietic cell

value: primary cell

value: adult

value: 6 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS391XAU at ENCODE; https://www.encodeproject.org/ENCBS391XAU/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: DNase-seq from heart (ENCLB749RWM)

description:
https://www.encodeproject.org/experiments/ENCSR677CPE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR677CPE
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB749RWM

source_name: Mus musculus strain B6CASTF1/J male adult (18-20 months) heart tissue

value: heart

value: tissue

value: B6Cast F1 DPN18-20months

value: male

value: 18-20 month

value: Barbara Wold, Caltech

value: ENCBS909PXG at ENCODE; https://www.encodeproject.org/ENCBS909PXG/


title: [RNA-Seq] Human brain pericytes_Ct_replicate2

description:
RNA-seq profile
T0-5.csv

value: Control

value: 0 min

value: Growth medium


title: [RNA-Seq] Human brain pericytes_Ct

description:
RNA-seq profile
T0-5.csv


title: DNase-seq from adrenal gland (ENCLB289HIG)

description:
https://www.encodeproject.org/experiments/ENCSR428CWD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR428CWD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB289HIG
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Mus musculus strain B6CASTF1/J male (25 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND25 Male 06 adrenal gland for Altius Stam core

value: unknown

value: 25 day

value: The Jackson Laboratory

value: ENCBS747FLY at ENCODE; https://www.encodeproject.org/ENCBS747FLY/

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


title: DNase-seq from layer of hippocampus (ENCLB912SWA)

description:
https://www.encodeproject.org/experiments/ENCSR424JJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR424JJO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB912SWA

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

value: layer of hippocampus

value: B6Cast F1 PND10 3x female Hippocampus

value: female

value: 10 day

value: ENCBS522TXQ at ENCODE; https://www.encodeproject.org/ENCBS522TXQ/


title: DNase-seq from lung (ENCLB514ATX)

description:
https://www.encodeproject.org/experiments/ENCSR536FZI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR536FZI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB514ATX

source_name: Mus musculus strain B6CASTF1/J female (2 months) lung tissue

value: lung

value: tissue

value: B6Cast F1 PND 2 months Female 05 lung for Altius Stam biobank

value: 2 month

value: Barbara Wold, Caltech

value: ENCBS764TMU at ENCODE; https://www.encodeproject.org/ENCBS764TMU/


title: DNase-seq from layer of hippocampus (ENCLB892CRI)

description:
https://www.encodeproject.org/experiments/ENCSR424JJO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR424JJO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB892CRI

value: ENCBS424YMR at ENCODE; https://www.encodeproject.org/ENCBS424YMR/


title: Control ChIP-seq from macrophage (ENCLB207RWT)

description:
https://www.encodeproject.org/experiments/ENCSR601NNP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on combined fragement DNA without pulled down which is pooled from BMDM cell with no stimulation
experiment encode accession: ENCSR601NNP
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2021-07-21
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB207RWT
size range: 350-480
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: macrophage

value: primary cell

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS130SJN at ENCODE; https://www.encodeproject.org/ENCBS130SJN/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: Control ChIP-seq from macrophage (ENCLB581BZU)

description:
https://www.encodeproject.org/experiments/ENCSR698GIN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on combined fragement DNA without pulled down which is pooled from BMDM cell with no stimulation
experiment encode accession: ENCSR698GIN
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2021-07-21
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB581BZU
size range: 350-480
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: ENCBS102VIU at ENCODE; https://www.encodeproject.org/ENCBS102VIU/


title: acentabular bone reamings [127]

city: CHARLOTTESVILLE

first: Abdullah

last: Abood

state: VA

address: OMS, Room 3817B

institute: University of Virginia

data_processing:
Alignment HISAT2 default parameters
Assembly using stringtie default parameters
Genome_build: grch38
Supplementary_files_format_and_content: gtf files with normalized counts

extract_protocol:
Bone fragments were isolated from the 17 patients. Total RNA was isolated from bone fragments as previously described in reference 39
Total RNA-Seq libraries were constructed from bone as well as hFOB RNA samples using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits. Constructed libraries contained all RNAs greater than 100 nt (both unpolyadenylated and polyadenylated) minus cytoplasmic and mitochondrial rRNAs. Samples were sequenced to achieve a minimum of 50 million reads 2 x 75 bp paired-end reads on an Illumina NextSeq500.

tag: tissue

value: acentabular bone

tag: gender

value: female

tag: race

value: African American


title: DNase-seq from heart (ENCLB807MEB)

description:
https://www.encodeproject.org/experiments/ENCSR677CPE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR677CPE
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB807MEB

value: heart

value: tissue

tag: description

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS023MIC at ENCODE; https://www.encodeproject.org/ENCBS023MIC/

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


title: acentabular bone reamings [134]

source_name: acentabular bone_male_White

value: White


title: acentabular bone reamings [128]


title: acentabular bone reamings [133]


title: acentabular bone reamings [123]

source_name: acentabular bone_female_White


title: Control ChIP-seq from macrophage (ENCLB337MVU)

description:
https://www.encodeproject.org/experiments/ENCSR601NNP/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on combined fragement DNA without pulled down which is pooled from BMDM cell with no stimulation
experiment encode accession: ENCSR601NNP
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2021-07-21
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB337MVU
size range: 350-480
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: macrophage

value: primary cell

tag: biosample encode accession

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS294JWF at ENCODE; https://www.encodeproject.org/ENCBS294JWF/


title: acentabular bone reamings [126]

value: acentabular bone

value: female


title: acentabular bone reamings [131]


title: DNase-seq from urinary bladder (ENCLB326XMX)

description:
https://www.encodeproject.org/experiments/ENCSR529VRP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR529VRP
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB326XMX

source_name: Mus musculus strain B6CASTF1/J male (14 days) urinary bladder tissue

value: urinary bladder

value: tissue

value: B6Cast F1 PND14 Male 06 urinary bladder for Altius Stam biobank

tag: Sex

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS761UOS at ENCODE; https://www.encodeproject.org/ENCBS761UOS/


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB410NRB)

description:
https://www.encodeproject.org/experiments/ENCSR597XTS/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR597XTS
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB410NRB
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus strain Foxp3GFP-DTRCD4CreERT2R26tdTomato male adult (16 weeks) inflammation-experienced regulatory T-cells primary cell originated from whole organism

value: male

tag: dev stage

value: adult

value: 16 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS236ZIY at ENCODE; https://www.encodeproject.org/ENCBS236ZIY/

value: Derived from ENCODE donor ENCDO717MZS; https://www.encodeproject.org/ENCDO717MZS/


title: acentabular bone reamings [117]

tag: age

value: African American


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB904MHZ)

description:
https://www.encodeproject.org/experiments/ENCSR646QSC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR646QSC
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB904MHZ
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: primary cell

value: 6 month

tag: lab

value: ENCBS391XAU at ENCODE; https://www.encodeproject.org/ENCBS391XAU/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: Control ChIP-seq from macrophage (ENCLB118EMU)

description:
https://www.encodeproject.org/experiments/ENCSR698GIN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on combined fragement DNA without pulled down which is pooled from BMDM cell with no stimulation
experiment encode accession: ENCSR698GIN
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2021-07-21
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB118EMU
size range: 350-480
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: macrophage

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

tag: source

value: Alexander Hoffmann

value: ENCBS507SZZ at ENCODE; https://www.encodeproject.org/ENCBS507SZZ/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: acentabular bone reamings [116]

source_name: acentabular bone_female_Hispanic

value: acentabular bone

value: female

value: Hispanic


title: DNase-seq from urinary bladder (ENCLB583SID)

description:
https://www.encodeproject.org/experiments/ENCSR529VRP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR529VRP
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB583SID

value: urinary bladder

value: tissue

value: B6Cast F1 PND14 3x Males 05 urinary bladder for Altius Stam biobank

value: male

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

tag: link

value: ENCBS840SCS at ENCODE; https://www.encodeproject.org/ENCBS840SCS/

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


title: acentabular bone reamings [115]

value: White


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB076IWG)

description:
https://www.encodeproject.org/experiments/ENCSR597XTS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR597XTS
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB076IWG
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: primary cell

value: adult

value: 16 week

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS236ZIY at ENCODE; https://www.encodeproject.org/ENCBS236ZIY/

value: Derived from ENCODE donor ENCDO717MZS; https://www.encodeproject.org/ENCDO717MZS/


title: acentabular bone reamings [114]

source_name: acentabular bone_male_African American

value: acentabular bone

value: African American


title: DNase-seq from testis (ENCLB322IGK)

description:
https://www.encodeproject.org/experiments/ENCSR671SQM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR671SQM
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB322IGK

source_name: Mus musculus strain B6CASTF1/J male (10 days) testis tissue

value: testis

value: tissue

value: B6Cast F1 PND10 Male 05 testis for Altius Stam biobank

value: unknown

value: 10 day

value: ENCBS457BCZ at ENCODE; https://www.encodeproject.org/ENCBS457BCZ/


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB747WJB)

description:
https://www.encodeproject.org/experiments/ENCSR597XTS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR597XTS
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB747WJB
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: male


title: acentabular bone reamings [135]

value: female

value: White


title: DNase-seq from testis (ENCLB767OZZ)

description:
https://www.encodeproject.org/experiments/ENCSR671SQM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR671SQM
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB767OZZ

value: B6Cast F1 PND10 Male 06 testis for Altius Stam biobank

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS442SNW at ENCODE; https://www.encodeproject.org/ENCBS442SNW/

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


title: Histone ChIP-seq from inflammation-experienced regulatory T-cells (ENCLB693YPD)

description:
https://www.encodeproject.org/experiments/ENCSR528PQK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR528PQK
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB693YPD

value: primary cell

value: adult

value: 6 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS304YTA at ENCODE; https://www.encodeproject.org/ENCBS304YTA/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: acentabular bone reamings [103]

value: acentabular bone

value: African American


title: acentabular bone reamings [108]


title: acentabular bone reamings [105]

value: male


title: DNase-seq from spleen (ENCLB454EWV)

description:
https://www.encodeproject.org/experiments/ENCSR585JUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR585JUM
assay title: DNase-seq
assembly: mm10
encode release date: 2021-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB454EWV

source_name: Mus musculus strain B6CASTF1/J male (14 days) spleen tissue

value: spleen

value: tissue

value: B6Cast F1 PND14 3x Males 05 spleen for Altius Stam biobank

value: unknown

value: 14 day

value: ENCBS995XTV at ENCODE; https://www.encodeproject.org/ENCBS995XTV/


title: Sample 49 Illumina

city: Eastbourne

first: Guan

last: Wang

address: 30 Carlisle Rd

department: School of Sport and Health Sciences

country: United Kingdom

institute: University of Brighton

description: Illumina_RNAseq_raw_counts_EnsemblID.txt

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

source_name: Whole blood

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

tag: age (year)

value: Male

tag: disease state

value: Healthy

tag: time (day)


title: acentabular bone reamings [119]

value: female


title: acentabular bone reamings [102]


title: DNase-seq from lung (ENCLB385WJY)

description:
https://www.encodeproject.org/experiments/ENCSR536FZI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR536FZI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB385WJY

value: lung

value: B6Cast F1 PND 2 months Female 06 lung for Altius Stam biobank

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS237MEY at ENCODE; https://www.encodeproject.org/ENCBS237MEY/

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


title: Histone ChIP-seq from activated regulatory T cell (ENCLB962ELX)

description:
https://www.encodeproject.org/experiments/ENCSR585IGO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR585IGO
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB962ELX

source_name: Mus musculus strain Foxp3CreERT2 x Rosa26YFP male adult (4 months) activated regulatory T primary cell originated from bone marrow hematopoietic cell

tag: antibody

value: activated regulatory T cell

value: primary cell

value: male

value: adult

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS107SNL at ENCODE; https://www.encodeproject.org/ENCBS107SNL/

value: Derived from ENCODE donor ENCDO820VCL; https://www.encodeproject.org/ENCDO820VCL/


title: Histone ChIP-seq from inflammation-experienced regulatory T-cells (ENCLB444IUL)

description:
https://www.encodeproject.org/experiments/ENCSR528PQK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR528PQK
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB444IUL

value: 6 month

value: ENCBS304YTA at ENCODE; https://www.encodeproject.org/ENCBS304YTA/


title: DNase-seq from heart (ENCLB708DYP)

description:
https://www.encodeproject.org/experiments/ENCSR671NPO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR671NPO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB708DYP

source_name: Mus musculus strain B6CASTF1/J male (2 months) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND 2 months Male 05 heart for Altius Stam biobank

value: unknown

value: ENCBS339ZOK at ENCODE; https://www.encodeproject.org/ENCBS339ZOK/


title: Histone ChIP-seq from activated regulatory T cell (ENCLB658BJS)

description:
https://www.encodeproject.org/experiments/ENCSR585IGO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR585IGO
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB658BJS


title: Sample 46 Illumina

value: Male

value: Healthy


title: Sample 45 Illumina


title: Sample 44 Illumina


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB987LSQ)

description:
https://www.encodeproject.org/experiments/ENCSR582PLJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR582PLJ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB987LSQ
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus strain Foxp3GFP-DTRCD4CreERT2R26tdTomato male adult (9 weeks) activated regulatory T primary cell originated from whole organism

value: activated regulatory T cell

value: primary cell

value: 9 week

value: ENCBS138ASO at ENCODE; https://www.encodeproject.org/ENCBS138ASO/

value: Derived from ENCODE donor ENCDO717MZS; https://www.encodeproject.org/ENCDO717MZS/


title: Sample 43 Illumina


title: Sample 48 Illumina


title: DNase-seq from heart (ENCLB769QWA)

description:
https://www.encodeproject.org/experiments/ENCSR671NPO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR671NPO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB769QWA

value: B6Cast F1 PND 2 months Male 06 heart for Altius Stam biobank

value: male

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS725EZT at ENCODE; https://www.encodeproject.org/ENCBS725EZT/

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


title: Sample 42 Illumina

value: Base2 (0)


title: Sample 47 Illumina


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB690EVW)

description:
https://www.encodeproject.org/experiments/ENCSR582PLJ/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR582PLJ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB690EVW
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: adult

value: Christina Leslie, MSKCC

value: Christina Leslie


title: DNase-seq from thymus (ENCLB308ZUW)

description:
https://www.encodeproject.org/experiments/ENCSR671JNA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR671JNA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB308ZUW

source_name: Mus musculus strain B6CASTF1/J female (14 days) thymus tissue

value: thymus

value: tissue

value: B6Cast F1 PND14 Female 05 thymus for Altius Stam biobank

value: female

value: unknown

value: 14 day

value: ENCBS891VRM at ENCODE; https://www.encodeproject.org/ENCBS891VRM/


title: Sample 41 Illumina

value: Male

value: Healthy


title: DNase-seq from thymus (ENCLB927TRR)

description:
https://www.encodeproject.org/experiments/ENCSR671JNA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR671JNA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB927TRR

value: B6Cast F1 PND14 Female 06 thymus for Altius Stam biobank

value: Barbara Wold, Caltech

value: ENCBS759YCE at ENCODE; https://www.encodeproject.org/ENCBS759YCE/


title: DNase-seq from spleen (ENCLB353STL)

description:
https://www.encodeproject.org/experiments/ENCSR585JUM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR585JUM
assay title: DNase-seq
assembly: mm10
encode release date: 2021-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB353STL

value: spleen

value: B6Cast F1 PND14 Male 06 spleen for Altius Stam biobank

value: male

value: The Jackson Laboratory

value: ENCBS734WJS at ENCODE; https://www.encodeproject.org/ENCBS734WJS/

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