title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB685GYY)

description:
https://www.encodeproject.org/experiments/ENCSR078ATS/
***************
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: ENCSR078ATS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR243EIU
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB685GYY

value: unknown

value: David Hafler


title: MybBGFP_r1_hr06

status: Public on Jun 15 2021

type: SRA

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
After demultiplexing and filtering illumina adapter sequences, the data was mapped to the D. discoideum genome with bowtie version 1.0.0. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with "_rc.tab" contain raw expression values while files ending with "_nor.tab" contain normalized expression values.

molecule: total RNA

organism: Dictyostelium discoideum

growth_protocol: Twenty strains were cultured axenically in HL5.

extract_protocol:
At each time point, we harvested the cells directly into 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries of all samples. 434 individual libraries were separately prepared and divided to 22 sets. We added a unique barcode to each library in each set at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced those pools by Illumina HiSeq2500 (single-end sequencing, read length = 50 or 100 bases) or (paired-end sequencing, read length = 93 or 100 bases) or by NovaSeq6000 (paired-end sequencing, read length = 150 bases).

treatment_protocol: Cells were washed with PDF and plated on nitrocellulse filter on filter paper saturated in PDF at 1.8x106 cells/cm2.

tag: strain

value: MybBGFP

tag: phenotype group

value: WT

tag: replicate

tag: developmental time


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB197LTY)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR077DVZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR077DVZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR034OUM
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB197LTY
fragmentation methods: none

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 CD4-positive, alpha-beta T primary cell

tag: antibody

value: primary cell

tag: description

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

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: healthy

tag: dev stage

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

tag: link

value: ENCBS928WKW at ENCODE; https://www.encodeproject.org/ENCBS928WKW/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB931CYT)

description:
https://www.encodeproject.org/experiments/ENCSR077DVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR077DVZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR034OUM
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB931CYT
fragmentation methods: none


title: MybBGFP_r1_hr16


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB657BQI)

description:
https://www.encodeproject.org/experiments/ENCSR276NGH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR276NGH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR456XXL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB657BQI
fragmentation methods: none

source_name: Homo sapiens CD4-positive, CD25-positive, alpha-beta regulatory T primary cell with multiple sclerosis

value: multiple sclerosis

value: ENCBS269FKR at ENCODE; https://www.encodeproject.org/ENCBS269FKR/

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


title: Mint-ChIP-seq from brain (ENCLB606FXI)

description:
https://www.encodeproject.org/experiments/ENCSR264ZTG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR264ZTG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB606FXI
fragmentation methods: none

source_name: Homo sapiens male adult (53 years) brain organoid, 90 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: ENCBS377FQM at ENCODE; https://www.encodeproject.org/ENCBS377FQM/

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


title: Mint-ChIP-seq from brain (ENCLB650PCY)

description:
https://www.encodeproject.org/experiments/ENCSR264ZTG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR264ZTG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB650PCY
fragmentation methods: none


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB449SVX)

description:
https://www.encodeproject.org/experiments/ENCSR276NGH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR276NGH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR456XXL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB449SVX
fragmentation methods: none

value: primary cell

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

value: not collected

value: unknown

value: David Hafler


title: MybBGFP_r1_hr04

value: MybBGFP

value: WT


title: MybBGFP_r1_hr03


title: MybBGFP_r1_hr02


title: Mint-ChIP-seq from brain (ENCLB184MOD)

description:
https://www.encodeproject.org/experiments/ENCSR264ZTG/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR264ZTG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB184MOD
fragmentation methods: none

value: Bradley Bernstein, Broad

value: ENCBS524OMS at ENCODE; https://www.encodeproject.org/ENCBS524OMS/


title: MybBGFP_r1_hr05


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB758ZWR)

description:
https://www.encodeproject.org/experiments/ENCSR267NWZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR267NWZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR867UMZ
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB758ZWR
fragmentation methods: none

source_name: Homo sapiens CD14-positive monocyte primary cell with multiple sclerosis, preserved by cryopreservation

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: multiple sclerosis

value: ENCBS522LRV at ENCODE; https://www.encodeproject.org/ENCBS522LRV/

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


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB487RII)

description:
https://www.encodeproject.org/experiments/ENCSR267NWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR267NWZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR867UMZ
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB487RII
fragmentation methods: none


title: MybBGFP_r1_hr01


title: MybBGFP_r1_hr00


title: AX4_SE_r7_hr24


title: Mint-ChIP-seq from brain (ENCLB276ISJ)

description:
https://www.encodeproject.org/experiments/ENCSR264ZTG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR264ZTG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB276ISJ
fragmentation methods: none

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: ENCBS291HMT at ENCODE; https://www.encodeproject.org/ENCBS291HMT/


title: AX4_SE_r7_hr16


title: Mint-ChIP-seq from brain (ENCLB961CSJ)

description:
https://www.encodeproject.org/experiments/ENCSR073GDR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR073GDR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB961CSJ
fragmentation methods: none

value: ENCBS377FQM at ENCODE; https://www.encodeproject.org/ENCBS377FQM/

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


title: Mint-ChIP-seq from brain (ENCLB219UNT)

description:
https://www.encodeproject.org/experiments/ENCSR073GDR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR073GDR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB219UNT
fragmentation methods: none

value: Bradley Bernstein, Broad


title: AX4_SE_r7_hr06

value: WT


title: Mint-ChIP-seq from brain (ENCLB385WVW)

description:
https://www.encodeproject.org/experiments/ENCSR264ZTG/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR264ZTG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB385WVW
fragmentation methods: none


title: AX4_SE_r7_hr08


title: Mint-ChIP-seq from brain (ENCLB774UTD)

description:
https://www.encodeproject.org/experiments/ENCSR073GDR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR073GDR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB774UTD
fragmentation methods: none


title: AX4_SE_r7_hr12


title: Mint-ChIP-seq from brain (ENCLB377YBX)

description:
https://www.encodeproject.org/experiments/ENCSR073GDR/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR073GDR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB377YBX
fragmentation methods: none

value: ENCBS524OMS at ENCODE; https://www.encodeproject.org/ENCBS524OMS/


title: Mint-ChIP-seq from brain (ENCLB047MGI)

description:
https://www.encodeproject.org/experiments/ENCSR073GDR/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR073GDR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB047MGI
fragmentation methods: none


title: AX4_SE_r7_hr03


title: AX4_SE_r7_hr04


title: AX4_SE_r7_hr05


title: AX4_SE_r7_hr02


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB153ZBY)

description:
https://www.encodeproject.org/experiments/ENCSR264WXE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR264WXE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR887UYJ
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB153ZBY
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: primary cell

value: CD4+ memory cells from healthy donor

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS963BXF at ENCODE; https://www.encodeproject.org/ENCBS963BXF/

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


title: AX4_SE_r7_hr01


title: AX4_SE_r7_hr00


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB103ZLL)

description:
https://www.encodeproject.org/experiments/ENCSR264WXE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR264WXE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR887UYJ
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB103ZLL
fragmentation methods: none


title: AX4_SE_r6_hr24


title: AX4_SE_r6_hr12


title: Mint-ChIP-seq from brain (ENCLB819LUX)

description:
https://www.encodeproject.org/experiments/ENCSR264ZTG/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR264ZTG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB819LUX
fragmentation methods: none

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


title: AX4_SE_r7_hr20

value: WT


title: AX4_SE_r6_hr20


title: AX4_SE_r6_hr06


title: AX4_SE_r6_hr16


title: Mint-ChIP-seq from brain (ENCLB562ZSO)

description:
https://www.encodeproject.org/experiments/ENCSR073GDR/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR073GDR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB562ZSO
fragmentation methods: none

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS377FQM at ENCODE; https://www.encodeproject.org/ENCBS377FQM/

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


title: Mint-ChIP-seq from nephron (ENCLB939MYW)

description:
https://www.encodeproject.org/experiments/ENCSR071SPR/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR071SPR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB939MYW
fragmentation methods: none

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

value: nephron

value: H9 derived nephron organoid 21 days

value: female

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: Mint-ChIP-seq from nephron (ENCLB155NRN)

description:
https://www.encodeproject.org/experiments/ENCSR071SPR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR071SPR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB155NRN
fragmentation methods: none

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

value: organoid

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

value: healthy

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


title: Mint-ChIP-seq from nephron (ENCLB340IPR)

description:
https://www.encodeproject.org/experiments/ENCSR071SPR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR071SPR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB340IPR
fragmentation methods: none


title: Mint-ChIP-seq from neural progenitor cell (ENCLB072DRE)

description:
https://www.encodeproject.org/experiments/ENCSR259VGN/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR259VGN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB072DRE
fragmentation methods: none

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

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: Kevin Eggan and Ralda Nehme

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


title: Mint-ChIP-seq from nephron (ENCLB612GUR)

description:
https://www.encodeproject.org/experiments/ENCSR071SPR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR071SPR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB612GUR
fragmentation methods: none

value: nephron

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from neural progenitor cell (ENCLB973QWT)

description:
https://www.encodeproject.org/experiments/ENCSR259VGN/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR259VGN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB973QWT
fragmentation methods: none

value: female

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


title: AX4_SE_r6_hr04

value: WT


title: AX4_SE_r6_hr03


title: AX4_SE_r6_hr05


title: AX4_SE_r6_hr02


title: Mint-ChIP-seq from neural progenitor cell (ENCLB243PEV)

description:
https://www.encodeproject.org/experiments/ENCSR259VGN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR259VGN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB243PEV
fragmentation methods: none

value: embryonic

value: 5 day

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB640ZMO)

description:
https://www.encodeproject.org/experiments/ENCSR259VGN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR259VGN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB640ZMO
fragmentation methods: none

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB607FNK)

description:
https://www.encodeproject.org/experiments/ENCSR259VGN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR259VGN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB607FNK
fragmentation methods: none


title: AX4_SE_r6_hr00


title: Mint-ChIP-seq from neural progenitor cell (ENCLB900XLR)

description:
https://www.encodeproject.org/experiments/ENCSR259VGN/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR259VGN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB900XLR
fragmentation methods: none


title: AX4_SE_r6_hr08


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB121HSL)

description:
https://www.encodeproject.org/experiments/ENCSR071LSL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR071LSL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR958CUX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB121HSL
fragmentation methods: none

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS929PLQ at ENCODE; https://www.encodeproject.org/ENCBS929PLQ/

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


title: AX4_SE_r6_hr01


title: AX4_SE_r5_hr20


title: AX4_SE_r5_hr08


title: AX4_SE_r5_hr06


title: AX4_SE_r5_hr12


title: Mint-ChIP-seq from brain (ENCLB152SKF)

description:
https://www.encodeproject.org/experiments/ENCSR070JEZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR070JEZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152SKF
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) brain organoid, 180 days post differentiation

value: brain

value: organoid

value: healthy

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS615FKW at ENCODE; https://www.encodeproject.org/ENCBS615FKW/


title: Mint-ChIP-seq from brain (ENCLB799AEE)

description:
https://www.encodeproject.org/experiments/ENCSR070JEZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR070JEZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB799AEE
fragmentation methods: none

value: female

value: embryonic

value: 5 day

value: ENCBS358VQQ at ENCODE; https://www.encodeproject.org/ENCBS358VQQ/


title: AX4_SE_r5_hr05

value: WT


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB232SUH)

description:
https://www.encodeproject.org/experiments/ENCSR191YDG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR191YDG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR958CUX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB232SUH
fragmentation methods: none

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected


title: Mint-ChIP-seq from brain (ENCLB255ABM)

description:
https://www.encodeproject.org/experiments/ENCSR070JEZ/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR070JEZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB255ABM
fragmentation methods: none

value: ENCBS598CLB at ENCODE; https://www.encodeproject.org/ENCBS598CLB/

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


title: AX4_SE_r5_hr04


title: AX4_SE_r5_hr24


title: Mint-ChIP-seq from brain (ENCLB048KFX)

description:
https://www.encodeproject.org/experiments/ENCSR070JEZ/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR070JEZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB048KFX
fragmentation methods: none

value: brain


title: Mint-ChIP-seq from brain (ENCLB592BYZ)

description:
https://www.encodeproject.org/experiments/ENCSR070JEZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR070JEZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB592BYZ
fragmentation methods: none

value: organoid


title: Mint-ChIP-seq from brain (ENCLB858OKL)

description:
https://www.encodeproject.org/experiments/ENCSR070JEZ/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR070JEZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR389BJR
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB858OKL
fragmentation methods: none

value: healthy


title: AX4_SE_r5_hr16


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB501URU)

description:
https://www.encodeproject.org/experiments/ENCSR259EBS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR259EBS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR469VTN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB501URU
fragmentation methods: none

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

value: IgD-negative memory B cell

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

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS677QPD at ENCODE; https://www.encodeproject.org/ENCBS677QPD/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB845FLW)

description:
https://www.encodeproject.org/experiments/ENCSR185TFI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR185TFI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB845FLW
fragmentation methods: none

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

value: ENCBS370LJB at ENCODE; https://www.encodeproject.org/ENCBS370LJB/


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB676DIZ)

description:
https://www.encodeproject.org/experiments/ENCSR185TFI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR185TFI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB676DIZ
fragmentation methods: none

value: primary cell


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB734WJW)

description:
https://www.encodeproject.org/experiments/ENCSR191YDG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR191YDG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR958CUX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB734WJW
fragmentation methods: none

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: multiple sclerosis

value: ENCBS929PLQ at ENCODE; https://www.encodeproject.org/ENCBS929PLQ/

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


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB696YRW)

description:
https://www.encodeproject.org/experiments/ENCSR259EBS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR259EBS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR469VTN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB696YRW
fragmentation methods: none

value: not collected


title: AX4_SE_r5_hr01

value: WT


title: AX4_SE_r5_hr00


title: AX4_SE_r5_hr02


title: Red light 1 hr rep3

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
BS-seq reads were removed PCR duplicates by using "FilterReads.py" in BS-Seeker2.
BS-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Trimmomatic.
BS-seq reads were aligned to the TAIR10 genome using BS-Seeker2, and in each read, at most 4 bp mismatches will be allowed. If multiple alignments mapped to the same location only one is kept.
Calling methylation levels and removing BS-seq reads with incomplete bisulfite conversion (#(mCH sites)/#(all CH sites)>0.8 and #(mCH sites)>5 for one read) by using BS-Seeker2.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

organism: Arabidopsis thaliana

source_name: Red light 1 hr, seedling

growth_protocol: Seeds were sown on Petri plates and stratified for 1 d at 4 degree in the dark, and then transferred to a growth chamber at 21 degree under long-days condition (16 hr light/8 hr dark light intensity: 70 µmol m-2s-1). One-week-old  seedlings were transferred to the dark for 3 days, and then irradiated under red or blue light for 1 and 4 hours before harvesting.

extract_protocol:
Genomic DNA was isolated from seeding using a MasterPure plant leaf DNA Purification kit MPP92100 (epcentre). The procedure involves extract DNA, RNase digestion, protein precipitation, centrifugation, precipitation of DNA from the supernatant using isopropanol, followed by a wash step with 70% ethanol. After pelleting the precipitated DNA by centrifugation, it was dried under a vacuum and rehydrated in sterile nuclease free water.
Genomic DNA was sheared by sonication to generate DNA fragments in the 100-700 bp size range. Then library preparation included end-repair, A-tailing, methylated adaptor ligation and bisulfite conversion. Finally, the libraries were amplified to enrichment ideal libary for sequencing. The resulting libraries were sequenced with  Illumina sequencing technology.

tag: tissue

value: seedling

tag: culture condition

value: red-light

tag: time


title: Blue light 1 hr rep3

source_name: Blue light 1 hr, seedling

treatment_protocol: One-week-old  seedlings were transferred to the dark for 3 days, and then irradiated under red or blue light for 1 and 4 hours before harvesting.

value: blue-light


title: Red light 4 hr rep2

source_name: Red light 4 hr, seedling


title: Red light 4 hr rep1


title: Blue light 1 hr rep2


title: Red light 4 hr rep3


title: Blue light 4 hr rep2

source_name: Blue light 4 hr, seedling


title: Blue light 1 hr rep1


title: Blue light 4 hr rep3


title: Mint-ChIP-seq from nephron (ENCLB732ZQE)

description:
https://www.encodeproject.org/experiments/ENCSR248DHY/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR248DHY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB732ZQE
fragmentation methods: none

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

value: nephron

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: ENCBS165DBC at ENCODE; https://www.encodeproject.org/ENCBS165DBC/

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB203BUE)

description:
https://www.encodeproject.org/experiments/ENCSR069EIG/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR069EIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB203BUE
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: Kevin Eggan and Ralda Nehme

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


title: Red light 1 hr rep2

value: seedling

value: red-light


title: Mint-ChIP-seq from neural progenitor cell (ENCLB342VKP)

description:
https://www.encodeproject.org/experiments/ENCSR069EIG/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR069EIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB342VKP
fragmentation methods: none

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


title: Blue light 4 hr rep1

value: blue-light


title: Mint-ChIP-seq from neural progenitor cell (ENCLB133PFU)

description:
https://www.encodeproject.org/experiments/ENCSR069EIG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR069EIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB133PFU
fragmentation methods: none

value: female

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB266OFE)

description:
https://www.encodeproject.org/experiments/ENCSR069EIG/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR069EIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB266OFE
fragmentation methods: none

value: healthy

value: embryonic


title: Dark rep4

source_name: Dark, seedling

value: dark


title: Mint-ChIP-seq from neural progenitor cell (ENCLB473SMU)

description:
https://www.encodeproject.org/experiments/ENCSR069EIG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR069EIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB473SMU
fragmentation methods: none

value: 5 day

value: Bradley Bernstein, Broad


title: Dark rep3


title: Mint-ChIP-seq from immature natural killer cell (ENCLB515CEN)

description:
https://www.encodeproject.org/experiments/ENCSR246TTM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR246TTM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731LOB
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB515CEN
fragmentation methods: none

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

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: ENCBS255ELL at ENCODE; https://www.encodeproject.org/ENCBS255ELL/

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


title: Dark rep2

value: seedling


title: Dark rep1


title: Mint-ChIP-seq from nephron (ENCLB156JKO)

description:
https://www.encodeproject.org/experiments/ENCSR248DHY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR248DHY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB156JKO
fragmentation methods: none

value: nephron

value: organoid

value: female

value: Joseph Bonventre

value: ENCBS165DBC at ENCODE; https://www.encodeproject.org/ENCBS165DBC/

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB995DZX)

description:
https://www.encodeproject.org/experiments/ENCSR069EIG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR069EIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB995DZX
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: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

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


title: WGS from transverse colon (ENCLB480CRB)

description:
https://www.encodeproject.org/experiments/ENCSR246MMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The data contained in this experiment correspond to Illumina-based whole genome shotgun sequencing of EN-TEX donor ENCDO845WKR, a 37 year old male. There are two libraries: PCR-based (9-cycle, ENCLB436FSE) and PCR-free (ENCLB480CRB), both sequenced on multiple lanes to a combined depth of ~ 60X in PE125 format.
experiment encode accession: ENCSR246MMZ
assay title: WGS
assembly: GRCh38
encode release date: 2016-04-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB480CRB
fragmentation methods: see document

source_name: Homo sapiens transverse colon tissue male adult (37 years)

value: transverse colon

value: tissue

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS767MGS at ENCODE; https://www.encodeproject.org/ENCBS767MGS/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Mint-ChIP-seq from immature natural killer cell (ENCLB082FHR)

description:
https://www.encodeproject.org/experiments/ENCSR246TTM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR246TTM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731LOB
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB082FHR
fragmentation methods: none

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: ENCBS255ELL at ENCODE; https://www.encodeproject.org/ENCBS255ELL/

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


title: WGS from transverse colon (ENCLB436FSE)

description:
https://www.encodeproject.org/experiments/ENCSR246MMZ/
***************
biological replicate number: 1
technical replicate number: 2
description: The data contained in this experiment correspond to Illumina-based whole genome shotgun sequencing of EN-TEX donor ENCDO845WKR, a 37 year old male. There are two libraries: PCR-based (9-cycle, ENCLB436FSE) and PCR-free (ENCLB480CRB), both sequenced on multiple lanes to a combined depth of ~ 60X in PE125 format.
experiment encode accession: ENCSR246MMZ
assay title: WGS
assembly: GRCh38
encode release date: 2016-04-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB436FSE
fragmentation methods: see document

value: transverse colon

value: tissue


title: Mint-ChIP-seq from brain (ENCLB478UQN)

description:
https://www.encodeproject.org/experiments/ENCSR246IBU/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR246IBU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB478UQN
fragmentation methods: none

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: 53 year

value: Bradley Bernstein, Broad

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 brain (ENCLB470DCZ)

description:
https://www.encodeproject.org/experiments/ENCSR246IBU/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR246IBU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB470DCZ
fragmentation methods: none

value: male

value: adult

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


title: Mint-ChIP-seq from brain (ENCLB704DKC)

description:
https://www.encodeproject.org/experiments/ENCSR246IBU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR246IBU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB704DKC
fragmentation methods: none


title: Mint-ChIP-seq from brain (ENCLB781MIX)

description:
https://www.encodeproject.org/experiments/ENCSR246IBU/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR246IBU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB781MIX
fragmentation methods: none


title: Mint-ChIP-seq from brain (ENCLB303QDI)

description:
https://www.encodeproject.org/experiments/ENCSR246IBU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR246IBU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB303QDI
fragmentation methods: none

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


title: Dnmt1 CKO  E18.5 lung - strong phenotype MUT_S_860_3

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description:
Dnmt1 CKO  E18.5 lung - strong phenotype
strong  phenotype -> widespread hemorrhages within the lung parenchyma

data_processing:
quality assessment - FastQC v0.11.8
adapter removal - Cutadapt 2.5
read quality trimming - Trimmomatic 0.36
alignment to Gencode m23 - STAR with GeneCounts 2.7.1a
generation of RPKM - edgeR 3.28.1
Genome_build: Gencode m19 (GRCm38.p6)
Supplementary_files_format_and_content: RPKM

organism: Mus musculus

source_name: E18.5 lung

extract_protocol:
Embryonic E18.5 lungs were homogenized and dissolved in Trizol (Thermo Fisher Scientific). RNA was extracted from the upper aqueous phase with Qiagen RNeasy Mini Spin Columns. In columns-DNAse treatment was performed according to the Qiagen manual. The quality of the purified RNA was confirmed by Agilent Bioanalyzer System, and reverse cDNA library synthesis and sequencing was performed at the Genomic Core at USC (50 M reads, 75 SR per sample).
Illumina TruSeq

value: Lung

tag: genotype


title: Dnmt1 CKO  E18.5 lung - strong phenotype MUT_S_265_5


title: Wildtype E18.5 lung WT_549_2

description: Wildtype E18.5 lung

value: Wild type


title: Dnmt1 CKO  E18.5 lung - weak phenotype MUT_W_549_3

description:
Dnmt1 CKO  E18.5 lung - weak phenotype
weak phenotype -> no hemorrhage


title: Dnmt1 CKO  E18.5 lung - weak phenotype MUT_W_265_2


title: Wildtype E18.5 lung WT_265_1

description: Wildtype E18.5 lung


title: LK1108 cell line grown with CAF in 3D

type: RNA

city: Linköping

first: Emilia

last: Wiechec

address: Sandbäcksgatan 7

department: Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

description:
Gene expression data; SST-RMA expression value derived from TAC software
Gene expression data from HNSCC cell lines grown with or without CAFs in 3D

hyb_protocol: Hybridization was done according to the GeneChip® WT Plus Reagent Kit manufacturer's instructions. A total of 5.5 µg of sscDNA was fragmented and hybridized on a Human Transcriptome 2.0 Array.

scan_protocol: Hybridized arrays were scanned with an Affymetrix GeneChip® 3000 fluorescent scanner.

data_processing: Raw intensity CEL files generated by the GeneChip Command Console were imported into Transcriptome Analysis Console (TAC) and CHP files were generated for gene level analysis using the SST-RMA summarization method.

label: biotin

source_name: cell co-culture with CAF

label_protocol: Labeling was done according to the GeneChip® WT Plus Reagent Kit manufacturer’s instructions The starting amount of total RNA was 150 ng. 15 µg of cRNA was used for single-stranded cDNA-synthesis (sscDNA).

growth_protocol: Tumor cells and CAFs were co-cultured in 3D. To achieve spheroids of tumor cells or co-cultures of tumor cells and CAFs, 15,000 tumor cells or 10,000 tumor cells with 5,000 CAFs were seeded into each well of ultra-low at-tachment (ULA) 96-well round-bottomed plates (Corning, Amsterdam, The Netherlands) and were thereafter cultured in standard culture conditions

extract_protocol: Total RNA extraction was performed using the RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Tumor cells were separated from CAFs by magnetic activated cell sorting (MACS).

value: HNSCC cell line (hypopharynx)


title: Dnmt1 CKO  E18.5 lung - weak phenotype MUT_W_268_3


title: Wildtype E18.5 lung WT_268_1

description: Wildtype E18.5 lung


title: AX4_SE_r5_hr03

tag: strain

tag: phenotype group

value: WT


title: LK1108 cell line grown without CAF in 3D

source_name: cell culture without CAF


title: LK0902 cell line grown with CAF in 3D

value: HNSCC cell line (tongue)


title: Dnmt1 CKO P7 myofibroblasts rep2

data_processing:
quality assessment: FastQC v0.11.8
adapter removal: Cutadapt 2.5
read quality trimming: Trimmomatic 0.36
alignment to Gencode m23: STAR with GeneCounts 2.7.1a
generation of RPKM: edgeR 3.28.1
Genome_build: Gencode m23 (GRCm38.p6)
Supplementary_files_format_and_content: fastq format raw data

source_name: P7 lungs

extract_protocol:
Two WT-Pdgfrb-GFP+/- and two CKO Pdgfrb-GFP+/- lungs were harvested from P7 animals. Blood was removed by infusing PBS into the right ventricle. Lungs were then minced and digested with collagenase IV (1mg/ml, Sigma), DNase I (0.16 mg/ml, Sigma) and dispase II (2mb/ml, Roche) for 45 minutes at 37C. Tissue homogenate was filtered through a 70 um filter to obtain single cells suspension. Pdgfrb-GFP+/- positive cells were retrieved via FACS. Dead cells were detected with DAPI. Approximately 300000-350000 cells were purified from each sample. Cell pellet was resuspended in Trizol (Thermo Fisher Scientific) and RNA was extracted from the upper aqueous phase with Qiagen RNeasy Mini Spin Columns. In column DNase treatment was performed according to the Qiagen manual. Quality of the purified RNA was confirmed with Agilent Bioanalyzer System.
Kapa low


title: LK0902 cell line grown without CAF in 3D


title: LK0917 cell line grown with CAF in 3D

value: HNSCC cell line (gingiva)


title: Wildtype P7 myofibroblasts rep2

value: Wild type PDGFRb-GFP


title: Mint-ChIP-seq from GM23338 (ENCLB587TDU)

description:
https://www.encodeproject.org/experiments/ENCSR068ZVD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR068ZVD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB587TDU
fragmentation methods: none

source_name: Homo sapiens GM23338 cell line, preserved by cryopreservation

tag: line

value: cell line

value: PGP1 iPSCs

value: George Church

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


title: Dnmt1 CKO P7 myofibroblasts rep1


title: Mint-ChIP-seq from brain (ENCLB740AKF)

description:
https://www.encodeproject.org/experiments/ENCSR246IBU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR246IBU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB740AKF
fragmentation methods: none

tag: antibody

value: brain

value: organoid

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

value: 53 year

value: Bradley Bernstein, Broad

value: Paola Arlotta


title: Dnmt1 CKO  E18.5 lung - strong phenotype MUT_S_268_4

value: Lung


title: exosome2

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

country: China

institute: Tongji University

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Genome_build: mm9
Supplementary_files_format_and_content: xls file containing the miRNA id, pre-miRNA_seq ,normalized abundance

source_name: Bone marrow

extract_protocol:
Total RNA was isolated from the samples and RNA integrity was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The miRNA-seq library was constructed using the TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) according to the manufacturer's instructions.

tag: cell type

value: Bone marrow stem cell (BMSC)


title: exosome1


title: Mint-ChIP-seq from H9 (ENCLB562AQF)

description:
https://www.encodeproject.org/experiments/ENCSR243FOM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR243FOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB562AQF
fragmentation methods: none

source_name: Homo sapiens H9 cell line

tag: biosample encode accession

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

tag: passage number

value: ENCBS965ZIX at ENCODE; https://www.encodeproject.org/ENCBS965ZIX/

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


title: Mint-ChIP-seq from H9 (ENCLB702ZHJ)

description:
https://www.encodeproject.org/experiments/ENCSR243FOM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR243FOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB702ZHJ
fragmentation methods: none

value: cell line

tag: Sex

tag: health state

value: ENCBS877WZR at ENCODE; https://www.encodeproject.org/ENCBS877WZR/


title: Wildtype P7 myofibroblasts rep1

value: Wild type PDGFRb-GFP


title: Red light 1 hr rep1

value: seedling

value: red-light


title: Th9 Areg-/- rep1

city: Faridabad

first: Abhay

middle: Deep

last: Pandey

address: 3rd Milestone, Faridabad-Gurgaon Expressway

department: Virology

country: India

institute: Regional Centre for Biotechnology

data_processing:
RNA extracted from Th9 cells was subjected to next-generation sequencing (NGS) to generate deep coverage RNA-Seq data. Sequencing libraries of Poly A selected mRNA were generated from the double-stranded cDNA using the Illumina TruSeq kit according to the manufacturer's protocol. Library quality control was checked using the Agilent DNA High Sensitivity Chip and qPCR. High quality libraries were sequenced on an Illumina HiSeq 2500.
The Quality check of the sequenced read were performed by FASTQC and FASTX to remove the adaptor and unwanted low quality reads. Tophat2 and Bowtie2 packages were used to align the cleaned reads to the reference mouse genome (GRCm38). The read count-based gene expression data were normalized on the basis of library complexity and gene variation using the Cuffdiff.
Genome_build: GRCm38
Supplementary_files_format_and_content: exp_diff.txt

source_name: T lymphocytes

extract_protocol:
RNA was extracted from in vitro differentiated Th9 cells from WT and Areg-/- mice using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Areg-/-

value: Th9 cells


title: Th9 WT rep2

value: Wild type


title: Mint-ChIP-seq from H9 (ENCLB574HRV)

description:
https://www.encodeproject.org/experiments/ENCSR243FOM/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR243FOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB574HRV
fragmentation methods: none

tag: dev stage

tag: age

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from H9 (ENCLB468ZFZ)

description:
https://www.encodeproject.org/experiments/ENCSR243FOM/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR243FOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB468ZFZ
fragmentation methods: none

tag: lab

tag: source


title: Mint-ChIP-seq from H9 (ENCLB961KLR)

description:
https://www.encodeproject.org/experiments/ENCSR243FOM/
***************
biological replicate number: 1
technical replicate number: 4
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR243FOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB961KLR
fragmentation methods: none

tag: link


title: Th9 WT rep1


title: Mint-ChIP-seq from H9 (ENCLB240LUL)

description:
https://www.encodeproject.org/experiments/ENCSR243FOM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR243FOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB240LUL
fragmentation methods: none


title: Mint-ChIP-seq from GM23338 (ENCLB676FBW)

description:
https://www.encodeproject.org/experiments/ENCSR068ZVD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR068ZVD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB676FBW
fragmentation methods: none

tag: description

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: LK0917 cell line grown without CAF in 3D

tag: tissue

value: HNSCC cell line (gingiva)


title: CCR2LO_3_4

city: BEIJING

first: SHIYUE

last: HOU

state: China Mainland

address: ROOM A104, MEDICAL SCIENCE BUILDING, TSINGHUA UNIVERSITY

institute: TSINGHUA UNIVERSITY

data_processing:
The raw data were processed with CASAVA (Illumina) for generating fastq files, followed by aligning reads to the Mus musculus reference genome (NCBI build 37.2) with TopHat2 and assembling Cufflinks  (version 2.2.1)  to calculate the FPKM for each transcript.
Supplementary_files_format_and_content: The matrix table is a spreadsheet containing the normalized gene counts comparable across rows and Samples.

source_name: Splenic CD8 T cells

growth_protocol: Splenic CD8 T cells from SPF Ccr2rfp/+ mice of 6-8 weeks old were isolated with CD8+ T cell isolation kit (Miltenyi Biotec).

extract_protocol: RNA extraction, reverse transcription and sequence library preparation is described in Wang, et.al., 2017(PMID: 28650481)

treatment_protocol: After antibody staining, CD8+CD44+CD62L+RFP+/RFP- cells were sorted as 200 cells in tubes with lysis buffer.

value: spleen

value: CCR2- virtual memory CD8 T cells

value: 6-8 weeks SPF mice

tag: cell markers


title: CCR2LO_3_1

tag: strain


title: Th9 Areg-/- rep2

tag: genotype


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB244KVC)

description:
https://www.encodeproject.org/experiments/ENCSR158UEK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR158UEK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242OUP
encode release date: 2020-09-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB244KVC
fragmentation methods: none

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

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS764TKE at ENCODE; https://www.encodeproject.org/ENCBS764TKE/

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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB671TCK)

description:
https://www.encodeproject.org/experiments/ENCSR158UEK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR158UEK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242OUP
encode release date: 2020-09-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB671TCK
fragmentation methods: none

value: Bradley Bernstein, Broad


title: CCR2LO_2_1


title: CCR2LO_2_2


title: Mint-ChIP-seq from immature natural killer cell (ENCLB980RSI)

description:
https://www.encodeproject.org/experiments/ENCSR158VSE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR158VSE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731LOB
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB980RSI
fragmentation methods: none

value: immature natural killer cell

value: multiple sclerosis

value: ENCBS255ELL at ENCODE; https://www.encodeproject.org/ENCBS255ELL/

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


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB168KEN)

description:
https://www.encodeproject.org/experiments/ENCSR157JIS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR157JIS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR469VTN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB168KEN
fragmentation methods: none

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

value: IgD-negative memory B cell

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

value: ENCBS677QPD at ENCODE; https://www.encodeproject.org/ENCBS677QPD/


title: CCR2LO_1_3

value: spleen

value: CCR2- virtual memory CD8 T cells

value: 6-8 weeks SPF mice


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB552OQP)

description:
https://www.encodeproject.org/experiments/ENCSR157JIS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR157JIS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR469VTN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB552OQP
fragmentation methods: none

value: primary cell

value: not collected


title: CCR2LO_1_4


title: CCR2LO_1_2


title: Mint-ChIP-seq from immature natural killer cell (ENCLB061WLS)

description:
https://www.encodeproject.org/experiments/ENCSR061ATV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR061ATV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731LOB
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB061WLS
fragmentation methods: none

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

value: unknown


title: CCR2LO_1_1


title: CCR2LO_3_3


title: Mint-ChIP-seq from immature natural killer cell (ENCLB406UXV)

description:
https://www.encodeproject.org/experiments/ENCSR158VSE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR158VSE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731LOB
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406UXV
fragmentation methods: none

value: David Hafler


title: Mint-ChIP-seq from immature natural killer cell (ENCLB772LKF)

description:
https://www.encodeproject.org/experiments/ENCSR061ATV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR061ATV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731LOB
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB772LKF
fragmentation methods: none


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB100XHA)

description:
https://www.encodeproject.org/experiments/ENCSR243EIU/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR243EIU
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB100XHA

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

value: ENCBS771DND at ENCODE; https://www.encodeproject.org/ENCBS771DND/

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


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB468GIL)

description:
https://www.encodeproject.org/experiments/ENCSR242ARJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR242ARJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB468GIL

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS142IVK at ENCODE; https://www.encodeproject.org/ENCBS142IVK/

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


title: Control Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB327JGE)

description:
https://www.encodeproject.org/experiments/ENCSR242OUP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR242OUP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB327JGE

value: ENCBS764TKE at ENCODE; https://www.encodeproject.org/ENCBS764TKE/


title: CCR2HI_3_1

value: CCR2+ virtual memory CD8 T cells


title: Control Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB169EZW)

description:
https://www.encodeproject.org/experiments/ENCSR242OUP/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR242OUP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB169EZW


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB445JJS)

description:
https://www.encodeproject.org/experiments/ENCSR243EIU/
***************
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: ENCSR243EIU
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB445JJS

value: multiple sclerosis


title: CCR2HI_3_4

value: spleen


title: CCR2HI_3_2

value: 6-8 weeks SPF mice


title: CCR2HI_3_3


title: CCR2LO_3_2

value: CCR2- virtual memory CD8 T cells


title: CCR2HI_2_2


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB111IPS)

description:
https://www.encodeproject.org/experiments/ENCSR239OWL/
***************
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: ENCSR239OWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128KDZ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB111IPS

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

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

value: primary cell

value: not collected

value: ENCBS757PLC at ENCODE; https://www.encodeproject.org/ENCBS757PLC/


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB890MPL)

description:
https://www.encodeproject.org/experiments/ENCSR242ARJ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR242ARJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB890MPL

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

value: unknown

value: David Hafler


title: CCR2HI_1_3


title: CCR2HI_1_4


title: CCR2HI_2_1


title: CCR2HI_1_2


title: WGS from transverse colon (ENCLB590TZQ)

description:
https://www.encodeproject.org/experiments/ENCSR997HAI/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this Experiment corresponds to 10X Genomics Chromium prepared WGS.
experiment encode accession: ENCSR997HAI
assay title: WGS
assembly: GRCh38
encode release date: 2017-08-01
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB590TZQ

source_name: Homo sapiens transverse colon tissue female adult (53 years)

value: transverse colon

value: tissue

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: female

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS974EYF at ENCODE; https://www.encodeproject.org/ENCBS974EYF/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: CCR2HI_1_1

value: spleen

value: CCR2+ virtual memory CD8 T cells

value: 6-8 weeks SPF mice


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB554JPN)

description:
https://www.encodeproject.org/experiments/ENCSR991KBE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR991KBE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR165PMH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB554JPN
fragmentation methods: none

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

value: CD14-positive monocyte

value: primary cell

value: male

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

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

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


title: Mint-ChIP-seq from brain (ENCLB831YUR)

description:
https://www.encodeproject.org/experiments/ENCSR236SCE/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR236SCE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB831YUR
fragmentation methods: none

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: adult

value: Bradley Bernstein, Broad

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 brain (ENCLB221GVW)

description:
https://www.encodeproject.org/experiments/ENCSR236SCE/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR236SCE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB221GVW
fragmentation methods: none

value: 53 year


title: Mint-ChIP-seq from brain (ENCLB047RVU)

description:
https://www.encodeproject.org/experiments/ENCSR236SCE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR236SCE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB047RVU
fragmentation methods: none

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


title: Mint-ChIP-seq from brain (ENCLB806GLE)

description:
https://www.encodeproject.org/experiments/ENCSR236SCE/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR236SCE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB806GLE
fragmentation methods: none

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


title: Mint-ChIP-seq from brain (ENCLB084BAR)

description:
https://www.encodeproject.org/experiments/ENCSR236SCE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR236SCE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB084BAR
fragmentation methods: none

value: male


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB650HOU)

description:
https://www.encodeproject.org/experiments/ENCSR991KBE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR991KBE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR165PMH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB650HOU
fragmentation methods: none

value: CD14-positive monocyte

value: primary cell

value: 30 year


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB474CHW)

description:
https://www.encodeproject.org/experiments/ENCSR239OWL/
***************
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: ENCSR239OWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128KDZ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB474CHW

value: CD8-positive, alpha-beta memory T 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: ENCBS757PLC at ENCODE; https://www.encodeproject.org/ENCBS757PLC/

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


title: Control Mint-ChIP-seq from activated T-cell (ENCLB554XYK)

description:
https://www.encodeproject.org/experiments/ENCSR897COL/
***************
biological replicate number: 2
technical replicate number: 1
description: Control Mint-ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR897COL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB554XYK

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: adult

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: Mint-ChIP-seq from brain (ENCLB340DFR)

description:
https://www.encodeproject.org/experiments/ENCSR236SCE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR236SCE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB340DFR
fragmentation methods: none

value: brain

value: organoid

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

value: male

value: 53 year

value: Paola Arlotta

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

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


title: Control Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB915RGP)

description:
https://www.encodeproject.org/experiments/ENCSR899DXS/
***************
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: ENCSR899DXS
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB915RGP
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS067WEN at ENCODE; https://www.encodeproject.org/ENCBS067WEN/

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


title: Control Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB149IEE)

description:
https://www.encodeproject.org/experiments/ENCSR899DXS/
***************
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: ENCSR899DXS
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB149IEE
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB672JSB)

description:
https://www.encodeproject.org/experiments/ENCSR151ARX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR151ARX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR881SIP
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB672JSB
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: healthy

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

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB287JRI)

description:
https://www.encodeproject.org/experiments/ENCSR057IZD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR057IZD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128CIX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB287JRI

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell with multiple sclerosis

value: ENCBS040CMJ at ENCODE; https://www.encodeproject.org/ENCBS040CMJ/

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


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB469MTN)

description:
https://www.encodeproject.org/experiments/ENCSR151ARX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR151ARX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR881SIP
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB469MTN
fragmentation methods: none


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB247XSD)

description:
https://www.encodeproject.org/experiments/ENCSR057IZD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR057IZD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128CIX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB247XSD


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB132TOP)

description:
https://www.encodeproject.org/experiments/ENCSR235WEI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR235WEI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB132TOP
fragmentation methods: none

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

value: ENCBS370LJB at ENCODE; https://www.encodeproject.org/ENCBS370LJB/


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB182FDA)

description:
https://www.encodeproject.org/experiments/ENCSR235WEI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR235WEI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182FDA
fragmentation methods: none


title: Control Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB943ERW)

description:
https://www.encodeproject.org/experiments/ENCSR890AQB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of CD8-positive, alpha-beta memory T cell male adult (30 years)
experiment encode accession: ENCSR890AQB
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB943ERW

source_name: Homo sapiens male adult (30 years) CD8-positive, alpha-beta memory T primary cell

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

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS122NLR at ENCODE; https://www.encodeproject.org/ENCBS122NLR/

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


title: Control Mint-ChIP-seq from activated T-cell (ENCLB985WHC)

description:
https://www.encodeproject.org/experiments/ENCSR897COL/
***************
biological replicate number: 2
technical replicate number: 2
description: Control Mint-ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR897COL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB985WHC

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

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


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB039YKC)

description:
https://www.encodeproject.org/experiments/ENCSR895OTJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR895OTJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR176HLK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039YKC
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: 43 year

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/

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


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB921QJL)

description:
https://www.encodeproject.org/experiments/ENCSR889GVN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR889GVN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB921QJL
fragmentation methods: none

source_name: Homo sapiens male adult (43 years) activated CD4 positive, naive alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

tag: antibody

value: male

value: adult

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: ENCBS377CVF at ENCODE; https://www.encodeproject.org/ENCBS377CVF/


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB140FNR)

description:
https://www.encodeproject.org/experiments/ENCSR895OTJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR895OTJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR176HLK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB140FNR
fragmentation methods: none

value: Yijun Ruan, JAX

value: AllCells


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB195VEE)

description:
https://www.encodeproject.org/experiments/ENCSR983MKX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR983MKX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR354FME
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB195VEE
fragmentation methods: none

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

value: IgD-negative memory B cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS091EUT at ENCODE; https://www.encodeproject.org/ENCBS091EUT/

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


title: Control Mint-ChIP-seq from brain (ENCLB382AII)

description:
https://www.encodeproject.org/experiments/ENCSR141MUD/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR141MUD
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB382AII

source_name: Homo sapiens male adult (53 years) brain organoid, 90 days post differentiation

value: brain

value: organoid

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

value: 53 year

value: Paola Arlotta

value: ENCBS291HMT at ENCODE; https://www.encodeproject.org/ENCBS291HMT/

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


title: Mint-ChIP-seq from naive B cell (ENCLB926RBX)

description:
https://www.encodeproject.org/experiments/ENCSR884MVN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR884MVN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR119CTT
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB926RBX
fragmentation methods: none

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

value: naive B cell

value: primary cell

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

value: healthy

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

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


title: Control Mint-ChIP-seq from brain (ENCLB624ARP)

description:
https://www.encodeproject.org/experiments/ENCSR141MUD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR141MUD
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB624ARP

value: male

value: adult

value: Bradley Bernstein, Broad


title: Control Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB511SFJ)

description:
https://www.encodeproject.org/experiments/ENCSR890AQB/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of CD8-positive, alpha-beta memory T cell male adult (30 years)
experiment encode accession: ENCSR890AQB
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB511SFJ

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

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS122NLR at ENCODE; https://www.encodeproject.org/ENCBS122NLR/

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