title: Mint-ChIP-seq from brain (ENCLB098QPY)

description:
https://www.encodeproject.org/experiments/ENCSR019BOC/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR019BOC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB098QPY
fragmentation methods: none

value: brain

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS337FMJ at ENCODE; https://www.encodeproject.org/ENCBS337FMJ/

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


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB379KEA)

status: Public on Jun 15 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/ENCSR923JIB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR923JIB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR034MTZ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB379KEA
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell with multiple sclerosis, preserved by cryopreservation

tag: antibody

value: primary cell

tag: description

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

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: multiple sclerosis

tag: dev stage

value: unknown

tag: age

tag: lab

tag: source

value: David Hafler

tag: link

value: ENCBS512HTQ at ENCODE; https://www.encodeproject.org/ENCBS512HTQ/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: Mint-ChIP-seq from GM23338 (ENCLB468ZRZ)

description:
https://www.encodeproject.org/experiments/ENCSR212MTU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR212MTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB468ZRZ
fragmentation methods: none

source_name: Homo sapiens GM23338 cell line, preserved by cryopreservation

tag: line

value: cell line

value: PGP1 iPSCs

value: male

value: adult

value: 53 year

value: George Church

value: ENCBS155WDP at ENCODE; https://www.encodeproject.org/ENCBS155WDP/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Mint-ChIP-seq from naive B cell (ENCLB704WWK)

description:
https://www.encodeproject.org/experiments/ENCSR821WMA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR821WMA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR119CTT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB704WWK
fragmentation methods: none

source_name: Homo sapiens naive B primary cell, preserved by cryopreservation

value: naive B cell

value: B naive CD3- CD14- CD19+ CD27- IgD+

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS182GUX at ENCODE; https://www.encodeproject.org/ENCBS182GUX/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB515IXQ)

description:
https://www.encodeproject.org/experiments/ENCSR923JIB/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR923JIB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR034MTZ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB515IXQ
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB925FIK)

description:
https://www.encodeproject.org/experiments/ENCSR922UKO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR922UKO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546XZC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB925FIK
fragmentation methods: none

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: female

value: embryonic

value: 5 day

value: SESCC

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 naive B cell (ENCLB192WHX)

description:
https://www.encodeproject.org/experiments/ENCSR821WMA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR821WMA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR119CTT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB192WHX
fragmentation methods: none

value: naive B cell

value: B naive CD3- CD14- CD19+ CD27- IgD+

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS182GUX at ENCODE; https://www.encodeproject.org/ENCBS182GUX/


title: Mint-ChIP-seq from neural progenitor cell (ENCLB970GSF)

description:
https://www.encodeproject.org/experiments/ENCSR211MKD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR211MKD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB970GSF
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) neural progenitor in vitro differentiated cells

value: neural progenitor cell

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: Kevin Eggan and Ralda Nehme

value: ENCBS959UMI at ENCODE; https://www.encodeproject.org/ENCBS959UMI/


title: Mint-ChIP-seq from neural progenitor cell (ENCLB420VGW)

description:
https://www.encodeproject.org/experiments/ENCSR211MKD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR211MKD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB420VGW
fragmentation methods: none

value: in vitro differentiated cells


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB114BGU)

description:
https://www.encodeproject.org/experiments/ENCSR922UKO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR922UKO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546XZC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB114BGU

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

value: progenitor cell of endocrine pancreas

value: WA09 derived pancreatic progenitor cells

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB961GFL)

description:
https://www.encodeproject.org/experiments/ENCSR211MKD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR211MKD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB961GFL
fragmentation methods: none

value: female

value: embryonic

value: 5 day

value: ENCBS606NEX at ENCODE; https://www.encodeproject.org/ENCBS606NEX/


title: Mint-ChIP-seq from neural progenitor cell (ENCLB613ASG)

description:
https://www.encodeproject.org/experiments/ENCSR211MKD/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR211MKD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB613ASG
fragmentation methods: none

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


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB125YAI)

description:
https://www.encodeproject.org/experiments/ENCSR922UKO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR922UKO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546XZC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB125YAI
fragmentation methods: none

value: SESCC

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


title: Control Mint-ChIP-seq from HFFc6 (ENCLB753XPD)

description:
https://www.encodeproject.org/experiments/ENCSR114FEG/
***************
biological replicate number: 2
technical replicate number: 2
description: Control Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR114FEG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB753XPD

source_name: Homo sapiens HFFc6 cell line, preserved by cryopreservation

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

tag: passage number

value: ENCBS794NUP at ENCODE; https://www.encodeproject.org/ENCBS794NUP/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: Mint-ChIP-seq from neural progenitor cell (ENCLB476MFE)

description:
https://www.encodeproject.org/experiments/ENCSR211MKD/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR211MKD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB476MFE
fragmentation methods: none

value: neural progenitor cell

value: in vitro differentiated cells

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: female

value: healthy

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

value: ENCBS167WAM at ENCODE; https://www.encodeproject.org/ENCBS167WAM/


title: Control Mint-ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB489XAS)

description:
https://www.encodeproject.org/experiments/ENCSR820SXH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of CD8-positive, alpha-beta T cell male adult (21 years)
experiment encode accession: ENCSR820SXH
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB489XAS

source_name: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS832HZD at ENCODE; https://www.encodeproject.org/ENCBS832HZD/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: Mint-ChIP-seq from neural progenitor cell (ENCLB418RZR)

description:
https://www.encodeproject.org/experiments/ENCSR211MKD/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR211MKD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB418RZR
fragmentation methods: none

value: embryonic

value: 5 day

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


title: Mint-ChIP-seq from brain (ENCLB548ZHL)

description:
https://www.encodeproject.org/experiments/ENCSR019BOC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR019BOC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB548ZHL
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) brain organoid, 30 days post differentiation

value: brain

value: organoid

value: Paola Arlotta

value: ENCBS219JHY at ENCODE; https://www.encodeproject.org/ENCBS219JHY/


title: Control Mint-ChIP-seq from HFFc6 (ENCLB866EGS)

description:
https://www.encodeproject.org/experiments/ENCSR114FEG/
***************
biological replicate number: 2
technical replicate number: 1
description: Control Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR114FEG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB866EGS

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: ENCBS794NUP at ENCODE; https://www.encodeproject.org/ENCBS794NUP/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: Control Mint-ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB908UAC)

description:
https://www.encodeproject.org/experiments/ENCSR820SXH/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of CD8-positive, alpha-beta T cell male adult (21 years)
experiment encode accession: ENCSR820SXH
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB908UAC

value: CD8-positive, alpha-beta T cell

value: primary cell

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS832HZD at ENCODE; https://www.encodeproject.org/ENCBS832HZD/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB770VCW)

description:
https://www.encodeproject.org/experiments/ENCSR114AZZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR114AZZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR570TYL
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB770VCW
fragmentation methods: none

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

value: CD4-positive, alpha-beta memory T cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS300QBR at ENCODE; https://www.encodeproject.org/ENCBS300QBR/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB567XXU)

description:
https://www.encodeproject.org/experiments/ENCSR922UKO/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR922UKO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546XZC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB567XXU

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: female

value: embryonic

value: 5 day

value: SESCC

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

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


title: Control Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB375QJX)

description:
https://www.encodeproject.org/experiments/ENCSR817QVK/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on CD4-positive, alpha-beta memory T cell male adult (43 years)
experiment encode accession: ENCSR817QVK
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB375QJX

source_name: Homo sapiens male adult (43 years) CD4-positive, alpha-beta memory T primary cell

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: male

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS050OWF at ENCODE; https://www.encodeproject.org/ENCBS050OWF/

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB675YVC)

description:
https://www.encodeproject.org/experiments/ENCSR114AZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR114AZZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR570TYL
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB675YVC
fragmentation methods: none

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS300QBR at ENCODE; https://www.encodeproject.org/ENCBS300QBR/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Control Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB820YIP)

description:
https://www.encodeproject.org/experiments/ENCSR817QVK/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on CD4-positive, alpha-beta memory T cell male adult (43 years)
experiment encode accession: ENCSR817QVK
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB820YIP

value: CD4-positive, alpha-beta memory T cell


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB382QLE)

description:
https://www.encodeproject.org/experiments/ENCSR813EKK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR813EKK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR176HLK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB382QLE
fragmentation methods: none

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

tag: treatments

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

value: ENCBS514SPI at ENCODE; https://www.encodeproject.org/ENCBS514SPI/


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB030NTO)

description:
https://www.encodeproject.org/experiments/ENCSR119DDY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR119DDY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR881SIP
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB030NTO
fragmentation methods: none

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

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: ENCBS135XFB at ENCODE; https://www.encodeproject.org/ENCBS135XFB/


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB207RKJ)

description:
https://www.encodeproject.org/experiments/ENCSR914UYO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR914UYO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310ZGH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB207RKJ
fragmentation methods: none

source_name: Homo sapiens CD4-positive, CD25-positive, alpha-beta regulatory T primary cell, preserved by cryopreservation

value: Treg CD3+ CD4+ CD8- CD25+ CD127-

value: ENCBS862LJK at ENCODE; https://www.encodeproject.org/ENCBS862LJK/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Control Mint-ChIP-seq from HFFc6 (ENCLB585OJM)

description:
https://www.encodeproject.org/experiments/ENCSR114FEG/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR114FEG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB585OJM

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: ENCBS217PYK at ENCODE; https://www.encodeproject.org/ENCBS217PYK/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: Mint-ChIP-seq from B cell (ENCLB400AKN)

description:
https://www.encodeproject.org/experiments/ENCSR812IND/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR812IND
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR051DHR
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB400AKN
fragmentation methods: none

source_name: Homo sapiens male adult (22 years) B primary cell

value: B cell

value: primary cell

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS852RUN at ENCODE; https://www.encodeproject.org/ENCBS852RUN/

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


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB733SSU)

description:
https://www.encodeproject.org/experiments/ENCSR813EKK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR813EKK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR176HLK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB733SSU
fragmentation methods: none

value: 43 year

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

value: ENCBS514SPI at ENCODE; https://www.encodeproject.org/ENCBS514SPI/

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB504POX)

description:
https://www.encodeproject.org/experiments/ENCSR018JXB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR018JXB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR749PSE
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB504POX
fragmentation methods: none

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

value: CD8-positive, alpha-beta memory T cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS020LPJ at ENCODE; https://www.encodeproject.org/ENCBS020LPJ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Control Mint-ChIP-seq from HFFc6 (ENCLB134XGD)

description:
https://www.encodeproject.org/experiments/ENCSR114FEG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR114FEG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB134XGD

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: ENCBS217PYK at ENCODE; https://www.encodeproject.org/ENCBS217PYK/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB048JSS)

description:
https://www.encodeproject.org/experiments/ENCSR914UYO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR914UYO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310ZGH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB048JSS
fragmentation methods: none

value: primary cell

value: Treg CD3+ CD4+ CD8- CD25+ CD127-

value: not collected

value: ENCBS862LJK at ENCODE; https://www.encodeproject.org/ENCBS862LJK/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Control Mint-ChIP-seq from naive B cell (ENCLB471EYE)

description:
https://www.encodeproject.org/experiments/ENCSR111MNI/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR111MNI
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB471EYE
instrument models: Illumina HiSeq 2500,Illumina NovaSeq 6000

source_name: Homo sapiens naive B primary cell with multiple sclerosis, preserved by cryopreservation

value: naive B cell

value: B naive CD3- CD14- CD19+ CD27- IgD+

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS743ZAV at ENCODE; https://www.encodeproject.org/ENCBS743ZAV/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: Control Mint-ChIP-seq from neural progenitor cell (ENCLB833DNN)

description:
https://www.encodeproject.org/experiments/ENCSR010GRX/
***************
biological replicate number: 2
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR010GRX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB833DNN

value: neural progenitor cell

value: in vitro differentiated cells

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: female

value: healthy

value: embryonic

value: 5 day

value: Kevin Eggan and Ralda Nehme

value: ENCBS606NEX at ENCODE; https://www.encodeproject.org/ENCBS606NEX/

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


title: Control Mint-ChIP-seq from neural progenitor cell (ENCLB182AFV)

description:
https://www.encodeproject.org/experiments/ENCSR010GRX/
***************
biological replicate number: 3
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR010GRX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182AFV

value: ENCBS167WAM at ENCODE; https://www.encodeproject.org/ENCBS167WAM/


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB969KQM)

description:
https://www.encodeproject.org/experiments/ENCSR911DCW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR911DCW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR779CPT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB969KQM
fragmentation methods: none

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS736STX at ENCODE; https://www.encodeproject.org/ENCBS736STX/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: Mint-ChIP-seq from B cell (ENCLB685RJG)

description:
https://www.encodeproject.org/experiments/ENCSR812IND/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR812IND
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR051DHR
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB685RJG
fragmentation methods: none

value: B cell

value: 22 year

value: ENCBS852RUN at ENCODE; https://www.encodeproject.org/ENCBS852RUN/

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


title: Control Mint-ChIP-seq from neural progenitor cell (ENCLB069FAL)

description:
https://www.encodeproject.org/experiments/ENCSR010GRX/
***************
biological replicate number: 3
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR010GRX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB069FAL

value: neural progenitor cell

value: in vitro differentiated cells

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme


title: Mint-ChIP-seq from nephron (ENCLB834THH)

description:
https://www.encodeproject.org/experiments/ENCSR007ZSS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR007ZSS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB834THH
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid originated from H9, 21 days post differentiation

value: nephron

value: organoid

value: derived from H9 nephron progenitor cells (NPCs) harvested at day 21

value: Joseph Bonventre

value: ENCBS378CGA at ENCODE; https://www.encodeproject.org/ENCBS378CGA/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB212VZL)

description:
https://www.encodeproject.org/experiments/ENCSR807NUW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR807NUW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR688UBO
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB212VZL
fragmentation methods: none

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

value: primary cell

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

value: not collected

value: unknown

value: David Hafler

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

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB177QKT)

description:
https://www.encodeproject.org/experiments/ENCSR018JXB/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR018JXB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR749PSE
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB177QKT
fragmentation methods: none

value: CD8-positive, alpha-beta memory T cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: healthy

value: ENCBS020LPJ at ENCODE; https://www.encodeproject.org/ENCBS020LPJ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Control Mint-ChIP-seq from neural progenitor cell (ENCLB810QKG)

description:
https://www.encodeproject.org/experiments/ENCSR010GRX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR010GRX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB810QKG

value: neural progenitor cell

value: in vitro differentiated cells

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

value: ENCBS959UMI at ENCODE; https://www.encodeproject.org/ENCBS959UMI/


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB338WIG)

description:
https://www.encodeproject.org/experiments/ENCSR911DCW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR911DCW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR779CPT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB338WIG
fragmentation methods: none

value: primary cell

value: male

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS736STX at ENCODE; https://www.encodeproject.org/ENCBS736STX/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: Mint-ChIP-seq from nephron (ENCLB707OZD)

description:
https://www.encodeproject.org/experiments/ENCSR007ZSS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR007ZSS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB707OZD
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid originated from H9, preserved by cryopreservation

value: nephron

value: organoid

value: H9 derived nephron organoid 21 days

value: healthy

value: Joseph Bonventre

value: ENCBS202RGJ at ENCODE; https://www.encodeproject.org/ENCBS202RGJ/

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


title: microRNA-seq from GM23338 (ENCLB866KYZ)

description:
https://www.encodeproject.org/experiments/ENCSR804CAP/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA Evaluation PGP1 iPSC microRNA-seq from Mortazavi
experiment encode accession: ENCSR804CAP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-01-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB866KYZ
size range: <30

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens GM23338 cell line, preserved by cryopreservation

value: cell line

value: PGP1 iPSCs

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS155WDP at ENCODE; https://www.encodeproject.org/ENCBS155WDP/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Mint-ChIP-seq from nephron (ENCLB073RBD)

description:
https://www.encodeproject.org/experiments/ENCSR007ZSS/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR007ZSS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB073RBD
fragmentation methods: none

value: derived from H9 nephron progenitor cells (NPCs) harvested at day 21

value: female

value: embryonic

value: 5 day

value: ENCBS378CGA at ENCODE; https://www.encodeproject.org/ENCBS378CGA/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB367AOP)

description:
https://www.encodeproject.org/experiments/ENCSR802MXQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq of CD4-positive, alpha-beta memory T cell originated from CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR802MXQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR131SAQ
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB367AOP
fragmentation methods: none

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell with multiple sclerosis, preserved by cryopreservation

value: CD4-positive, alpha-beta memory T cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS702KJW at ENCODE; https://www.encodeproject.org/ENCBS702KJW/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: Mint-ChIP-seq from activated CD8-positive, alpha-beta T cell (ENCLB649NAZ)

description:
https://www.encodeproject.org/experiments/ENCSR801PPM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR801PPM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR741YCX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB649NAZ
fragmentation methods: none

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: male

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS458XCC at ENCODE; https://www.encodeproject.org/ENCBS458XCC/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB705ISV)

description:
https://www.encodeproject.org/experiments/ENCSR204YIP/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR204YIP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB705ISV

source_name: Homo sapiens immature natural killer primary cell with multiple sclerosis

value: immature natural killer cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: Bradley Bernstein, Broad

value: ENCBS745FCE at ENCODE; https://www.encodeproject.org/ENCBS745FCE/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB896TAL)

description:
https://www.encodeproject.org/experiments/ENCSR802MXQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq of CD4-positive, alpha-beta memory T cell originated from CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR802MXQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR131SAQ
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB896TAL
fragmentation methods: none

value: CD4-positive, alpha-beta memory T cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown


title: Mint-ChIP-seq from nephron (ENCLB146BQQ)

description:
https://www.encodeproject.org/experiments/ENCSR007ZSS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR007ZSS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB146BQQ
fragmentation methods: none

value: nephron

value: organoid

value: H9 derived nephron organoid 21 days

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS202RGJ at ENCODE; https://www.encodeproject.org/ENCBS202RGJ/

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


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB476PVY)

description:
https://www.encodeproject.org/experiments/ENCSR205FKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR205FKJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB476PVY

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS006RRW at ENCODE; https://www.encodeproject.org/ENCBS006RRW/

value: Derived from ENCODE donor ENCDO258PRN; https://www.encodeproject.org/ENCDO258PRN/


title: Control Mint-ChIP-seq from endodermal cell (ENCLB355BKS)

description:
https://www.encodeproject.org/experiments/ENCSR901NYG/
***************
biological replicate number: 2
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR901NYG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB355BKS

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

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: SESCC

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/


title: Mint-ChIP-seq from activated CD8-positive, alpha-beta T cell (ENCLB923TWU)

description:
https://www.encodeproject.org/experiments/ENCSR801PPM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR801PPM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR741YCX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB923TWU
fragmentation methods: none

value: primary cell

value: male

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS458XCC at ENCODE; https://www.encodeproject.org/ENCBS458XCC/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: Control Mint-ChIP-seq from neural progenitor cell (ENCLB071ETI)

description:
https://www.encodeproject.org/experiments/ENCSR010GRX/
***************
biological replicate number: 2
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR010GRX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB071ETI

source_name: Homo sapiens female embryo (5 days) neural progenitor in vitro differentiated cells

value: neural progenitor cell

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

value: ENCBS606NEX at ENCODE; https://www.encodeproject.org/ENCBS606NEX/

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


title: microRNA-seq from GM23338 (ENCLB595LKS)

description:
https://www.encodeproject.org/experiments/ENCSR804CAP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation PGP1 iPSC microRNA-seq from Mortazavi
experiment encode accession: ENCSR804CAP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-01-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB595LKS
size range: <30

value: cell line

value: PGP1 iPSCs

value: male

value: adult

value: 53 year

value: George Church

value: ENCBS155WDP at ENCODE; https://www.encodeproject.org/ENCBS155WDP/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB037KFD)

description:
https://www.encodeproject.org/experiments/ENCSR204YIP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR204YIP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB037KFD

value: immature natural killer cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS745FCE at ENCODE; https://www.encodeproject.org/ENCBS745FCE/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Control Mint-ChIP-seq from endodermal cell (ENCLB673PIF)

description:
https://www.encodeproject.org/experiments/ENCSR901NYG/
***************
biological replicate number: 2
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR901NYG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB673PIF

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB231BUZ)

description:
https://www.encodeproject.org/experiments/ENCSR807NUW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR807NUW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR688UBO
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB231BUZ
fragmentation methods: none

value: primary cell

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

value: not collected

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

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


title: Control Mint-ChIP-seq from endodermal cell (ENCLB094DSK)

description:
https://www.encodeproject.org/experiments/ENCSR901NYG/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR901NYG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB094DSK

value: ENCBS958FWY at ENCODE; https://www.encodeproject.org/ENCBS958FWY/


title: Control Mint-ChIP-seq from endodermal cell (ENCLB378DPZ)

description:
https://www.encodeproject.org/experiments/ENCSR901NYG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR901NYG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB378DPZ

value: endodermal cell


title: Control Mint-ChIP-seq from brain (ENCLB636INX)

description:
https://www.encodeproject.org/experiments/ENCSR106WDX/
***************
biological replicate number: 3
technical replicate number: 1
description: Control Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR106WDX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB636INX

source_name: Homo sapiens male adult (53 years) brain organoid, 180 days post differentiation

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: male

value: adult

value: 53 year

value: Paola Arlotta

value: ENCBS412HPI at ENCODE; https://www.encodeproject.org/ENCBS412HPI/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Mint-ChIP-seq from activated T-cell (ENCLB939QIF)

description:
https://www.encodeproject.org/experiments/ENCSR696ILA/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR696ILA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB939QIF
fragmentation methods: none

source_name: Homo sapiens male adult (38 years) activated T-cell primary cell

value: activated T-cell

value: Activated with 1:1 ratio of CD3, CD28 beads for 24 hours by Stam lab at Altius.

value: 38 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS693BEC at ENCODE; https://www.encodeproject.org/ENCBS693BEC/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: Control Mint-ChIP-seq from neural progenitor cell (ENCLB268PRH)

description:
https://www.encodeproject.org/experiments/ENCSR010GRX/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR010GRX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB268PRH

value: neural progenitor cell

value: in vitro differentiated cells

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: female

value: healthy

value: embryonic

value: 5 day

value: Kevin Eggan and Ralda Nehme

value: ENCBS959UMI at ENCODE; https://www.encodeproject.org/ENCBS959UMI/

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


title: Control Mint-ChIP-seq from brain (ENCLB719OBD)

description:
https://www.encodeproject.org/experiments/ENCSR106WDX/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR106WDX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB719OBD

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: male

value: adult

value: 53 year

value: Paola Arlotta

value: ENCBS344QAP at ENCODE; https://www.encodeproject.org/ENCBS344QAP/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Control Mint-ChIP-seq from brain (ENCLB720CWU)

description:
https://www.encodeproject.org/experiments/ENCSR106WDX/
***************
biological replicate number: 3
technical replicate number: 2
description: Control Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR106WDX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB720CWU

value: Bradley Bernstein, Broad

value: ENCBS412HPI at ENCODE; https://www.encodeproject.org/ENCBS412HPI/


title: Mint-ChIP-seq from activated T-cell (ENCLB431VKJ)

description:
https://www.encodeproject.org/experiments/ENCSR696ILA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR696ILA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB431VKJ
fragmentation methods: none

value: activated T-cell

value: primary cell

value: Activated with 1:1 ratio of CD3, CD28 beads for 24 hours by Stam lab at Altius.

value: 38 year

value: John Stamatoyannopoulos

value: ENCBS833ENP at ENCODE; https://www.encodeproject.org/ENCBS833ENP/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: Control Mint-ChIP-seq from brain (ENCLB677PJG)

description:
https://www.encodeproject.org/experiments/ENCSR106WDX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR106WDX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB677PJG

value: brain

value: organoid


title: Mint-ChIP-seq from activated T-cell (ENCLB152HGT)

description:
https://www.encodeproject.org/experiments/ENCSR696ILA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR696ILA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152HGT
fragmentation methods: none

value: male

value: ENCBS693BEC at ENCODE; https://www.encodeproject.org/ENCBS693BEC/


title: Control Mint-ChIP-seq from brain (ENCLB482KCJ)

description:
https://www.encodeproject.org/experiments/ENCSR106WDX/
***************
biological replicate number: 2
technical replicate number: 1
description: Control Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR106WDX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB482KCJ

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: adult

value: 53 year

value: ENCBS252LAB at ENCODE; https://www.encodeproject.org/ENCBS252LAB/


title: Mint-ChIP-seq from nephron (ENCLB754ELD)

description:
https://www.encodeproject.org/experiments/ENCSR007HIL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR007HIL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801AJD
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB754ELD
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid

value: nephron

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: ENCBS047TRT at ENCODE; https://www.encodeproject.org/ENCBS047TRT/

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


title: Control Mint-ChIP-seq from brain (ENCLB907FEG)

description:
https://www.encodeproject.org/experiments/ENCSR106WDX/
***************
biological replicate number: 2
technical replicate number: 2
description: Control Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR106WDX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB907FEG

value: brain

value: Paola Arlotta

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Mint-ChIP-seq from activated T-cell (ENCLB773SPE)

description:
https://www.encodeproject.org/experiments/ENCSR696ILA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR696ILA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB773SPE
fragmentation methods: none

value: activated T-cell

value: primary cell

value: Activated with 1:1 ratio of CD3, CD28 beads for 24 hours by Stam lab at Altius.

value: male

value: 38 year

value: John Stamatoyannopoulos

value: ENCBS833ENP at ENCODE; https://www.encodeproject.org/ENCBS833ENP/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: Mint-ChIP-seq from activated CD8-positive, alpha-beta T cell (ENCLB857CAI)

description:
https://www.encodeproject.org/experiments/ENCSR689XCY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq of activated CD8-positive, alpha-beta T cell male adult (21 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR689XCY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR741YCX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB857CAI
fragmentation methods: none

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS458XCC at ENCODE; https://www.encodeproject.org/ENCBS458XCC/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: Mint-ChIP-seq from activated CD8-positive, alpha-beta T cell (ENCLB087PSG)

description:
https://www.encodeproject.org/experiments/ENCSR689XCY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq of activated CD8-positive, alpha-beta T cell male adult (21 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR689XCY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR741YCX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB087PSG
fragmentation methods: none


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB069YTL)

description:
https://www.encodeproject.org/experiments/ENCSR685XAS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR685XAS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR053AWV
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB069YTL
fragmentation methods: none

source_name: Homo sapiens male adult (43 years) activated CD4 positive, naive alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: 43 year

value: ENCBS212SYV at ENCODE; https://www.encodeproject.org/ENCBS212SYV/

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


title: Control Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB177BJX)

description:
https://www.encodeproject.org/experiments/ENCSR688UBO/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR688UBO
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB177BJX

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: Control Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB530KPK)

description:
https://www.encodeproject.org/experiments/ENCSR688UBO/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR688UBO
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB530KPK


title: Mint-ChIP-seq from activated B cell (ENCLB630USI)

description:
https://www.encodeproject.org/experiments/ENCSR685KZA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on B cell male adult (22 years)
experiment encode accession: ENCSR685KZA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR784EZW
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB630USI
fragmentation methods: none

source_name: Homo sapiens male adult (22 years) activated B primary cell treated with 0.5 uM CpG ODN for 24 hours

value: activated B cell

value: male

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS860GIC at ENCODE; https://www.encodeproject.org/ENCBS860GIC/

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


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB874LXR)

description:
https://www.encodeproject.org/experiments/ENCSR685XAS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR685XAS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR053AWV
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB874LXR
fragmentation methods: none

value: primary cell

value: 43 year

value: AllCells

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

value: ENCBS212SYV at ENCODE; https://www.encodeproject.org/ENCBS212SYV/

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


title: Mint-ChIP-seq from naive B cell (ENCLB042XJC)

description:
https://www.encodeproject.org/experiments/ENCSR104CUK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR104CUK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR906UGW
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB042XJC

source_name: Homo sapiens naive B primary cell

value: naive B cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS973SPF at ENCODE; https://www.encodeproject.org/ENCBS973SPF/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from naive B cell (ENCLB003LGP)

description:
https://www.encodeproject.org/experiments/ENCSR104CUK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR104CUK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR906UGW
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB003LGP


title: Mint-ChIP-seq from activated B cell (ENCLB897UMI)

description:
https://www.encodeproject.org/experiments/ENCSR685KZA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on B cell male adult (22 years)
experiment encode accession: ENCSR685KZA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR784EZW
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB897UMI
fragmentation methods: none

value: activated B cell

value: male

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS860GIC at ENCODE; https://www.encodeproject.org/ENCBS860GIC/


title: Control Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCLB179LVM)

description:
https://www.encodeproject.org/experiments/ENCSR692OOM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (43 years)
experiment encode accession: ENCSR692OOM
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB179LVM

source_name: Homo sapiens male adult (43 years) CD4-positive naive resting alpha-beta T primary cell

value: primary cell

value: 43 year

value: AllCells

value: ENCBS527XSO at ENCODE; https://www.encodeproject.org/ENCBS527XSO/

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


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB660VAC)

description:
https://www.encodeproject.org/experiments/ENCSR677ZMY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR677ZMY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR165PMH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB660VAC
fragmentation methods: none

source_name: Homo sapiens male adult (30 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: 30 year

value: ENCBS615HXL at ENCODE; https://www.encodeproject.org/ENCBS615HXL/

value: Derived from ENCODE donor ENCDO544CHQ; https://www.encodeproject.org/ENCDO544CHQ/


title: sgNT#1_Rep3

city: Boston

first: Jiye

last: Liu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR with parameters (--outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000
Reads Per Kilobase of exon per Megabase of library size (RPKM) and ranscripts Per Kilobase Million (TPM) were calculated by using RSEM (Li et al, BMC bioinformatics, 2011)
Differential analysis was performed by DESeq2 (Love et al, Genome biology, 2018)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each Sample ...

growth_protocol: MM1S cells were cultured in RPMI 1640 with 10%FBS

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
1ug of RNA was used to make the libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: No treatment

tag: cell type

value: myeloma derived cell line

tag: genotype

value: wildtype


title: Mint-ChIP-seq from activated T-cell (ENCLB051MFS)

description:
https://www.encodeproject.org/experiments/ENCSR677RWJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR677RWJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB051MFS
fragmentation methods: none

value: activated T-cell

value: Activated with 1:1 ratio of CD3, CD28 beads for 24 hours by Stam lab at Altius.

value: male

value: 38 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS833ENP at ENCODE; https://www.encodeproject.org/ENCBS833ENP/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: sgTRAF2#2_Rep1

value: TRAF2 KO


title: sgTRAF2#2_Rep2


title: sgNT#1_Rep2


title: Mint-ChIP-seq from activated T-cell (ENCLB301TZM)

description:
https://www.encodeproject.org/experiments/ENCSR677RWJ/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR677RWJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB301TZM
fragmentation methods: none

value: primary cell

value: adult

value: ENCBS693BEC at ENCODE; https://www.encodeproject.org/ENCBS693BEC/


title: Mint-ChIP-seq from activated T-cell (ENCLB022IXE)

description:
https://www.encodeproject.org/experiments/ENCSR677RWJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR677RWJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB022IXE
fragmentation methods: none


title: Mint-ChIP-seq from activated T-cell (ENCLB841KGY)

description:
https://www.encodeproject.org/experiments/ENCSR677RWJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR677RWJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB841KGY
fragmentation methods: none


title: Control Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCLB060MAL)

description:
https://www.encodeproject.org/experiments/ENCSR692OOM/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (43 years)
experiment encode accession: ENCSR692OOM
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB060MAL

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS527XSO at ENCODE; https://www.encodeproject.org/ENCBS527XSO/

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


title: WGS from GM23248 (ENCLB234AQO)

description:
https://www.encodeproject.org/experiments/ENCSR674PQI/
***************
biological replicate number: 1
technical replicate number: 1
description: The data contained in this experiment correspond to Illumina-based whole genome shotgun sequencing of the Personal Genomes Project 1 donor (PGP1) donor ENCDO336AAA. They were made using a PCR-based (9-cycle, ENCLB234AQO) protocol sequenced on multiple lanes to a combined depth of ~ 60X in PE125 format.
experiment encode accession: ENCSR674PQI
assay title: WGS
assembly: GRCh38
encode release date: 2016-04-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB234AQO
fragmentation methods: see document

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: cell line

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: Mint-ChIP-seq from nephron (ENCLB153TWO)

description:
https://www.encodeproject.org/experiments/ENCSR007HIL/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR007HIL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801AJD
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB153TWO
fragmentation methods: none

value: nephron

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: ENCBS047TRT at ENCODE; https://www.encodeproject.org/ENCBS047TRT/

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


title: Control Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB656WUK)

description:
https://www.encodeproject.org/experiments/ENCSR674JPB/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (20 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR674JPB
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB656WUK

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS896OLN at ENCODE; https://www.encodeproject.org/ENCBS896OLN/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB155NAC)

description:
https://www.encodeproject.org/experiments/ENCSR677ZMY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR677ZMY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR165PMH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB155NAC
fragmentation methods: none

value: CD14-positive monocyte

value: 30 year

value: ENCBS615HXL at ENCODE; https://www.encodeproject.org/ENCBS615HXL/

value: Derived from ENCODE donor ENCDO544CHQ; https://www.encodeproject.org/ENCDO544CHQ/


title: Control Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB349FUS)

description:
https://www.encodeproject.org/experiments/ENCSR674JPB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (20 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR674JPB
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB349FUS


title: lib B_Pom_D7

data_processing:
The sequence reads were trimmed to remove a constant portion of the sgRNA sequences and mapped to the GeCKO v2 genome-wide CRISPR library with MAGeCK “count” module, which computes read counts for each sgRNA. We used MAGeCK “test” module to identify pomalidomide resistance regulators, for which targeting sgRNA were significantly enriched in the treated populations compared to the control untreated populations grown in parallel.
Genome_build: hg19
Supplementary_files_format_and_content: The read count files returned from the MAGeCK

growth_protocol: We perfomred CRISPR/cas9 screening to identify regulators of pomalidomide sensitivity. We transduced MM1S cells with GeCKO v2 libraries at MOI=0.3 to ensure that most transduced cells received only 1 virion. We cultured transduced cells for 2 days in RPMI 1640 completed medium, selected with 1ug/ml puromycin for 7 days, and cultured for

extract_protocol:
We extracted genomic DNA from each froup population by DNeasy Blood & Tissue Kits (Qiagen)
1 step PCR to construct the barcode-indexed sequencing library for each sample
CRISPR screening

value: myeloma derived cell line

value: wildtype

tag: treatment

value: Pom


title: lib B_baseline


title: Mint-ChIP-seq from T-cell (ENCLB772TSA)

description:
https://www.encodeproject.org/experiments/ENCSR789VME/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on T-cell male adult (38 years)
experiment encode accession: ENCSR789VME
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR203XDG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB772TSA
fragmentation methods: none

source_name: Homo sapiens male adult (38 years) T-cell primary cell

value: T-cell

value: CD3+ unactivated cells from Stam Lab at Altius.

value: 38 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS059XUY at ENCODE; https://www.encodeproject.org/ENCBS059XUY/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: lib B_veh_D21

value: DMSO


title: Mint-ChIP-seq from activated B cell (ENCLB743NJK)

description:
https://www.encodeproject.org/experiments/ENCSR791CAF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on B cell male adult (22 years)
experiment encode accession: ENCSR791CAF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR784EZW
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB743NJK
fragmentation methods: none

value: activated B cell

value: primary cell

value: male

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS860GIC at ENCODE; https://www.encodeproject.org/ENCBS860GIC/

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


title: lib A_Pom_D14

value: myeloma derived cell line

value: wildtype

value: Pom


title: Mint-ChIP-seq from endodermal cell (ENCLB669ARC)

description:
https://www.encodeproject.org/experiments/ENCSR788UDH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR788UDH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB669ARC
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS958FWY at ENCODE; https://www.encodeproject.org/ENCBS958FWY/

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


title: lib A_Pom_D7


title: Mint-ChIP-seq from endodermal cell (ENCLB743SJN)

description:
https://www.encodeproject.org/experiments/ENCSR788UDH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR788UDH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB743SJN
fragmentation methods: none


title: Mint-ChIP-seq from T-cell (ENCLB185CDP)

description:
https://www.encodeproject.org/experiments/ENCSR789VME/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on T-cell male adult (38 years)
experiment encode accession: ENCSR789VME
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR203XDG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB185CDP
fragmentation methods: none

value: T-cell

value: primary cell

value: CD3+ unactivated cells from Stam Lab at Altius.

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos

value: ENCBS059XUY at ENCODE; https://www.encodeproject.org/ENCBS059XUY/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: sgTRAF2#2_Rep3

value: myeloma derived cell line

value: TRAF2 KO


title: lib B_veh_D7

value: wildtype

value: DMSO


title: lib A_veh_D21


title: Mint-ChIP-seq from endodermal cell (ENCLB400QYM)

description:
https://www.encodeproject.org/experiments/ENCSR788UDH/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR788UDH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB400QYM
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/


title: lib B_Pom_D21

value: Pom


title: lib A_baseline


title: Mint-ChIP-seq from endodermal cell (ENCLB479WVV)

description:
https://www.encodeproject.org/experiments/ENCSR788UDH/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR788UDH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB479WVV
fragmentation methods: none

value: SESCC

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


title: lib A_veh_D14


title: lib A_veh_D7


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB155RPU)

description:
https://www.encodeproject.org/experiments/ENCSR788TEF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR788TEF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR426RVC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB155RPU
fragmentation methods: none

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell with multiple sclerosis, preserved by cryopreservation

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS671UYD at ENCODE; https://www.encodeproject.org/ENCBS671UYD/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: sgNT#1_Rep1

value: myeloma derived cell line

value: wildtype


title: Mint-ChIP-seq from activated B cell (ENCLB300OPC)

description:
https://www.encodeproject.org/experiments/ENCSR791CAF/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on B cell male adult (22 years)
experiment encode accession: ENCSR791CAF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR784EZW
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB300OPC
fragmentation methods: none

value: activated B cell

value: male

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS860GIC at ENCODE; https://www.encodeproject.org/ENCBS860GIC/

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


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB482CVM)

description:
https://www.encodeproject.org/experiments/ENCSR788TEF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR788TEF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR426RVC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB482CVM
fragmentation methods: none

value: primary cell

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

value: not collected

value: Bradley Bernstein, Broad


title: Con1  from normal control 1

city: Nanjing

first: Minmin

last: Song

address: 321 Zhongshan Rd.

country: China

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
To identify differentially expressed circRNAs and miRNAs across samples or groups, the edgeR package (http://www.r-project.org/) was used. We identified circRNAs with a fold change ≥2 and a P value <0.05 in a comparison between samples or groups as significant differentially expressed circRNAs and miRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample .

source_name: Endometrium

extract_protocol:
Endometria were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-200-0048) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: endometrium

tag: diagnosis

value: healthy control

value: untreated


title: Con3  from normal control 3


title: Con2  from normal control 2


title: lib B_veh_D14

value: myeloma derived cell line

value: wildtype

value: DMSO


title: Ba3 from IUA patient 3

value: Intrauterine adhesions (IUA)


title: lib A_Pom_D21

value: Pom


title: Control Mint-ChIP-seq from activated B cell (ENCLB971HMM)

description:
https://www.encodeproject.org/experiments/ENCSR784EZW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on B cell male adult (22 years)
experiment encode accession: ENCSR784EZW
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB971HMM

value: activated B cell

value: male

value: adult

value: 22 year

value: Yijun Ruan, JAX


title: Ba1 from IUA patient 1


title: Control Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB324IPC)

description:
https://www.encodeproject.org/experiments/ENCSR779CPT/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (20 years) treated with 10 ng
experiment encode accession: ENCSR779CPT
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB324IPC

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: 20 year

value: AllCells

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS736STX at ENCODE; https://www.encodeproject.org/ENCBS736STX/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB625EUE)

description:
https://www.encodeproject.org/experiments/ENCSR651XKR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq of IgD-negative memory B cell originated from IgD-negative memory B cell
experiment encode accession: ENCSR651XKR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519VQC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB625EUE
fragmentation methods: none

source_name: Homo sapiens IgD-negative memory B primary cell, preserved by cryopreservation

tag: antibody

value: IgD-negative memory B cell

tag: description

value: B memory CD3- CD14- CD19+ CD27+ IgD-

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS318ZNB at ENCODE; https://www.encodeproject.org/ENCBS318ZNB/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Control Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB538LHV)

description:
https://www.encodeproject.org/experiments/ENCSR779CPT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (20 years) treated with 10 ng
experiment encode accession: ENCSR779CPT
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB538LHV

tag: biosample encode accession

tag: Sex

value: male

value: adult


title: Control Mint-ChIP-seq from activated B cell (ENCLB432COZ)

description:
https://www.encodeproject.org/experiments/ENCSR784EZW/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on B cell male adult (22 years)
experiment encode accession: ENCSR784EZW
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB432COZ

value: activated B cell

value: primary cell

tag: dev stage

value: 22 year

value: Yijun Ruan, JAX

value: treatment_term_name:CpG ODN; treatment_type:chemical; duration:24; duration_units:hour;

value: ENCBS860GIC at ENCODE; https://www.encodeproject.org/ENCBS860GIC/

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


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB174NJI)

description:
https://www.encodeproject.org/experiments/ENCSR651XKR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq of IgD-negative memory B cell originated from IgD-negative memory B cell
experiment encode accession: ENCSR651XKR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519VQC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB174NJI
fragmentation methods: none

value: IgD-negative memory B cell

value: B memory CD3- CD14- CD19+ CD27+ IgD-

tag: health state

tag: age


title: lib B_Pom_D14

value: myeloma derived cell line

value: wildtype

value: Pom


title: Control Mint-ChIP-seq from activated CD8-positive, alpha-beta T cell (ENCLB081JSB)

description:
https://www.encodeproject.org/experiments/ENCSR651JZJ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of activated CD8-positive, alpha-beta T cell male adult (21 years) treated with 10 ng
experiment encode accession: ENCSR651JZJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB081JSB

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: 21 year

tag: lab

tag: source

value: AllCells

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS387CPR at ENCODE; https://www.encodeproject.org/ENCBS387CPR/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: Control Mint-ChIP-seq from CD4-positive, alpha-beta T cell (ENCLB185DYG)

description:
https://www.encodeproject.org/experiments/ENCSR774CGN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on CD4-positive, alpha-beta T cell male adult (20 years)
experiment encode accession: ENCSR774CGN
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB185DYG

source_name: Homo sapiens male adult (20 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: male

value: adult

value: 20 year

tag: link

value: ENCBS151VTD at ENCODE; https://www.encodeproject.org/ENCBS151VTD/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/