title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB905HGF)

description:
https://www.encodeproject.org/experiments/ENCSR486XJK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR486XJK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283LWF
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB905HGF
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

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

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

value: ENCBS812ZCI at ENCODE; https://www.encodeproject.org/ENCBS812ZCI/

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


title: Mint-ChIP-seq from naive B cell (ENCLB941OEG)

status: Public on Jun 15 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR486SZN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR486SZN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR111MNI
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB941OEG
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

value: naive B cell

value: primary cell

tag: description

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

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: multiple sclerosis

tag: dev stage

value: unknown

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

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


title: gtaI_r1_hr12

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
GSM3767616
GEO: GSE131209
gtaI_bio1_hr12: gtaI_development 12h : replicate 1
gtaI_r1_hr12

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 through the web application dictyExpress GenBoard or Genialis platform. 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: polyA RNA

organism: Dictyostelium discoideum

source_name: gtaI–

growth_protocol: Dictyostelium discoideum cells were grown in nutrient media (HL-5)

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.

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: gtaI-

tag: phenotype group

value: culmination defective

tag: replicate

tag: developmental time


title: Mint-ChIP-seq from T-cell (ENCLB432HJD)

description:
https://www.encodeproject.org/experiments/ENCSR381QKQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR381QKQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB432HJD
fragmentation methods: none

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

value: T-cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS038FPK at ENCODE; https://www.encodeproject.org/ENCBS038FPK/

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


title: gtaI_r1_hr00

description:
GSM3767613
GEO: GSE131209
gtaI_bio1_hr00: gtaI_development 0h : replicate 1
gtaI_r1_hr00


title: gtaI_r1_hr08

description:
GSM3767615
GEO: GSE131209
gtaI_bio1_hr08: gtaI_development 8h : replicate 1
gtaI_r1_hr08


title: gtaI_r1_hr04

description:
GSM3767614
GEO: GSE131209
gtaI_bio1_hr04: gtaI_development 4h : replicate 1
gtaI_r1_hr04


title: amiB_r2_hr20

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

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).

value: amiB

value: aggregation minus


title: Mint-ChIP-seq from T-cell (ENCLB187KJT)

description:
https://www.encodeproject.org/experiments/ENCSR381QKQ/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR381QKQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB187KJT
fragmentation methods: none

value: primary cell


title: Mint-ChIP-seq from T-cell (ENCLB529VDK)

description:
https://www.encodeproject.org/experiments/ENCSR381QKQ/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR381QKQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB529VDK
fragmentation methods: none


title: amiB_r2_hr24


title: amiB_r2_hr16


title: amiB_r2_hr08


title: Mint-ChIP-seq from T-cell (ENCLB527ZQE)

description:
https://www.encodeproject.org/experiments/ENCSR381QKQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR381QKQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB527ZQE
fragmentation methods: none


title: amiB_r2_hr12


title: Mint-ChIP-seq from naive B cell (ENCLB919PVT)

description:
https://www.encodeproject.org/experiments/ENCSR486SZN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR486SZN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR111MNI
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919PVT
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: naive B cell

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

value: not collected

value: multiple sclerosis

value: unknown

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB314ODL)

description:
https://www.encodeproject.org/experiments/ENCSR485JEQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR485JEQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR820SXH
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB314ODL
fragmentation methods: none

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

value: CD8-positive, alpha-beta T cell

value: 21 year

value: Yijun Ruan, JAX

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

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


title: amiB_r1_hr20


title: amiB_r2_hr04


title: amiB_r1_hr24


title: Control Mint-ChIP-seq from type B pancreatic cell (ENCLB983JDD)

description:
https://www.encodeproject.org/experiments/ENCSR380ZKL/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR380ZKL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB983JDD

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

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS779FCS at ENCODE; https://www.encodeproject.org/ENCBS779FCS/

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


title: amiB_r1_hr12

value: amiB

value: aggregation minus


title: amiB_r2_hr00


title: amiB_r2_hr02


title: Mint-ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB416SYX)

description:
https://www.encodeproject.org/experiments/ENCSR485JEQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR485JEQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR820SXH
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB416SYX
fragmentation methods: none

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 21 year

value: AllCells


title: Control Mint-ChIP-seq from type B pancreatic cell (ENCLB984LZT)

description:
https://www.encodeproject.org/experiments/ENCSR380ZKL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR380ZKL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB984LZT

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells


title: amiB_r1_hr08


title: amiB_r1_hr06


title: amiB_r1_hr16


title: Mint-ChIP-seq from immature natural killer cell (ENCLB269FIK)

description:
https://www.encodeproject.org/experiments/ENCSR578KKD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR578KKD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR314IFB
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB269FIK
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS497KWS at ENCODE; https://www.encodeproject.org/ENCBS497KWS/

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


title: amiB_r1_hr04

value: amiB

value: aggregation minus


title: amiB_r1_hr02


title: Mint-ChIP-seq from immature natural killer cell (ENCLB548VFN)

description:
https://www.encodeproject.org/experiments/ENCSR578KKD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR578KKD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR314IFB
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB548VFN
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: primary cell

value: Bradley Bernstein, Broad


title: amiB_r1_hr00


title: gbfA_r2_hr24

value: gbfA

value: disaggregation


title: gbfA_r2_hr20


title: gbfA_r2_hr14


title: amiB_r2_hr06


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB893BRO)

description:
https://www.encodeproject.org/experiments/ENCSR573RAO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR573RAO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB893BRO
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

value: male

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

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/

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


title: gbfA_r2_hr12


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB619SCK)

description:
https://www.encodeproject.org/experiments/ENCSR573RAO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR573RAO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB619SCK
fragmentation methods: none


title: gbfA_r2_hr06


title: gbfA_r2_hr10


title: gbfA_r2_hr04


title: gbfA_r1_hr24


title: gbfA_r2_hr00


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB369PLR)

description:
https://www.encodeproject.org/experiments/ENCSR571SOT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR571SOT
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB369PLR
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: immature natural killer cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS493KVP at ENCODE; https://www.encodeproject.org/ENCBS493KVP/

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


title: Mint-ChIP-seq from naive B cell (ENCLB471XWE)

description:
https://www.encodeproject.org/experiments/ENCSR480ITK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR480ITK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR163IRW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB471XWE
fragmentation methods: none

value: naive B cell

value: primary cell

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

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: ENCBS345AAH at ENCODE; https://www.encodeproject.org/ENCBS345AAH/

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


title: gbfA_r1_hr16

value: gbfA

value: disaggregation


title: gbfA_r1_hr14


title: Mint-ChIP-seq from activated T-cell (ENCLB931FKL)

description:
https://www.encodeproject.org/experiments/ENCSR569XQS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq of activated T-cell male adult (42 years)
experiment encode accession: ENCSR569XQS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR975DSD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB931FKL
fragmentation methods: none

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

value: activated T-cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

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

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


title: gbfA_r1_hr12


title: gbfA_r1_hr10


title: gbfA_r1_hr20


title: Mint-ChIP-seq from activated T-cell (ENCLB567KND)

description:
https://www.encodeproject.org/experiments/ENCSR569XQS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq of activated T-cell male adult (42 years)
experiment encode accession: ENCSR569XQS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR975DSD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB567KND
fragmentation methods: none


title: gbfA_r1_hr06


title: gbfA_r1_hr04


title: Ucp2-wildtype NAC treatment replicate 2

city: Bethesda

first: Eytan

last: Ruppin

address: 9000 Rockville Pike

institute: National Institutes of Health

description: Ucp2-wildtype NAC treatment replicate 2

data_processing:
The HiSeq Real Time Analysis software (RTA 1.18.64) was used for processing raw data files, the Illumina bcl2fastq2.17 was used to demultiplex and convert binary base calls and qualities to fastq format.  The sequencing reads were trimmed adapters and low-quality bases using Cutadapt (version 1.18), the trimmed reads were mapped to mouse reference genome (mm10) and Gencode annotation GENCODE M21 using STAR (version 2.7.0f) with two-pass alignment option. RSEM (version 1.3.1) was used for gene and transcript quantification.
Genome_build: Mouse reference genome (mm10) and GENCODE M21
Supplementary_files_format_and_content: The RSEM result for each sample is given in a separate file, containing the expected read count, TPM and FPKM across genes and transcripts

organism: Mus musculus

source_name: Pmel-1 CD8 T cell

growth_protocol: CD8+ T cells from pmel-1 mice were stimulated in vitro with 1 μM hgp10025–33 peptide or plate-bound anti-CD3 (2 μg/ml; 145-2C11; BD Biosciences) and soluble anti-CD28 (1 μg/ml; 37.5 l; BD Biosciences) and expanded in culture medium containing 10 ng•ml–1 IL-2 (Chiron) for 4 days.

extract_protocol:
The TruSeq Stranded Total RNA library preparation kit from Illumina was used. This protocol involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads.
The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to produce a sequencing ready library. The final purified product is then quantitated by qPCR before cluster generation and sequencing.  The libraries were run on the Illumina HiSeq3000/4000 using HiSeq 3000/4000 SBS kit chemistry, 2x150bp paired-end sequencing run.

treatment_protocol: CD8+ T cells from pmel-1 mice were incubated with genipin, or NAC (Sigma-Aldrich) or vehicle (culture media) at the indicated doses.

tag: cell type

value: Pmel-1 CD8 T cell

tag: treatment

value: NAC

tag: ucp2 genotype

value: wildtype


title: gbfA_r2_hr16


title: Ucp2-wildtype NAC treatment replicate 3

description: Ucp2-wildtype NAC treatment replicate 3


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB471AGI)

description:
https://www.encodeproject.org/experiments/ENCSR472ZFJ/
***************
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: ENCSR472ZFJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR521SOP
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB471AGI
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

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

tag: antibody

value: primary cell

tag: description

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS892TKW at ENCODE; https://www.encodeproject.org/ENCBS892TKW/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB271NFV)

description:
https://www.encodeproject.org/experiments/ENCSR472ZFJ/
***************
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: ENCSR472ZFJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR521SOP
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB271NFV
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

tag: biosample encode accession

tag: Sex

value: Bradley Bernstein, Broad


title: gbfA_r1_hr00

value: gbfA

value: disaggregation


title: Ucp2-wildtype NAC treatment replicate 1

description: Ucp2-wildtype NAC treatment replicate 1


title: gbfA_r2_hr08


title: Mint-ChIP-seq from naive B cell (ENCLB406WVG)

description:
https://www.encodeproject.org/experiments/ENCSR480ITK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR480ITK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR163IRW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406WVG
fragmentation methods: none

value: naive B cell

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

tag: health state

value: multiple sclerosis

tag: dev stage

value: ENCBS345AAH at ENCODE; https://www.encodeproject.org/ENCBS345AAH/

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


title: Mint-ChIP-seq from H9 (ENCLB807LQH)

description:
https://www.encodeproject.org/experiments/ENCSR373TMA/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR373TMA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB807LQH
fragmentation methods: none

source_name: Homo sapiens H9 cell line originated from H9

tag: line

value: cell line

value: WA09 ES cells

value: female

value: embryonic

tag: age

value: 5 day

tag: lab

value: SESCC

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/

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


title: tgrC1_r2_hr24

tag: strain


title: tgrC1_r2_hr20

tag: phenotype group


title: Ucp2-wildtype genipin+NAC treatment replicate 3

value: Pmel-1 CD8 T cell

value: genipin+NAC

value: wildtype


title: Mint-ChIP-seq from H9 (ENCLB842AMK)

description:
https://www.encodeproject.org/experiments/ENCSR373TMA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR373TMA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB842AMK
fragmentation methods: none

value: healthy

value: Bradley Bernstein, Broad

tag: source

tag: link

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/


title: tgrC1_r2_hr14

value: disaggregation

tag: replicate

tag: developmental time


title: tgrC1_r2_hr12


title: tgrC1_r2_hr10


title: gbfA_r1_hr08

value: gbfA


title: Ucp2-wildtype genipin+NAC treatment replicate 2

tag: cell type

tag: treatment


title: Ucp2-wildtype genipin+NAC treatment replicate 1

tag: ucp2 genotype


title: Mint-ChIP-seq from H9 (ENCLB622IYY)

description:
https://www.encodeproject.org/experiments/ENCSR373TMA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR373TMA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB622IYY
fragmentation methods: none

tag: antibody

tag: description


title: tgrC1_r2_hr06


title: tgrC1_r2_hr08


title: Ucp2-wildtype genipin treatment replicate 2

value: genipin


title: Ucp2-wildtype genipin treatment replicate 1


title: tgrC1_r1_hr24


title: tgrC1_r1_hr20


title: tgrC1_r2_hr00


title: tgrC1_r2_hr16


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB842KBD)

description:
https://www.encodeproject.org/experiments/ENCSR372LPU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq of CD8-positive naive resting alpha-beta T cell male adult (30 years)
experiment encode accession: ENCSR372LPU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR761HQT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB842KBD
fragmentation methods: none

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

value: primary cell

tag: biosample encode accession

tag: Sex

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS845PJM at ENCODE; https://www.encodeproject.org/ENCBS845PJM/

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


title: tgrC1_r1_hr12


title: tgrC1_r1_hr10


title: tgrC1_r1_hr14


title: Ucp2-wildtype vehicle treatment replicate 3

value: Pmel-1 CD8 T cell

value: vehicle (culture media)


title: tgrC1_r1_hr08


title: Mint-ChIP-seq from H9 (ENCLB303BPM)

description:
https://www.encodeproject.org/experiments/ENCSR372FFA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR372FFA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB303BPM
fragmentation methods: none

value: cell line

value: WA09 ES cells

value: female

tag: health state

tag: dev stage

value: embryonic

value: 5 day

value: SESCC

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/

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


title: Ucp2-wildtype vehicle treatment replicate 2

value: wildtype


title: Mint-ChIP-seq from H9 (ENCLB417JBH)

description:
https://www.encodeproject.org/experiments/ENCSR373TMA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR373TMA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB417JBH
fragmentation methods: none

tag: line

value: healthy

tag: age

value: Bradley Bernstein, Broad


title: Ucp2-wildtype genipin treatment replicate 3

value: genipin


title: tgrC1_r1_hr06

tag: strain

value: disaggregation


title: infected macrophage rep3

city: Freiburg

first: Sebastian

last: Baasch

address: Breisacher Str.

department: Institute for Immunodeficiency; Center for Chronic Immunodeficiency

country: Germany

institute: University Medical Center

data_processing:
De-multiplexing: Illumina bcl2fastq
Trimming: Skewer (V0.2.2)
Read count: STAR (V2.5.2b)
Quality control reads: FASTQC
Alignment: STAR (V2.5.2b)
Differentially expressed genes: DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab seperated values-files of raw_reads, normalized_reads and differentially expressed genes (fold change and adjusted p-values) comparing infected vs control BMDM and infected vs bystanding BMDM

source_name: Bone marrow-derived macrophages

growth_protocol: Murine bone marrow was cultured in RPMI with 10% fetal calve serum, 0,5% ciprofloxacin and M-CSF (20ng/ml) for 7 days to obtain differentiated bone marrow-derived macrophages (BMDM). Medium was changed after 4 days of culture.

extract_protocol:
100ng of total RNA, obtained with QIAGEN microkit, was subjected to library synthesis using the TruSeq Stranded  mRNA Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDM were infected with a murine cytomegalovirus, which expresses GFP during replication. BMDM were sorted 24 hours post infection into bystanding (uninfected GFP-) and infected (GFP+) macrophages. Control macrophages were sorted without infection. After sorting the macrophages were cultured until 3 dpi before cell lysis.

value: Bone marrow-derived macrophages

tag: genotype

value: wild type

tag: condition

value: infected


title: Mint-ChIP-seq from H9 (ENCLB473WHB)

description:
https://www.encodeproject.org/experiments/ENCSR372FFA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR372FFA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB473WHB
fragmentation methods: none

tag: lab

tag: source

tag: link

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/


title: tgrC1_r1_hr00

tag: phenotype group

tag: replicate

tag: developmental time


title: tgrB1C1_r2_hr24


title: tgrC1_r1_hr04


title: tgrC1_r2_hr04


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB869NZX)

description:
https://www.encodeproject.org/experiments/ENCSR372LPU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq of CD8-positive naive resting alpha-beta T cell male adult (30 years)
experiment encode accession: ENCSR372LPU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR761HQT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB869NZX
fragmentation methods: none

tag: antibody

value: primary cell

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS845PJM at ENCODE; https://www.encodeproject.org/ENCBS845PJM/

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


title: Mint-ChIP-seq from H9 (ENCLB087JAK)

description:
https://www.encodeproject.org/experiments/ENCSR372FFA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR372FFA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB087JAK
fragmentation methods: none

value: cell line

tag: description

value: WA09 ES cells

value: female

value: embryonic

value: 5 day

value: SESCC

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


title: tgrB1C1_r2_hr20

value: disaggregation


title: Ucp2-wildtype vehicle treatment replicate 1

tag: cell type

value: Pmel-1 CD8 T cell

tag: treatment

value: vehicle (culture media)

tag: ucp2 genotype

value: wildtype


title: tgrB1C1_r2_hr16


title: bystanding macrophage rep3

value: Bone marrow-derived macrophages

value: wild type

value: bystanding


title: control macrophage rep3

value: uninfected - control


title: tgrC1_r1_hr16


title: Mint-ChIP-seq from H9 (ENCLB825HGH)

description:
https://www.encodeproject.org/experiments/ENCSR372FFA/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR372FFA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB825HGH
fragmentation methods: none

tag: biosample encode accession

tag: Sex

tag: health state

value: healthy

tag: dev stage

value: Bradley Bernstein, Broad

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB995KCK)

description:
https://www.encodeproject.org/experiments/ENCSR555VYM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR555VYM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR165PMH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB995KCK
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: adult

tag: age

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: tgrB1C1_r2_hr14

tag: strain

value: disaggregation


title: infected macrophage rep2

value: Bone marrow-derived macrophages

tag: genotype

tag: condition

value: infected


title: tgrB1C1_r2_hr08


title: tgrB1C1_r2_hr06


title: tgrB1C1_r2_hr10


title: tgrB1C1_r2_hr12


title: bystanding macrophage rep2

value: wild type

value: bystanding


title: tgrB1C1_r2_hr04


title: control macrophage rep2

value: uninfected - control


title: tgrB1C1_r2_hr00


title: tgrB1C1_r1_hr20


title: tgrB1C1_r1_hr12


title: tgrB1C1_r1_hr16


title: tgrB1C1_r1_hr14


title: infected macrophage rep1


title: bystanding macrophage rep1


title: tgrB1C1_r1_hr10


title: tgrB1C1_r1_hr24


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB848LYZ)

description:
https://www.encodeproject.org/experiments/ENCSR467UCT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR467UCT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR779CPT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB848LYZ
fragmentation methods: none

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

value: 20 year

tag: lab

tag: source

tag: treatments

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;

tag: link

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

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


title: tgrB1C1_r1_hr06

tag: phenotype group

tag: replicate

tag: developmental time


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB879IJX)

description:
https://www.encodeproject.org/experiments/ENCSR555VYM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR555VYM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR165PMH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB879IJX
fragmentation methods: none

tag: antibody

value: CD14-positive monocyte

value: primary cell

value: male


title: tgrB1C1_r1_hr08


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB309LUM)

description:
https://www.encodeproject.org/experiments/ENCSR371GOJ/
***************
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: ENCSR371GOJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB309LUM

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

tag: description

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS044FCF at ENCODE; https://www.encodeproject.org/ENCBS044FCF/

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


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB726CXG)

description:
https://www.encodeproject.org/experiments/ENCSR371GOJ/
***************
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: ENCSR371GOJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB726CXG

tag: biosample encode accession


title: tgrB1C1_r1_hr00

value: disaggregation


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB372JRF)

description:
https://www.encodeproject.org/experiments/ENCSR554KDG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR554KDG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB372JRF
fragmentation methods: none

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

tag: Sex

value: female

value: embryonic

value: 5 day

value: SESCC

value: ENCBS779FCS at ENCODE; https://www.encodeproject.org/ENCBS779FCS/

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


title: tgrB1_r2_hr24


title: tgrB1_r2_hr16


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB950TMQ)

description:
https://www.encodeproject.org/experiments/ENCSR554KDG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR554KDG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB950TMQ
fragmentation methods: none

tag: health state


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB148OCX)

description:
https://www.encodeproject.org/experiments/ENCSR467UCT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR467UCT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR779CPT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB148OCX
fragmentation methods: none

value: primary cell

value: male

tag: dev stage

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

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

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

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


title: tgrB1_r2_hr20

value: disaggregation


title: tgrB1_r2_hr14


title: control macrophage rep1

tag: cell type

value: Bone marrow-derived macrophages

value: wild type

value: uninfected - control


title: tgrB1_r2_hr12

tag: strain


title: Control Mint-ChIP-seq from chondrocyte (ENCLB575DHZ)

description:
https://www.encodeproject.org/experiments/ENCSR466ZEA/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of chondrocyte originated from chondrocyte
experiment encode accession: ENCSR466ZEA
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB575DHZ

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

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: female

value: healthy

value: embryonic

tag: age

value: 5 day

value: Bradley Bernstein, Broad

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


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB140ADJ)

description:
https://www.encodeproject.org/experiments/ENCSR554KDG/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR554KDG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB140ADJ

value: type B pancreatic cell

value: WA09 derived insulin producing beta-like cells

value: SESCC

value: ENCBS251SEQ at ENCODE; https://www.encodeproject.org/ENCBS251SEQ/

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


title: Control Mint-ChIP-seq from chondrocyte (ENCLB927HHS)

description:
https://www.encodeproject.org/experiments/ENCSR466ZEA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of chondrocyte originated from chondrocyte
experiment encode accession: ENCSR466ZEA
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB927HHS


title: tgrB1C1_r1_hr04

value: disaggregation


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB784RHF)

description:
https://www.encodeproject.org/experiments/ENCSR554KDG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR554KDG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB784RHF


title: tgrB1_r2_hr04


title: tgrB1_r2_hr06


title: COV434-shFTO-IP, rep2

city: Shanghai

first: Zhongxin

last: Jiang

address: No.515 Fengyang Road

department: Reproductive medical center，Changzheng Hospital

country: China

institute: Naval Medical university

description:
RNA of Cov434 cells transfected by FTO-knockdown lentivirus were were Immunoprecipitat with FTO antibody.
SH2.ip

data_processing:
paired-end reads were harvested from an Illumina HiSeq 4000 sequencer and quality controlled by Q30. After 3’ adaptor trimming and low-quality read removal, cutadapt software (v1.9.3) was used.
First, clean reads of all libraries were aligned to the reference genome (UCSC HG19) by Hisat2 software (v2.0.4).
For the RNA m6A sequence, methylated sites on the RNAs (peaks) were identified by MACS software.Differentially methylated sites were identified by diffReps.
These peaks identified by both software packages that overlapping with exons of the mRNA were determined and chosen by homemade scripts.
Supplementary_files_format_and_content: mRNA Expression Profiling.xlsx, Methylated_RNA_sites.mRNA.xlsx

growth_protocol: COV434 with STR (short tandem repeat) identification were cultured in DMEM (HyClone, Logan, UT, USA) containing 10% fetal bovine serum (FBS) (Gibco, Detroit, MI, USA) and 100 IU/mL penicillin-streptomycin in a humidified atmosphere of 5% CO2 and 95% air at 37°C.

extract_protocol:
Total RNA was extracted with RNAiso Plus (TAKARA, Beijing, China) from stable shFTO COV434 cells and the controls, which was used to remove the rRNAs by Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Ten pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on an Illumina HiSeq Sequencer according to the manufacturer’s instructions.

tag: cell line

tag: transfection

value: FTO-knockdown lentivirus

tag: rip antibody

value: FTO antibody


title: COV434-shNC-IP, rep3

description:
RNA of Cov434 cells transfected by negative control lentivirus were were Immunoprecipitat with FTO antibody.
NC3.ip

value: negative control lentivirus


title: COV434-shFTO-IP, rep1

description:
RNA of Cov434 cells transfected by FTO-knockdown lentivirus were were Immunoprecipitat with FTO antibody.
SH1.ip


title: COV434-shNC-IP, rep2

description:
RNA of Cov434 cells transfected by negative control lentivirus were were Immunoprecipitat with FTO antibody.
NC2.ip


title: Control Mint-ChIP-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB785ZIK)

description:
https://www.encodeproject.org/experiments/ENCSR466PQY/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of activated CD8-positive, alpha-beta T cell male adult (30 years) treated with 10 ng
experiment encode accession: ENCSR466PQY
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB785ZIK

source_name: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male

value: adult

value: 30 year

tag: lab

value: Yijun Ruan, JAX

tag: source

value: AllCells

tag: treatments

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: ENCBS039WVH at ENCODE; https://www.encodeproject.org/ENCBS039WVH/

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


title: Control Mint-ChIP-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB471NUY)

description:
https://www.encodeproject.org/experiments/ENCSR466PQY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of activated CD8-positive, alpha-beta T cell male adult (30 years) treated with 10 ng
experiment encode accession: ENCSR466PQY
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB471NUY

tag: link


title: COV434-shNC-IP, rep1

description:
RNA of Cov434 cells transfected by negative control lentivirus were were Immunoprecipitat with FTO antibody.
NC1.ip


title: tgrB1_r2_hr00

tag: phenotype group

tag: replicate

tag: developmental time


title: COV434-shFTO-IP, rep3

description:
RNA of Cov434 cells transfected by FTO-knockdown lentivirus were were Immunoprecipitat with FTO antibody.
SH3.ip


title: COV434-shFTO, rep3

description:
Cov434 cells transfected by FTO-knockdown lentivirus
SH3.input


title: COV434-shFTO, rep2

description:
Cov434 cells transfected by FTO-knockdown lentivirus
SH2.input


title: COV434-shFTO, rep1

description:
Cov434 cells transfected by FTO-knockdown lentivirus
SH1.input


title: tgrB1_r1_hr14


title: tgrB1_r1_hr12


title: tgrB1_r1_hr16


title: tgrB1_r1_hr20


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB062RTB)

description:
https://www.encodeproject.org/experiments/ENCSR553QIO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of CD8-positive, alpha-beta memory T cell male adult (30 years)
experiment encode accession: ENCSR553QIO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR890AQB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB062RTB
fragmentation methods: none

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

tag: antibody

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

tag: biosample encode accession

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


title: tgrB1_r1_hr10


title: COV434-shNC, rep3

description:
Cov434 cells transfected by negative control lentivirus
NC3.input


title: tgrB1_r2_hr08


title: tgrB1_r2_hr10


title: tgrB1_r1_hr06


title: tgrB1_r1_hr08


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB670YQR)

description:
https://www.encodeproject.org/experiments/ENCSR553QIO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of CD8-positive, alpha-beta memory T cell male adult (30 years)
experiment encode accession: ENCSR553QIO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR890AQB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB670YQR
fragmentation methods: none

tag: Sex


title: COV434-shNC, rep2

description:
Cov434 cells transfected by negative control lentivirus
NC2.input


title: tgrB1_r1_hr24


title: tgrB1_r1_hr04


title: comH_r2_hr24

value: comH

value: tight aggregate arrest


title: COV434-shNC, rep1

description:
Cov434 cells transfected by negative control lentivirus
NC1.input


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB347LJK)

description:
https://www.encodeproject.org/experiments/ENCSR461QMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR461QMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR354FME
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB347LJK
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

tag: description

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

value: not collected

tag: health state

value: multiple sclerosis

tag: dev stage

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: comH_r2_hr12

tag: strain


title: comH_r2_hr28


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB833VLV)

description:
https://www.encodeproject.org/experiments/ENCSR551DOT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with 10 ng
experiment encode accession: ENCSR551DOT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB833VLV
fragmentation methods: none

value: primary cell

value: male

value: adult

tag: age

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

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

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


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB596QDO)

description:
https://www.encodeproject.org/experiments/ENCSR461QMZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR461QMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR354FME
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB596QDO
fragmentation methods: none

value: IgD-negative memory B cell


title: tgrB1_r1_hr00

value: disaggregation


title: comH_r2_hr20

value: comH

value: tight aggregate arrest


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB576KTZ)

description:
https://www.encodeproject.org/experiments/ENCSR551DOT/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with 10 ng
experiment encode accession: ENCSR551DOT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB576KTZ
fragmentation methods: none

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;


title: comH_r2_hr08


title: comH_r2_hr06


title: Mint-ChIP-seq from immature natural killer cell (ENCLB052JET)

description:
https://www.encodeproject.org/experiments/ENCSR369WMO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR369WMO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR050UUC
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB052JET
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: immature natural killer cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS620QTW at ENCODE; https://www.encodeproject.org/ENCBS620QTW/

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB363OQY)

description:
https://www.encodeproject.org/experiments/ENCSR458TOW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of CD8-positive, alpha-beta memory T cell originated from CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR458TOW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR231SVU
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB363OQY
fragmentation methods: none

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

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

value: primary cell

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

value: multiple sclerosis

value: David Hafler

value: ENCBS347VRW at ENCODE; https://www.encodeproject.org/ENCBS347VRW/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB771OBD)

description:
https://www.encodeproject.org/experiments/ENCSR458QEY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR458QEY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR899DXS
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB771OBD
fragmentation methods: none
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: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

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

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB643KST)

description:
https://www.encodeproject.org/experiments/ENCSR458QEY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR458QEY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR899DXS
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB643KST
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500


title: comH_r2_hr16

value: comH

value: tight aggregate arrest


title: comH_r2_hr00


title: comH_r1_hr24


title: comH_r2_hr04


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB455FGF)

description:
https://www.encodeproject.org/experiments/ENCSR458TOW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of CD8-positive, alpha-beta memory T cell originated from CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR458TOW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR231SVU
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB455FGF
fragmentation methods: none

value: not collected


title: comH_r1_hr28


title: comH_r1_hr12


title: comH_r1_hr20


title: comH_r1_hr16


title: comH_r1_hr08


title: comH_r1_hr06


title: dgcA_r2_hr24

value: dgcA

value: culmination defective


title: comH_r1_hr02


title: Mint-ChIP-seq from astrocyte (ENCLB119LPN)

description:
https://www.encodeproject.org/experiments/ENCSR547XUU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived astrocyte
experiment encode accession: ENCSR547XUU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731CEI
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB119LPN
fragmentation methods: none

source_name: Homo sapiens male adult (53 years) astrocyte in vitro differentiated cells originated from astrocyte, preserved by cryopreservation

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: male

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS534DJA at ENCODE; https://www.encodeproject.org/ENCBS534DJA/

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


title: comH_r1_hr00


title: comH_r2_hr02


title: WGS from transverse colon (ENCLB588HWR)

description:
https://www.encodeproject.org/experiments/ENCSR456SNK/
***************
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: ENCSR456SNK
assay title: WGS
assembly: GRCh38
encode release date: 2017-08-01
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB588HWR

source_name: Homo sapiens transverse colon tissue female adult (51 year)

value: transverse colon

value: tissue

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

value: female

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS999VTF at ENCODE; https://www.encodeproject.org/ENCBS999VTF/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: comH_r1_hr04

value: comH

value: tight aggregate arrest


title: Mint-ChIP-seq from immature natural killer cell (ENCLB864GTD)

description:
https://www.encodeproject.org/experiments/ENCSR369WMO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR369WMO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR050UUC
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB864GTD
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer 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: ENCBS620QTW at ENCODE; https://www.encodeproject.org/ENCBS620QTW/

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


title: dgcA_r2_hr14

value: dgcA

value: culmination defective


title: dgcA_r2_hr12


title: dgcA_r2_hr20


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB624OZO)

description:
https://www.encodeproject.org/experiments/ENCSR546YQN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR546YQN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR622ZKD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB624OZO
fragmentation methods: none

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

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

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

value: Bradley Bernstein, Broad

value: ENCBS235RVH at ENCODE; https://www.encodeproject.org/ENCBS235RVH/


title: dgcA_r2_hr08


title: dgcA_r2_hr00


title: dgcA_r1_hr24


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB107GJR)

description:
https://www.encodeproject.org/experiments/ENCSR546YQN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR546YQN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR622ZKD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB107GJR
fragmentation methods: none


title: dgcA_r2_hr04


title: dgcA_r2_hr16


title: Mint-ChIP-seq from astrocyte (ENCLB899XRV)

description:
https://www.encodeproject.org/experiments/ENCSR547XUU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived astrocyte
experiment encode accession: ENCSR547XUU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731CEI
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB899XRV
fragmentation methods: none

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: male

value: adult

value: 53 year

value: George Church

value: ENCBS534DJA at ENCODE; https://www.encodeproject.org/ENCBS534DJA/

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


title: dgcA_r1_hr18


title: dgcA_r1_hr16


title: dgcA_r1_hr12


title: dgcA_r1_hr20


title: Mint-ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB600NEB)

description:
https://www.encodeproject.org/experiments/ENCSR367EKE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR367EKE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR820SXH
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB600NEB
fragmentation methods: none

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

value: CD8-positive, alpha-beta T cell

value: primary cell

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

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

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


title: dgcA_r1_hr14

value: dgcA

value: culmination defective


title: Control Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB366IRC)

description:
https://www.encodeproject.org/experiments/ENCSR546XZC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR546XZC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB366IRC

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

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: healthy

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

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


title: Control Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCLB926EXG)

description:
https://www.encodeproject.org/experiments/ENCSR546XZC/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR546XZC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB926EXG


title: dgcA_r2_hr18


title: dgcA_r1_hr08


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB264UIY)

description:
https://www.encodeproject.org/experiments/ENCSR546UUS/
***************
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: ENCSR546UUS
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB264UIY

value: primary cell

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

value: not collected

value: unknown

value: David Hafler

value: ENCBS872QPK at ENCODE; https://www.encodeproject.org/ENCBS872QPK/

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


title: cudA_r2_hr14

value: cudA

value: culmination defective


title: Mint-ChIP-seq from naive B cell (ENCLB104KMT)

description:
https://www.encodeproject.org/experiments/ENCSR364OIK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR364OIK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR111MNI
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB104KMT
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

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

value: naive B cell

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

value: multiple sclerosis

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

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


title: cudA_r2_hr16


title: Control ChIP-seq from SK-N-SH (ENCLB288MXW)

description:
https://www.encodeproject.org/experiments/ENCSR973END/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR973END
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB288MXW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting SATB1 treated with 6 uM all-trans-retinoic acid for 48 hours

tag: line

value: SK-N-SH

value: cell line

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS524KYL at ENCODE; https://www.encodeproject.org/ENCBS524KYL/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: dgcA_r1_hr04

value: dgcA

value: culmination defective


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB152KJO)

description:
https://www.encodeproject.org/experiments/ENCSR546UUS/
***************
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: ENCSR546UUS
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152KJO

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS872QPK at ENCODE; https://www.encodeproject.org/ENCBS872QPK/

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


title: cudA_r2_hr12

value: cudA


title: dgcA_r1_hr00


title: Mint-ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB285MLS)

description:
https://www.encodeproject.org/experiments/ENCSR367EKE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR367EKE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR820SXH
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB285MLS
fragmentation methods: none

value: CD8-positive, alpha-beta T cell

value: male

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

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

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


title: Mint-ChIP-seq from naive B cell (ENCLB253BUC)

description:
https://www.encodeproject.org/experiments/ENCSR364OIK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR364OIK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR111MNI
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB253BUC
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

value: naive B cell

value: primary cell

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

value: multiple sclerosis

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

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


title: cudA_r2_hr04

value: culmination defective


title: cudA_r1_hr16


title: cudA_r1_hr24


title: cudA_r2_hr18


title: cudA_r1_hr20


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB512UCM)

description:
https://www.encodeproject.org/experiments/ENCSR360MUC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR360MUC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR156VQN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB512UCM
fragmentation methods: none

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

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS681GZX at ENCODE; https://www.encodeproject.org/ENCBS681GZX/

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


title: cudA_r1_hr12

value: cudA


title: cudA_r1_hr18


title: cudA_r2_hr20


title: cudA_r2_hr24


title: Control ChIP-seq from A549 (ENCLB574ERK)

description:
https://www.encodeproject.org/experiments/ENCSR855NLW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR855NLW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB574ERK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting HMGA2

value: cell line

value: male

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS088GDV at ENCODE; https://www.encodeproject.org/ENCBS088GDV/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: cudA_r1_hr08

value: culmination defective


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB688GOV)

description:
https://www.encodeproject.org/experiments/ENCSR360MUC/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR360MUC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR156VQN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB688GOV
fragmentation methods: none

value: primary cell

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

value: not collected


title: gtaG_r2_hr24

value: gtaG


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB939YYM)

description:
https://www.encodeproject.org/experiments/ENCSR360IRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR360IRQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310ZGH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB939YYM
fragmentation methods: none

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: cudA_r2_hr00

value: cudA


title: cudA_r1_hr14


title: gtaG_r2_hr20


title: cudA_r1_hr00


title: cudA_r1_hr04


title: Control ChIP-seq from K562 (ENCLB812LQB)

description:
https://www.encodeproject.org/experiments/ENCSR851OQN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR851OQN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB812LQB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting RFX7

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS768PNH at ENCODE; https://www.encodeproject.org/ENCBS768PNH/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: gtaG_r2_hr16

value: culmination defective


title: cudA_r2_hr08


title: gtaG_r2_hr12

value: gtaG


title: Mint-ChIP-seq from naive B cell (ENCLB385GMS)

description:
https://www.encodeproject.org/experiments/ENCSR541PLO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of naive B cell originated from naive B cell
experiment encode accession: ENCSR541PLO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR163IRW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB385GMS
fragmentation methods: none

value: naive B cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: ENCBS345AAH at ENCODE; https://www.encodeproject.org/ENCBS345AAH/

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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB815FWP)

description:
https://www.encodeproject.org/experiments/ENCSR360IRQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR360IRQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310ZGH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB815FWP
fragmentation methods: none

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

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB463EMZ)

description:
https://www.encodeproject.org/experiments/ENCSR541VWV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR541VWV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR176HLK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB463EMZ
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: male

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

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: gtaG_r2_hr04

value: gtaG

value: culmination defective


title: Mint-ChIP-seq from naive B cell (ENCLB220OLY)

description:
https://www.encodeproject.org/experiments/ENCSR541PLO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of naive B cell originated from naive B cell
experiment encode accession: ENCSR541PLO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR163IRW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB220OLY
fragmentation methods: none

value: naive B cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: ENCBS345AAH at ENCODE; https://www.encodeproject.org/ENCBS345AAH/

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


title: gtaG_r2_hr08


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB815VYY)

description:
https://www.encodeproject.org/experiments/ENCSR541VWV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR541VWV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR176HLK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB815VYY
fragmentation methods: none

value: male


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB832YXA)

description:
https://www.encodeproject.org/experiments/ENCSR540XNK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR540XNK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283LWF
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB832YXA
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

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

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

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

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS812ZCI at ENCODE; https://www.encodeproject.org/ENCBS812ZCI/

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


title: gtaG_r2_hr00

value: gtaG


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB867JJJ)

description:
https://www.encodeproject.org/experiments/ENCSR540XNK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR540XNK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283LWF
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB867JJJ
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500


title: gtaG_r1_hr24

value: culmination defective


title: gtaG_r1_hr12


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB507MGE)

description:
https://www.encodeproject.org/experiments/ENCSR358NBC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR358NBC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR201SEO
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB507MGE
fragmentation methods: none

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

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS677HEG at ENCODE; https://www.encodeproject.org/ENCBS677HEG/

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


title: gtaG_r1_hr20


title: gtaG_r1_hr04


title: gtaG_r1_hr08


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB319RAR)

description:
https://www.encodeproject.org/experiments/ENCSR358CSB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR358CSB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR156VQN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB319RAR
fragmentation methods: none

value: primary cell

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

value: not collected

value: healthy

value: ENCBS681GZX at ENCODE; https://www.encodeproject.org/ENCBS681GZX/

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


title: ac3PkaCoe_r2_hr16

value: acaA,acrA,acgA/PkaCoe

value: small fruiting body


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB725WLS)

description:
https://www.encodeproject.org/experiments/ENCSR448CEK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR448CEK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB725WLS
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

value: male

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


title: ac3PkaCoe_r2_hr12


title: ac3PkaCoe_r2_hr20


title: ac3PkaCoe_r2_hr08


title: gtaG_r1_hr00

value: gtaG

value: culmination defective


title: ac3PkaCoe_r2_hr04


title: ac3PkaCoe_r2_hr06


title: ac3PkaCoe_r2_hr24


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB824UOX)

description:
https://www.encodeproject.org/experiments/ENCSR448CEK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR448CEK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB824UOX
fragmentation methods: none

value: adult

value: 43 year

value: Yijun Ruan, JAX


title: ac3PkaCoe_r2_hr00


title: ac3PkaCoe_r1_hr24


title: Mint-ChIP-seq from activated B cell (ENCLB292BAR)

description:
https://www.encodeproject.org/experiments/ENCSR445LTM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on B cell male adult (22 years)
experiment encode accession: ENCSR445LTM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR784EZW
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB292BAR
fragmentation methods: none

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

value: activated B cell

value: 22 year

value: AllCells

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

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

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


title: Mint-ChIP-seq from activated B cell (ENCLB020QOA)

description:
https://www.encodeproject.org/experiments/ENCSR445LTM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on B cell male adult (22 years)
experiment encode accession: ENCSR445LTM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR784EZW
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB020QOA
fragmentation methods: none

value: primary cell


title: ac3PkaCoe_r1_hr12


title: gtaG_r1_hr16


title: ac3PkaCoe_r1_hr16


title: ac3PkaCoe_r1_hr20


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB450PVR)

description:
https://www.encodeproject.org/experiments/ENCSR358NBC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR358NBC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR201SEO
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB450PVR
fragmentation methods: none

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: ENCBS677HEG at ENCODE; https://www.encodeproject.org/ENCBS677HEG/

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


title: ac3PkaCoe_r1_hr08

value: acaA,acrA,acgA/PkaCoe

value: small fruiting body


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB076FCG)

description:
https://www.encodeproject.org/experiments/ENCSR358CSB/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR358CSB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR156VQN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB076FCG
fragmentation methods: none

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS681GZX at ENCODE; https://www.encodeproject.org/ENCBS681GZX/

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


title: ac3PkaCoe_r1_hr04


title: ac3PkaCoe_r1_hr00


title: Control Mint-ChIP-seq from T-cell (ENCLB779OOU)

description:
https://www.encodeproject.org/experiments/ENCSR445KDW/
***************
biological replicate number: 1
technical replicate number: 4
description: Control Mint-ChIP-seq of T-cell male adult (42 years)
experiment encode accession: ENCSR445KDW
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB779OOU

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

value: T-cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS038FPK at ENCODE; https://www.encodeproject.org/ENCBS038FPK/

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


title: PkaCoe_r2_hr24

value: PkaCoe

value: precocious development


title: Control Mint-ChIP-seq from T-cell (ENCLB639RRD)

description:
https://www.encodeproject.org/experiments/ENCSR445KDW/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of T-cell male adult (42 years)
experiment encode accession: ENCSR445KDW
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB639RRD

value: primary cell


title: Control Mint-ChIP-seq from T-cell (ENCLB158BZH)

description:
https://www.encodeproject.org/experiments/ENCSR445KDW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of T-cell male adult (42 years)
experiment encode accession: ENCSR445KDW
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB158BZH


title: ac3PkaCoe_r1_hr06

value: acaA,acrA,acgA/PkaCoe

value: small fruiting body


title: PkaCoe_r2_hr12


title: PkaCoe_r2_hr16


title: PkaCoe_r2_hr20


title: PkaCoe_r2_hr18


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB464PLS)

description:
https://www.encodeproject.org/experiments/ENCSR536AYF/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR536AYF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR996DNY
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB464PLS
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

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

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS274KKV at ENCODE; https://www.encodeproject.org/ENCBS274KKV/

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