title: polyA plus RNA-seq from activated regulatory T cell (ENCLB262LWI)

description:
https://www.encodeproject.org/experiments/ENCSR582PLJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR582PLJ
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB262LWI
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: activated regulatory T cell

value: primary cell

value: adult

value: 9 week

value: Christina Leslie, MSKCC

value: Christina Leslie

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

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


title: DNase-seq from spleen (ENCLB007POO)

status: Public on Nov 04 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR581ZXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR581ZXI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB007POO

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

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

value: spleen

value: tissue

tag: description

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

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: unknown

tag: age

value: 10 day

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS527TEO at ENCODE; https://www.encodeproject.org/ENCBS527TEO/

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


title: Sample 39 Illumina

city: Eastbourne

first: Guan

last: Wang

address: 30 Carlisle Rd

department: School of Sport and Health Sciences

country: United Kingdom

institute: University of Brighton

description: Illumina_RNAseq_raw_counts_EnsemblID.txt

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

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

tag: age (year)

value: Male

tag: disease state

value: Healthy

tag: time (day)


title: Sample 38 Illumina


title: Sample 37 Illumina

value: Base2 (0)


title: DNase-seq from spleen (ENCLB388TKV)

description:
https://www.encodeproject.org/experiments/ENCSR581ZXI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR581ZXI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB388TKV

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

value: ENCBS251NUV at ENCODE; https://www.encodeproject.org/ENCBS251NUV/


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB466PUZ)

description:
https://www.encodeproject.org/experiments/ENCSR306JBO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306JBO
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB466PUZ
fragmentation methods: shearing (Covaris generic)
size range: 100-300

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

value: activated regulatory T cell

value: primary cell

value: adult

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS562IGY at ENCODE; https://www.encodeproject.org/ENCBS562IGY/

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


title: Sample 36 Illumina


title: Sample 35 Illumina


title: Sample 50 Illumina


title: DNase-seq from layer of hippocampus (ENCLB491LFK)

description:
https://www.encodeproject.org/experiments/ENCSR503JJC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR503JJC
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB491LFK

source_name: Mus musculus strain B6CASTF1/J male (14 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: B6Cast F1 PND14 3x male Hippocampus

value: male

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS857RPA at ENCODE; https://www.encodeproject.org/ENCBS857RPA/


title: Sample 32 Illumina

value: Male

value: Healthy

value: Base2 (0)


title: Sample 34 Illumina


title: polyA plus RNA-seq from activated regulatory T cell (ENCLB320TBS)

description:
https://www.encodeproject.org/experiments/ENCSR306JBO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR306JBO
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB320TBS
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: activated regulatory T cell

value: primary cell

value: adult


title: Histone ChIP-seq from macrophage (ENCLB075LFO)

description:
https://www.encodeproject.org/experiments/ENCSR280NNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on fragement DNA which is part of BMDM cell with no stimulation
experiment encode accession: ENCSR280NNQ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR698GIN
encode release date: 2021-07-21
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB075LFO
size range: 350-480
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

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

tag: antibody

value: macrophage

value: not collected

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS253FAT at ENCODE; https://www.encodeproject.org/ENCBS253FAT/

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


title: DNase-seq from layer of hippocampus (ENCLB588FBZ)

description:
https://www.encodeproject.org/experiments/ENCSR503JJC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR503JJC
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB588FBZ

value: layer of hippocampus

value: tissue

value: B6Cast F1 PND14 3x male Hippocampus

value: male

value: The Jackson Laboratory

value: ENCBS349JKG at ENCODE; https://www.encodeproject.org/ENCBS349JKG/

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


title: Sample 30 Illumina

value: Male

value: Healthy


title: Sample 29 Illumina


title: Sample 31 Illumina


title: Histone ChIP-seq from activated regulatory T cell (ENCLB493OFP)

description:
https://www.encodeproject.org/experiments/ENCSR364HOR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR364HOR
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB493OFP

value: activated regulatory T cell

value: primary cell

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

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

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


title: Sample 27 Illumina

value: Base2 (0)


title: Sample 28 Illumina


title: Histone ChIP-seq from macrophage (ENCLB544UWC)

description:
https://www.encodeproject.org/experiments/ENCSR280NNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on fragement DNA which is part of BMDM cell with no stimulation
experiment encode accession: ENCSR280NNQ
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR698GIN
encode release date: 2021-07-21
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB544UWC
size range: 350-480
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: macrophage

value: not collected

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

value: ENCBS210FNH at ENCODE; https://www.encodeproject.org/ENCBS210FNH/

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


title: Sample 25 Illumina

value: Male


title: Histone ChIP-seq from regulatory T cell (ENCLB347DQD)

description:
https://www.encodeproject.org/experiments/ENCSR075MGD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR075MGD
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB347DQD

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

value: regulatory T cell

value: male

value: adult

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


title: Histone ChIP-seq from activated regulatory T cell (ENCLB300SLK)

description:
https://www.encodeproject.org/experiments/ENCSR364HOR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR364HOR
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB300SLK

value: activated regulatory T cell

value: primary cell

value: 4 month

value: Christina Leslie, MSKCC


title: Sample 26 Illumina

value: Healthy


title: DNase-seq from cerebellum (ENCLB630EIA)

description:
https://www.encodeproject.org/experiments/ENCSR414VXP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR414VXP
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB630EIA

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

value: cerebellum

value: tissue

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS521DKS at ENCODE; https://www.encodeproject.org/ENCBS521DKS/

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


title: Sample 23 Illumina

value: Male


title: Sample 22 Illumina


title: Histone ChIP-seq from regulatory T cell (ENCLB861RER)

description:
https://www.encodeproject.org/experiments/ENCSR075MGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR075MGD
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB861RER

value: regulatory T cell

value: male

value: Christina Leslie

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


title: DNase-seq from thymus (ENCLB759TFT)

description:
https://www.encodeproject.org/experiments/ENCSR398LUY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR398LUY
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB759TFT

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

value: thymus

value: B6Cast F1 PND10 Female 05 thymus for Altius Stam biobank

value: female

value: unknown

value: 10 day

value: ENCBS797NTQ at ENCODE; https://www.encodeproject.org/ENCBS797NTQ/


title: polyA plus RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB972UHL)

description:
https://www.encodeproject.org/experiments/ENCSR074OSI/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR074OSI
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB972UHL
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus strain C57BL/6J male adult (7 months) effector memory CD4-positive, alpha-beta T primary cell

value: primary cell

value: adult

value: 7 month

value: Christina Leslie, MSKCC

value: ENCBS532RFM at ENCODE; https://www.encodeproject.org/ENCBS532RFM/

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


title: Sample 20 Illumina

value: Male

value: Healthy


title: Sample 21 Illumina


title: Sample 19 Illumina


title: DNase-seq from thymus (ENCLB698ICQ)

description:
https://www.encodeproject.org/experiments/ENCSR398LUY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR398LUY
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB698ICQ

value: tissue

value: B6Cast F1 PND10 Female 06 thymus for Altius Stam biobank

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS077PHI at ENCODE; https://www.encodeproject.org/ENCBS077PHI/

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


title: DNase-seq from cerebellum (ENCLB520XKZ)

description:
https://www.encodeproject.org/experiments/ENCSR414VXP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR414VXP
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB520XKZ

value: cerebellum

value: B6Cast F1 DPN18-20months

value: male

value: 18-20 month

value: ENCBS083XQR at ENCODE; https://www.encodeproject.org/ENCBS083XQR/


title: polyA plus RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB704NKE)

description:
https://www.encodeproject.org/experiments/ENCSR074OSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR074OSI
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB704NKE
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: primary cell

value: adult

value: 7 month

value: Christina Leslie


title: Sample 18 Illumina

description: Illumina_RNAseq_raw_counts_EnsemblID.txt

value: Male


title: DNase-seq from gastrocnemius (ENCLB202HYJ)

description:
https://www.encodeproject.org/experiments/ENCSR391YHC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR391YHC
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB202HYJ

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

value: gastrocnemius

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

value: unknown

value: 25 day

value: ENCBS752IJW at ENCODE; https://www.encodeproject.org/ENCBS752IJW/


title: Sample 16 Illumina

value: Healthy


title: Sample 15 Illumina


title: DNase-seq from heart (ENCLB107HZV)

description:
https://www.encodeproject.org/experiments/ENCSR409LVQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR409LVQ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB107HZV

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

value: heart

value: tissue

value: B6Cast F1 PND10 Female 06 heart for Altius Stam biobank

value: female

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS918RUL at ENCODE; https://www.encodeproject.org/ENCBS918RUL/

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


title: DNase-seq from heart (ENCLB097QIF)

description:
https://www.encodeproject.org/experiments/ENCSR409LVQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR409LVQ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB097QIF

value: B6Cast F1 PND10 Female 05 heart for Altius Stam biobank

value: ENCBS846QKZ at ENCODE; https://www.encodeproject.org/ENCBS846QKZ/


title: Sample 14 Illumina

value: Male


title: polyA plus RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB706AMM)

description:
https://www.encodeproject.org/experiments/ENCSR255OLH/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR255OLH
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB706AMM
fragmentation methods: shearing (Covaris generic)
size range: 100-300

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

value: primary cell

value: male

value: adult

value: 5 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS798OBX at ENCODE; https://www.encodeproject.org/ENCBS798OBX/

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


title: Sample 13 Illumina

value: Healthy


title: DNase-seq from gastrocnemius (ENCLB020ADV)

description:
https://www.encodeproject.org/experiments/ENCSR104BED/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR104BED
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB020ADV

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

value: gastrocnemius

value: tissue

value: B6Cast F1 PND14 3x Females 06 gastrocnemius for Altius Stam core

value: female

value: unknown

value: 14 day

value: ENCBS492PQX at ENCODE; https://www.encodeproject.org/ENCBS492PQX/


title: Sample 24 Illumina

value: Male


title: polyA plus RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB455HHG)

description:
https://www.encodeproject.org/experiments/ENCSR074OSI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR074OSI
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB455HHG
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: primary cell

value: 7 month

value: ENCBS532RFM at ENCODE; https://www.encodeproject.org/ENCBS532RFM/

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


title: DNase-seq from adrenal gland (ENCLB061EZK)

description:
https://www.encodeproject.org/experiments/ENCSR385MRA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR385MRA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB061EZK
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Mus musculus strain B6CASTF1/J male (36 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND36 Male 05 adrenal gland for Altius Stam core

value: male

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS171ZHM at ENCODE; https://www.encodeproject.org/ENCBS171ZHM/

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


title: Sample 12 Illumina

value: Healthy

value: Base2 (0)


title: Sample 11 Illumina


title: polyA plus RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB284BLC)

description:
https://www.encodeproject.org/experiments/ENCSR255OLH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR255OLH
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB284BLC
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: adult

value: 5 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS798OBX at ENCODE; https://www.encodeproject.org/ENCBS798OBX/

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


title: Sample 09 Illumina

value: Male


title: DNase-seq from cerebellum (ENCLB361PRD)

description:
https://www.encodeproject.org/experiments/ENCSR097IUF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR097IUF
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB361PRD

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

value: cerebellum

value: tissue

value: B6Cast F1 DPN18-20months

value: female

value: 18-20 month

value: ENCBS062MAQ at ENCODE; https://www.encodeproject.org/ENCBS062MAQ/


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB035SJY)

description:
https://www.encodeproject.org/experiments/ENCSR128KAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR128KAW
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB035SJY
fragmentation methods: shearing (Covaris generic)
size range: 100-300

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

value: primary cell

value: male

value: 6 month

value: ENCBS799RXL at ENCODE; https://www.encodeproject.org/ENCBS799RXL/

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


title: Sample 10 Illumina

value: Healthy


title: Sample 08 Illumina


title: DNase-seq from cerebellum (ENCLB421ZRE)

description:
https://www.encodeproject.org/experiments/ENCSR097IUF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR097IUF
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB421ZRE

value: adult

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS431ZWY at ENCODE; https://www.encodeproject.org/ENCBS431ZWY/

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


title: Sample 17 Illumina

value: Male


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB156UZP)

description:
https://www.encodeproject.org/experiments/ENCSR128KAW/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR128KAW
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB156UZP
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: Christina Leslie, MSKCC

value: Christina Leslie


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCLB623EWA)

description:
https://www.encodeproject.org/experiments/ENCSR128KAW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR128KAW
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB623EWA
fragmentation methods: shearing (Covaris generic)
size range: 100-300


title: polyA plus RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB335TFY)

description:
https://www.encodeproject.org/experiments/ENCSR255OLH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR255OLH
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB335TFY
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: 5 month

value: ENCBS798OBX at ENCODE; https://www.encodeproject.org/ENCBS798OBX/

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


title: DNase-seq from adrenal gland (ENCLB701WGI)

description:
https://www.encodeproject.org/experiments/ENCSR204WCY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR204WCY
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB701WGI

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

value: adrenal gland

value: tissue

value: B6Cast F1 PND 2 months Male 05 adrenal gland for Altius Stam core

value: unknown

value: 2 month

value: ENCBS923QAR at ENCODE; https://www.encodeproject.org/ENCBS923QAR/


title: Sample 06 Illumina

value: Healthy


title: Histone ChIP-seq from inflammation-experienced regulatory T-cells (ENCLB871JGN)

description:
https://www.encodeproject.org/experiments/ENCSR118TPX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR118TPX
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB871JGN

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

value: primary cell

value: male

value: adult

value: 6 month

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

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


title: Sample 07 Illumina

description: Illumina_RNAseq_raw_counts_EnsemblID.txt

source_name: Whole blood

value: Male


title: Sample 04 Illumina


title: Sample 03 Illumina


title: Sample 02 Illumina


title: DNase-seq from left cerebral cortex (ENCLB576YQM)

description:
https://www.encodeproject.org/experiments/ENCSR370VVJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR370VVJ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB576YQM

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

value: left cerebral cortex

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS393GOD at ENCODE; https://www.encodeproject.org/ENCBS393GOD/

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


title: DNase-seq from adrenal gland (ENCLB402OTO)

description:
https://www.encodeproject.org/experiments/ENCSR205UJK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR205UJK
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB402OTO

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

value: adrenal gland

value: tissue

value: B6Cast F1 PND14 3x Males 05 adrenal gland for Altius Stam core

value: unknown

value: 14 day

value: ENCBS705PHY at ENCODE; https://www.encodeproject.org/ENCBS705PHY/


title: Histone ChIP-seq from inflammation-experienced regulatory T-cells (ENCLB692QEB)

description:
https://www.encodeproject.org/experiments/ENCSR118TPX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR118TPX
assay title: Histone ChIP-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB692QEB

value: primary cell

value: male

value: adult

value: 6 month

value: Christina Leslie, MSKCC

value: Christina Leslie


title: Patient_11_3E4D1L_ATAC

city: Chapel Hill

first: Hector

middle: L

last: Franco

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Lineberger Cancer Center

description:
3E4D1L_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq

data_processing:
scRNA-seq: The Cell Ranger Software Suite (version 3.1.0) was used for demultiplexing BCL files, alignment, barcode counting, and UMI counting for scRNA-seq libraries. GRCh38-3.0.0 was used as a reference transcriptome.
Specific details and instructions for running Cell Ranger can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
scATAC-seq: The Cell Ranger ATAC Software Suite (version 1.2.0) was used for demultiplexing BCL files, alignment, barcode counting, and generating fragments.tsv.gz files for scATAC-seq libraries. refdata-cellranger-atac-GRCh38-1.2.0 was used as a genomic reference.
Specific details and instructions for running Cell Ranger ATAC can be found at: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Cell Ranger scRNA filtered feature barcode matrices contain gene counts for cellular barcodes.
Supplementary_files_format_and_content: Cell Ranger scATAC fragments files list unique ATAC fragments per barcode sequence.

source_name: Tumor of the ovary

extract_protocol:
Tumor specimens were minced using two razor blades and digested overnight in 20-30 mL DMEM/F12 + 5% FBS, 15mM HEPES (Gibco), 1x Glutamax (Gibco), 1x Collagenase/Hyaluronidase (Stem Cell Technologies), 1% Penicillin/Streptomycin (Corning), and 0.48 µg/mL Hydrocortisone (Stem Cell Technologies) on a stir plate at 37°C and 180 rpm. For ovarian tumors, Gentle Collagenase/Hyaluronidase (Stem Cell Technologies) was used instead of Collagenase/Hyaluronidase. After digestion, tumor cells were washed twice with cold PBS + 2% FBS and 10mM HEPES (PBS-HF) and centrifuged at 1200 rpm for 5 min at room temperature. To remove red blood cells, the cell pellet was treated with 4 or 8 mL cold Ammonium Chloride Solution (Stem Cell Technologies) with 1 or 2 mL PBS-HF, respectively, for 1 minute, then centrifuged at 1200 rpm for 5 min. The amount of Ammonium Chloride Solution added was based on the size of the cell pellet and visual assessment of pink or red color present in the pellet. This step was repeated a second time if the pellet still exhibited a pink or red color after initial treatment. To further dissociate the cells, pellets were resuspended in 1-2 mL 0.05% Trypsin-EDTA (Gibco) and the suspension was gently pipetted up and down for 1 min. After 1 min, trypsin was inactivated by adding 10mL PBS-HF solution. The suspension was then centrifuged at 1200rpm for 5 min. If cell suspensions were clumpy, cells were resuspended with 1-2 mL Dispase (Stem Cell Technologies) and 200 µL 1mg/mL DNase I (Stem Cell Technologies) for 1 min, then inactivated with 10 mL PBS-HF. If the Dispase step was not necessary, cells were treated with DNase I during the trypsinization step. Cells were again centrifuged at 1200 rpm for 5 min, then washed in 10 mL PBS-HF and filtered through a 100µm cell strainer. A final centrifugation step was done at 1200 rpm for 5 min. The cell pellet was resuspended in DMEM/F12 + 5% FBS using a volume based on the final pellet size and filtered using a 40µm cell strainer. Single-cell suspension concentration and cell viability was measured by adding 10 µL 0.4% Trypan Blue to 10 µL cell suspension and measuring with the Countess II Automated Cell Counter (Thermo Fisher, AMQAX1000). We aimed for cell viability above 60% for the cells to be used for single-cell sequencing. Cell viability varied between 64% and 94% across all samples, with the majority of tumor suspensions being over 70% viable.
To continue with scRNA-seq, the cell suspension was diluted to 1200 cells/µL and 10,000 cells were used in library preparation using the 10x Genomics Chromium Single Cell 3’ GEM Kit v3 (PN-1000077) following the manufacturer’s protocol. To continue with scATAC-seq, 500,000 cells were used in nuclei isolation following the Nuclei Isolation for Single Cell ATAC Sequencing protocol from 10x Genomics. For the lysis step, cells were lysed for 4 min. For the resuspension step, nuclei were resuspended in 50 µL 1x Nuclei Buffer. Nuclei were counted by adding 10 µL 0.4% Trypan Blue to 10 µL nuclei suspension and counted with the Countess II Automated Cell Counter. 10,000 nuclei were then used in library preparation using the 10x Genomics Chromium Single Cell ATAC Library Kit v1 (PN-1000083) following the manufacturer’s protocol.
Libraries were sequenced on an Illumina NextSeq500 in the pair-end format using 10x Genomics recommended sequencing parameters.

value: Caucasian

tag: tissue

value: Tumor

value: Ovary

tag: histology

value: GIST

tag: metastatic status

value: Metastatic

tag: patient


title: polyA plus RNA-seq from regulatory T cell (ENCLB854BPC)

description:
https://www.encodeproject.org/experiments/ENCSR323OER/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR323OER
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB854BPC
fragmentation methods: shearing (Covaris generic)
size range: 100-300

source_name: Mus musculus male adult (4 months) regulatory T primary cell

value: regulatory T cell

value: 4 month

value: ENCBS377GTN at ENCODE; https://www.encodeproject.org/ENCBS377GTN/


title: Patient_10_3CCF1L_ATAC

description:
3CCF1L_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq

value: Carcinosarcoma

value: Primary/Non-metastatic


title: DNase-seq from left cerebral cortex (ENCLB025OSJ)

description:
https://www.encodeproject.org/experiments/ENCSR370VVJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR370VVJ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB025OSJ

value: left cerebral cortex

value: tissue

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS286VDM at ENCODE; https://www.encodeproject.org/ENCBS286VDM/

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


title: DNase-seq from adrenal gland (ENCLB303NTG)

description:
https://www.encodeproject.org/experiments/ENCSR204WCY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR204WCY
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB303NTG

value: adrenal gland

value: B6Cast F1 PND 2 months Male 06 adrenal gland for Altius Stam core

value: male

value: unknown

value: 2 month

value: ENCBS269NXW at ENCODE; https://www.encodeproject.org/ENCBS269NXW/


title: DNase-seq from spleen (ENCLB107FSQ)

description:
https://www.encodeproject.org/experiments/ENCSR087PCD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR087PCD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB107FSQ

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

value: spleen

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

value: ENCBS929LUE at ENCODE; https://www.encodeproject.org/ENCBS929LUE/


title: Sample 01 Illumina

value: Male

value: Healthy


title: Patient_9_3E5CFL_ATAC

description:
3E5CFL_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq

value: Asian

value: Tumor

value: Ovary

value: High-Grade Serous

value: Primary/Non-metastatic


title: polyA plus RNA-seq from regulatory T cell (ENCLB399HGG)

description:
https://www.encodeproject.org/experiments/ENCSR323OER/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR323OER
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB399HGG
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: regulatory T cell

value: primary cell

value: adult

value: 4 month

value: Christina Leslie, MSKCC

value: Christina Leslie

value: ENCBS377GTN at ENCODE; https://www.encodeproject.org/ENCBS377GTN/


title: Patient_8_3BAE2L_ATAC

description:
3BAE2L_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq

value: Caucasian


title: polyA plus RNA-seq from regulatory T cell (ENCLB762OQV)

description:
https://www.encodeproject.org/experiments/ENCSR323OER/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR323OER
assay title: polyA plus RNA-seq
assembly: mm10
encode release date: 2017-03-07
lab: Christina Leslie, MSKCC
library encode accession: ENCLB762OQV
fragmentation methods: shearing (Covaris generic)
size range: 100-300

value: male


title: Patient_6_37EACL_ATAC

description:
37EACL_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq

value: Serous

value: Metastatic


title: Sample 05 Illumina

value: Male

value: Healthy


title: DNase-seq from spleen (ENCLB435SDP)

description:
https://www.encodeproject.org/experiments/ENCSR087PCD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR087PCD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB435SDP

value: spleen

value: tissue

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

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS821BXD at ENCODE; https://www.encodeproject.org/ENCBS821BXD/

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


title: DNase-seq from adrenal gland (ENCLB256QIO)

description:
https://www.encodeproject.org/experiments/ENCSR365LKY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR365LKY
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB256QIO

source_name: Mus musculus strain B6CASTF1/J female (36 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND36 Female 06 adrenal gland for Altius Stam core

value: female

value: 36 day

value: ENCBS426MGT at ENCODE; https://www.encodeproject.org/ENCBS426MGT/


title: Patient_5_366C5L_ATAC

description:
366C5L_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq

source_name: Tumor of the endometrium

value: Caucasian

value: Tumor

value: Endometrium

value: Endometrioid

value: Primary/Non-metastatic


title: Patient_4_36639L_ATAC

description:
36639L_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq


title: Control-Pool2 [WES_25]

city: Pamplona

first: Ibai

last: Goicoechea

state: Navarra

address: Centro de Investigación Médica Aplicada (CIMA) Avenida Pío XII, 55

country: Spain

institute: Universidad de Navarra

data_processing:
Demultiplexing, alignment and gene counts were performed with Cell Ranger Single-Cell Software Suite (v3.01, 10X Genomics).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: NOT PROVIDED

source_name: Tail

extract_protocol:
For WES B cells were sorted and genomic DNA from viable cells was purified using the NucleoSpin® Tissue kit (Macherey-Nagel), according to the manufacturer’s instructions
SureSelectXT Target Enrichment System for Illumina  Paired-End Multiplexed Sequencing Library Version C2, Dec 2018
Exome capture libraries were prepared per the instructions of the SureSelectXT mouse all exon target enrichment system (Agilent Technologies)

tag: cell type

value: B cells

value: Tail

tag: strain background

tag: genotype/variation

value: control


title: Patient_3_36186L_ATAC

description:
36186L_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq


title: Control-1 [WES_24]


title: Patient_2_3571DL_ATAC

description:
3571DL_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq


title: Patient_1_3533EL_ATAC

description:
3533EL_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq

value: African American


title: 8961B-M88Yc [WES_23]

source_name: Spleen

value: Spleen


title: DNase-seq from adrenal gland (ENCLB231HAK)

description:
https://www.encodeproject.org/experiments/ENCSR365LKY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR365LKY
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB231HAK

value: tissue

tag: description

value: B6Cast F1 PND36 Female 05 adrenal gland for Altius Stam core

tag: biosample encode accession

tag: Sex

value: unknown

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS777RZR at ENCODE; https://www.encodeproject.org/ENCBS777RZR/


title: 8827GT-M88Yc [WES_22]

source_name: Gastric tumor

value: Gastric tumor


title: DNase-seq from left cerebral cortex (ENCLB613MNJ)

description:
https://www.encodeproject.org/experiments/ENCSR074RIB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR074RIB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB613MNJ

source_name: Mus musculus strain B6CASTF1/J male (10 days) left cerebral cortex tissue

value: left cerebral cortex

value: B6Cast F1 PND10 Male 05 left cerebral cortex for Altius Stam biobank

value: male

tag: dev stage

tag: age

value: 10 day

tag: lab

value: ENCBS732BTA at ENCODE; https://www.encodeproject.org/ENCBS732BTA/

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


title: Patient_9_3E5CFL_RNA

description:
3E5CFL_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

value: Asian

value: Tumor

value: Ovary

value: High-Grade Serous

value: Primary/Non-metastatic


title: DNase-seq from left cerebral cortex (ENCLB899BWS)

description:
https://www.encodeproject.org/experiments/ENCSR074RIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR074RIB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB899BWS

value: tissue

value: B6Cast F1 PND10 Male 06 left cerebral cortex for Altius Stam biobank

tag: source

tag: link

value: ENCBS329XBE at ENCODE; https://www.encodeproject.org/ENCBS329XBE/


title: Patient_11_3E4D1L_RNA

description:
3E4D1L_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

value: Caucasian

value: GIST

value: Metastatic


title: TF ChIP-seq from WTC11 (ENCLB362LOZ)

description:
https://www.encodeproject.org/experiments/ENCSR568LRK/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-JAZF1 ChIP-seq on human WTC11
experiment encode accession: ENCSR568LRK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB362LOZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens JAZF1

tag: line

value: cell line

value: adult

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS716HBH at ENCODE; https://www.encodeproject.org/ENCBS716HBH/

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


title: TF ChIP-seq from WTC11 (ENCLB526CGC)

description:
https://www.encodeproject.org/experiments/ENCSR568LRK/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-JAZF1 ChIP-seq on human WTC11
experiment encode accession: ENCSR568LRK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB526CGC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

value: male

value: ENCBS852KUV at ENCODE; https://www.encodeproject.org/ENCBS852KUV/


title: polyA plus RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB825MEM)

description:
https://www.encodeproject.org/experiments/ENCSR940EVD/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, CD25-positive, alpha-beta regulatory T cell with multiple sclerosis.
experiment encode accession: ENCSR940EVD
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB825MEM
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: primary cell

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

value: not collected

tag: health state

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: 8826SG-M88Yc [WES_21]

source_name: Salivary Gland

value: B cells

tag: tissue

value: Salivary Gland


title: 8757T-M88Yc [WES_20]

source_name: Thymus

value: Thymus


title: polyA plus RNA-seq from naive B cell (ENCLB375IIW)

description:
https://www.encodeproject.org/experiments/ENCSR936COT/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive B cell.
experiment encode accession: ENCSR936COT
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB375IIW
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: naive B cell

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

value: healthy

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

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


title: Patient_7_38FE7L_ATAC

description:
38FE7L_ATAC
single-cell ATAC-seq
Patient tumor tissue profiled by 10x scATAC-seq

value: Caucasian

value: Tumor

value: Ovary

tag: histology

value: Endometrioid

tag: metastatic status

value: Primary/Non-metastatic


title: Patient_10_3CCF1L_RNA

description:
3CCF1L_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

value: Carcinosarcoma

tag: patient


title: DNase-seq from lung (ENCLB440BSM)

description:
https://www.encodeproject.org/experiments/ENCSR059VAQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR059VAQ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB440BSM

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

value: lung

value: tissue

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

value: female

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS574UPG at ENCODE; https://www.encodeproject.org/ENCBS574UPG/

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


title: DNase-seq from cerebellum (ENCLB358GFG)

description:
https://www.encodeproject.org/experiments/ENCSR361FXJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR361FXJ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB358GFG

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

value: cerebellum

value: B6Cast F1 PND 2 months Female 06 cerebellum for Altius Stam core

value: 2 month

value: ENCBS584UAR at ENCODE; https://www.encodeproject.org/ENCBS584UAR/


title: Patient_8_3BAE2L_RNA

description:
3BAE2L_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

value: Caucasian

value: Tumor

value: Ovary

value: High-Grade Serous


title: ATAC-seq from T-cell (ENCLB288PFT)

description:
https://www.encodeproject.org/experiments/ENCSR934AWQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR934AWQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB288PFT
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: T-cell

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS701JOY at ENCODE; https://www.encodeproject.org/ENCBS701JOY/

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


title: 8701GT-M88Yc [WES_19]

tag: cell type

value: B cells

value: Gastric tumor

tag: strain background


title: 2885T-M88N [WES_17]

value: Thymus

tag: genotype/variation


title: Patient_7_38FE7L_RNA

description:
38FE7L_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

source_name: Tumor of the ovary

value: Endometrioid

value: Primary/Non-metastatic


title: DNase-seq from cerebellum (ENCLB258GMR)

description:
https://www.encodeproject.org/experiments/ENCSR361FXJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR361FXJ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB258GMR

value: cerebellum

value: tissue

tag: description

value: B6Cast F1 PND 2 months Female 05 cerebellum for Altius Stam core

tag: biosample encode accession

value: female

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS540EJY at ENCODE; https://www.encodeproject.org/ENCBS540EJY/

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


title: Patient_6_37EACL_RNA

description:
37EACL_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

value: Caucasian

value: Tumor

value: Ovary

value: Serous

value: Metastatic


title: Patient_5_366C5L_RNA

description:
366C5L_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

value: Endometrium

value: Endometrioid


title: DNase-seq from thymus (ENCLB216TUB)

description:
https://www.encodeproject.org/experiments/ENCSR179HEN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR179HEN
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB216TUB

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

value: thymus

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

tag: Sex

value: male

tag: dev stage

value: 10 day

value: ENCBS610QGR at ENCODE; https://www.encodeproject.org/ENCBS610QGR/


title: 2886LN-M88N [WES_18]

source_name: Lymph node

value: B cells

value: Lymph node


title: DNase-seq from thymus (ENCLB198WYA)

description:
https://www.encodeproject.org/experiments/ENCSR179HEN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR179HEN
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB198WYA

value: tissue

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

value: unknown

tag: age

tag: lab

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS235PCX at ENCODE; https://www.encodeproject.org/ENCBS235PCX/


title: 2483T-M88N [WES_15]

value: Thymus


title: polyA plus RNA-seq from CD8-positive, alpha-beta memory T cell (ENCLB654BHH)

description:
https://www.encodeproject.org/experiments/ENCSR849RVP/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD8-positive, alpha-beta memory T cell with multiple sclerosis.
experiment encode accession: ENCSR849RVP
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB654BHH
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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: not collected

value: multiple sclerosis

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

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

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


title: DNase-seq from head of caudate nucleus (ENCLB750QKA)

description:
https://www.encodeproject.org/experiments/ENCSR923BEY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR923BEY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB750QKA
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens female adult (90 or above years) with mild cognitive impairment; head of caudate nucleus tissue

value: head of caudate nucleus

value: female

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS816IOP at ENCODE; https://www.encodeproject.org/ENCBS816IOP/

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


title: 2486T-M88N [WES_16]

value: B cells

value: Thymus


title: DNase-seq from lung (ENCLB280KAZ)

description:
https://www.encodeproject.org/experiments/ENCSR059VAQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059VAQ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB280KAZ

value: lung

value: tissue

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

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS123AMC at ENCODE; https://www.encodeproject.org/ENCBS123AMC/

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


title: Patient_3_36186L_RNA

description:
36186L_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

source_name: Tumor of the endometrium

value: Caucasian

value: Tumor

value: Endometrium

value: Endometrioid

value: Primary/Non-metastatic


title: DNase-seq from heart (ENCLB485FKU)

description:
https://www.encodeproject.org/experiments/ENCSR168HGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR168HGB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB485FKU

source_name: Mus musculus strain B6CASTF1/J male (36 days) heart tissue

value: heart

value: B6Cast F1 PND36 Male 05 heart for Altius Stam biobank

value: male

value: 36 day

value: ENCBS785CSF at ENCODE; https://www.encodeproject.org/ENCBS785CSF/


title: DNase-seq from heart (ENCLB021YKE)

description:
https://www.encodeproject.org/experiments/ENCSR168HGB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR168HGB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB021YKE

value: tissue

value: B6Cast F1 PND36 Male 06 heart for Altius Stam biobank

value: ENCBS844PWB at ENCODE; https://www.encodeproject.org/ENCBS844PWB/


title: TF ChIP-seq from A549 (ENCLB716DSS)

description:
https://www.encodeproject.org/experiments/ENCSR913JBH/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TP63 ChIP-seq on human A549
experiment encode accession: ENCSR913JBH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR779AKU, ENCSR997RBV
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB716DSS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TP63

tag: antibody

tag: line

value: cell line

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS584AXO at ENCODE; https://www.encodeproject.org/ENCBS584AXO/

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


title: 2230SG-M88N [WES_13]

value: B cells

tag: tissue

value: Salivary Gland


title: Patient_2_3571DL_RNA

description:
3571DL_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

value: Caucasian

value: Tumor

value: Endometrium

tag: histology

value: Endometrioid

value: Primary/Non-metastatic


title: DNase-seq from cerebellum (ENCLB699HET)

description:
https://www.encodeproject.org/experiments/ENCSR240XYH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR240XYH
assay title: DNase-seq
assembly: mm10
encode release date: 2021-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB699HET

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

value: cerebellum

value: tissue

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

value: female

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS302IOD at ENCODE; https://www.encodeproject.org/ENCBS302IOD/

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


title: Patient_4_36639L_RNA

description:
36639L_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

tag: metastatic status


title: 2258SG-M88Ym [WES_14]

value: B cells


title: DNase-seq from cerebellum (ENCLB695TTU)

description:
https://www.encodeproject.org/experiments/ENCSR240XYH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR240XYH
assay title: DNase-seq
assembly: mm10
encode release date: 2021-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB695TTU

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

value: ENCBS703LGF at ENCODE; https://www.encodeproject.org/ENCBS703LGF/


title: TF ChIP-seq from A549 (ENCLB080VCW)

description:
https://www.encodeproject.org/experiments/ENCSR742KNZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TFCP2L1 ChIP-seq on human A549
experiment encode accession: ENCSR742KNZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR344EOM, ENCSR279OHT
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB080VCW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TFCP2L1

value: cell line

value: male

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS990MHF at ENCODE; https://www.encodeproject.org/ENCBS990MHF/

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


title: Patient_1_3533EL_RNA

description:
3533EL_RNA
single-cell RNA-seq
Patient tumor tissue profiled by 10x scRNA-seq

value: African American

value: Tumor

value: Endometrium

value: Endometrioid

value: Primary/Non-metastatic

tag: patient


title: 2223GT-M88N [WES_12]

source_name: Gastric tumor

tag: cell type

value: Gastric tumor


title: DNase-seq from kidney (ENCLB410HKI)

description:
https://www.encodeproject.org/experiments/ENCSR162TZA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR162TZA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-08-24
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB410HKI

source_name: Mus musculus strain B6CASTF1/J male (36 days) kidney tissue

value: kidney

value: tissue

value: B6Cast F1 PND36 Male 06 kidney for Altius Stam core

value: unknown

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS225PCE at ENCODE; https://www.encodeproject.org/ENCBS225PCE/

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


title: TF ChIP-seq from K562 (ENCLB428CHI)

description:
https://www.encodeproject.org/experiments/ENCSR829UCH/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-NFXL1 ChIP-seq on human K562
experiment encode accession: ENCSR829UCH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU, ENCSR957RYA
encode release date: 2021-08-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB428CHI
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NFXL1

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NFXL1.

value: female

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS511KLK at ENCODE; https://www.encodeproject.org/ENCBS511KLK/

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


title: 2220LN-M88N [WES_11]

value: B cells

value: Lymph node

tag: strain background

tag: genotype/variation


title: TF ChIP-seq from A549 (ENCLB184CHS)

description:
https://www.encodeproject.org/experiments/ENCSR742KNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TFCP2L1 ChIP-seq on human A549
experiment encode accession: ENCSR742KNZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR344EOM, ENCSR279OHT
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB184CHS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: biosample encode accession

value: male

value: 58 year

value: Michael Snyder

value: ENCBS309RHE at ENCODE; https://www.encodeproject.org/ENCBS309RHE/

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


title: Sample 17 Prostate Tumor

city: Happy Valley

first: Alex

middle: Daniel

last: Chitsazan

state: OR

address: 2720 S Moody Ave

institute: Oregon Health and Science University

data_processing:
Reads were then aligned using snaptools aligned-paired-end command using all of the default parameters (bwa) to hg19
 Reads were than preprocessed using the snaptools snap-pre command using the default parameters
a binned matrix where each counts were generated for each 5kb bin in the genome using the snaptools -- snap-add-bmat command
a peak matrix was made with the snapATAC command runMACS (MACS2  parameters: --nomodel --shift 100 --ext 200 --qval 5e-2 -B –SPMR.)
Downstream analysis down in R
Genome_build: hg19
Supplementary_files_format_and_content: peak matrix, binned matrix in triplicate spare file and meta data text file

source_name: Prostate adenocarcinoma

extract_protocol:
Nuclei Isolation Buffer (NIB) was used to extract nuclei from flash-frozen prostate tumors via dounce homogenizer.
Nuclei were tagmented with specific barcode sequences annealed to the Tn5 enzyme after being sorted to a 96-well plate. Tagmented nuclei were mixed and sorted to another 96-well plate. A second set of indices were introduced via PCR to generate sci-ATAC-seq libraries. Clean-up was done using Qiagen PCR purification kits, followed up by AMPure bead purification twice.
single-cell ATAC-seq

tag: gleason score


title: 2209T-M88N [WES_9]

source_name: Thymus

value: Thymus


title: Sample 18 Prostate Tumor


title: 2210T-M88N [WES_10]


title: polyA plus RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB364GHN)

description:
https://www.encodeproject.org/experiments/ENCSR816TAY/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, CD25-positive, alpha-beta regulatory T cell.
experiment encode accession: ENCSR816TAY
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-10-12
lab: David Hafler, Yale
library encode accession: ENCLB364GHN
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: primary cell

tag: description

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

tag: Sex

value: not collected

value: healthy

tag: dev stage

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: TF ChIP-seq from WTC11 (ENCLB349LCW)

description:
https://www.encodeproject.org/experiments/ENCSR742DAU/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-HMGA2 ChIP-seq on human WTC11
experiment encode accession: ENCSR742DAU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR979TXM, ENCSR712UWN
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB349LCW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HMGA2

value: cell line

value: adult

tag: age

value: 30 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Kevin White

value: ENCBS892MRW at ENCODE; https://www.encodeproject.org/ENCBS892MRW/

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


title: DNase-seq from adrenal gland (ENCLB316YNG)

description:
https://www.encodeproject.org/experiments/ENCSR021YHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR021YHN
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB316YNG

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

value: adrenal gland

value: tissue

value: B6Cast F1 DPN18-20months

value: male

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

tag: link

value: ENCBS374DGO at ENCODE; https://www.encodeproject.org/ENCBS374DGO/

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


title: 2157SG-M88N [WES_7]

source_name: Salivary Gland

value: B cells

tag: tissue

value: Salivary Gland


title: 2205LN-M88N [WES_8]

source_name: Lymph node

value: Lymph node


title: Sample 15 Prostate Tumor


title: TF ChIP-seq from K562 (ENCLB220YTV)

description:
https://www.encodeproject.org/experiments/ENCSR829UCH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-NFXL1 ChIP-seq on human K562
experiment encode accession: ENCSR829UCH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU, ENCSR957RYA
encode release date: 2021-08-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB220YTV
size range: 450-650

tag: antibody

tag: line

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NFXL1.

value: female

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS319LGP at ENCODE; https://www.encodeproject.org/ENCBS319LGP/

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


title: TF ChIP-seq from WTC11 (ENCLB746QPE)

description:
https://www.encodeproject.org/experiments/ENCSR807VQT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZMAT4 ChIP-seq on human WTC11
experiment encode accession: ENCSR807VQT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615YWF
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB746QPE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZMAT4

value: male

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS113VKH at ENCODE; https://www.encodeproject.org/ENCBS113VKH/

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


title: DNase-seq from adrenal gland (ENCLB119SRI)

description:
https://www.encodeproject.org/experiments/ENCSR021YHN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR021YHN
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB119SRI

value: adrenal gland

value: tissue

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS643OIJ at ENCODE; https://www.encodeproject.org/ENCBS643OIJ/

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


title: Sample 14 Prostate Tumor


title: TF ChIP-seq from WTC11 (ENCLB825LYI)

description:
https://www.encodeproject.org/experiments/ENCSR742DAU/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-HMGA2 ChIP-seq on human WTC11
experiment encode accession: ENCSR742DAU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR979TXM, ENCSR712UWN
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB825LYI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: adult

value: ENCBS079WAC at ENCODE; https://www.encodeproject.org/ENCBS079WAC/


title: 2114GT-M88N [WES_6]

value: B cells

value: Gastric tumor


title: DNase-seq from thymus (ENCLB966DXP)

description:
https://www.encodeproject.org/experiments/ENCSR021IRX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR021IRX
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB966DXP

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

value: thymus

value: B6Cast F1 PND4 Male 05 thymus for Altius Stam biobank

value: male

value: unknown

value: 4 day

value: ENCBS359DJG at ENCODE; https://www.encodeproject.org/ENCBS359DJG/


title: TF ChIP-seq from WTC11 (ENCLB481IDY)

description:
https://www.encodeproject.org/experiments/ENCSR807VQT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZMAT4 ChIP-seq on human WTC11
experiment encode accession: ENCSR807VQT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615YWF
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB481IDY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS033IAJ at ENCODE; https://www.encodeproject.org/ENCBS033IAJ/

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


title: DNase-seq from thymus (ENCLB009TIT)

description:
https://www.encodeproject.org/experiments/ENCSR021IRX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR021IRX
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB009TIT

value: tissue

value: B6Cast F1 PND4 Male 06 thymus for Altius Stam biobank

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS288LEA at ENCODE; https://www.encodeproject.org/ENCBS288LEA/

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


title: polyA plus RNA-seq from naive B cell (ENCLB143ASG)

description:
https://www.encodeproject.org/experiments/ENCSR804NGX/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of naive B cell with multiple sclerosis.
experiment encode accession: ENCSR804NGX
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB143ASG
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: naive B cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: DNase-seq from lung (ENCLB977HTN)

description:
https://www.encodeproject.org/experiments/ENCSR224ZGJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR224ZGJ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB977HTN

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

value: lung

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

value: female

value: unknown

value: 4 day

value: ENCBS332SDT at ENCODE; https://www.encodeproject.org/ENCBS332SDT/


title: Sample 12 Prostate Tumor


title: Sample 16 Prostate Tumor


title: DNase-seq from cerebellum (ENCLB670LIS)

description:
https://www.encodeproject.org/experiments/ENCSR026MFT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR026MFT
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB670LIS
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

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

value: cerebellum

value: tissue

value: B6Cast F1 PND14 3x Males 06 cerebellum for Altius Stam core

value: male

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS264XMR at ENCODE; https://www.encodeproject.org/ENCBS264XMR/


title: 2052GT-M88Ym [WES_4]

value: B cells

value: Gastric tumor


title: DNase-seq from lung (ENCLB159CZC)

description:
https://www.encodeproject.org/experiments/ENCSR224ZGJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR224ZGJ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB159CZC

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

value: ENCBS374KLN at ENCODE; https://www.encodeproject.org/ENCBS374KLN/

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


title: Sample 11 Prostate Tumor


title: DNase-seq from head of caudate nucleus (ENCLB291CBP)

description:
https://www.encodeproject.org/experiments/ENCSR802NBC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR802NBC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB291CBP
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens female adult (90 or above years) with Alzheimer's disease; head of caudate nucleus tissue

value: head of caudate nucleus

value: female

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS867PSC at ENCODE; https://www.encodeproject.org/ENCBS867PSC/

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


title: DNase-seq from heart (ENCLB858GAR)

description:
https://www.encodeproject.org/experiments/ENCSR145TJB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR145TJB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB858GAR

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

value: heart

value: tissue

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

value: male

value: unknown

value: 4 day

value: ENCBS527SLD at ENCODE; https://www.encodeproject.org/ENCBS527SLD/


title: Sample 10 Prostate Tumor


title: 1933LN-M88N [WES_2]

value: B cells

value: Lymph node


title: DNase-seq from WTC11 (ENCLB375JCC)

description:
https://www.encodeproject.org/experiments/ENCSR785ZUI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR785ZUI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-05-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB375JCC

source_name: Homo sapiens WTC11 cell line

value: cell line

value: 30 year

value: Yin Shen

value: ENCBS348ZLD at ENCODE; https://www.encodeproject.org/ENCBS348ZLD/

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


title: DNase-seq from WTC11 (ENCLB526HYQ)

description:
https://www.encodeproject.org/experiments/ENCSR785ZUI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR785ZUI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-05-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB526HYQ

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS794VBE at ENCODE; https://www.encodeproject.org/ENCBS794VBE/


title: Sample 13 Prostate Tumor


title: Sample 8 Prostate Tumor


title: 2017T-M88N [WES_1]

value: Thymus


title: Sample 7 Prostate Tumor


title: DNase-seq from heart (ENCLB580XHP)

description:
https://www.encodeproject.org/experiments/ENCSR145TJB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR145TJB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB580XHP

value: heart

value: tissue

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

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS276HLH at ENCODE; https://www.encodeproject.org/ENCBS276HLH/

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


title: polyA plus RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB824TYQ)

description:
https://www.encodeproject.org/experiments/ENCSR667OPL/
***************
biological replicate number: 1
technical replicate number: 1
description: polyA plus RNA-seq of CD4-positive, CD25-positive, alpha-beta regulatory T cell.
experiment encode accession: ENCSR667OPL
assay title: polyA plus RNA-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: David Hafler, Yale
library encode accession: ENCLB824TYQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 300-500

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

value: primary cell

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

value: not collected

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: DNase-seq from heart (ENCLB232QAM)

description:
https://www.encodeproject.org/experiments/ENCSR121JAB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR121JAB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB232QAM

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

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

value: male

value: 10 day

value: ENCBS722VSK at ENCODE; https://www.encodeproject.org/ENCBS722VSK/


title: Sample 6 Prostate Tumor

source_name: Prostate adenocarcinoma


title: DNase-seq from kidney (ENCLB393TYG)

description:
https://www.encodeproject.org/experiments/ENCSR113CGA/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR113CGA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB393TYG
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

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

value: kidney

value: tissue

value: B6Cast F1 PND14 3x Females 05 kidney for Altius Stam core

value: female

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS761GSR at ENCODE; https://www.encodeproject.org/ENCBS761GSR/


title: DNase-seq from heart (ENCLB999KXV)

description:
https://www.encodeproject.org/experiments/ENCSR121JAB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121JAB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB999KXV

value: heart

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

value: The Jackson Laboratory

value: ENCBS289KXY at ENCODE; https://www.encodeproject.org/ENCBS289KXY/

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


title: DNase-seq from thymus (ENCLB369OAS)

description:
https://www.encodeproject.org/experiments/ENCSR322AIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR322AIL
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB369OAS

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

value: thymus

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

value: unknown

value: 2 month

value: ENCBS755DQH at ENCODE; https://www.encodeproject.org/ENCBS755DQH/


title: TF ChIP-seq from HepG2 (ENCLB810IDF)

description:
https://www.encodeproject.org/experiments/ENCSR695WOH/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR695WOH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042HRU
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB810IDF
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MEIS1

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS734OGN at ENCODE; https://www.encodeproject.org/ENCBS734OGN/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: DNase-seq from thymus (ENCLB348IHL)

description:
https://www.encodeproject.org/experiments/ENCSR322AIL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR322AIL
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB348IHL

value: tissue

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

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS154TGC at ENCODE; https://www.encodeproject.org/ENCBS154TGC/


title: Sample 4 Prostate Tumor


title: Sample 3 Prostate Tumor


title: Bru-seq from Calu3 (ENCLB513LUX)

description:
https://www.encodeproject.org/experiments/ENCSR692DCF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR692DCF
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB513LUX
size range: 400-500

source_name: Homo sapiens Calu3 cell line

value: adult

value: 25 year

value: Mats Ljungman, UMichigan

value: ATCC

value: Lung adenocarcinoma

value: ENCBS520GAP at ENCODE; https://www.encodeproject.org/ENCBS520GAP/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: Control ChIP-seq from A549 (ENCLB059PDH)

description:
https://www.encodeproject.org/experiments/ENCSR997RBV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR997RBV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB059PDH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TP63

value: cell line

value: male

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS074BMC at ENCODE; https://www.encodeproject.org/ENCBS074BMC/

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


title: DNase-seq from thymus (ENCLB046DEA)

description:
https://www.encodeproject.org/experiments/ENCSR315TVO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR315TVO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB046DEA

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

value: thymus

value: tissue

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

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS943GSU at ENCODE; https://www.encodeproject.org/ENCBS943GSU/

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


title: Sample 9 Prostate Tumor


title: 204B-M88Yc [WES_3]

source_name: Spleen

value: B cells

value: Spleen


title: Sample 2 Prostate Tumor


title: DNase-seq from colonic mucosa (ENCLB184HJU)

description:
https://www.encodeproject.org/experiments/ENCSR994KTY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR994KTY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB184HJU

source_name: Homo sapiens female adult (41 years) colonic mucosa tissue, preserved by flash-freezing

value: colonic mucosa

value: female

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

value: adult

value: 41 year

value: Yiing Lin, MD, PhD

value: ENCBS936QHW at ENCODE; https://www.encodeproject.org/ENCBS936QHW/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: ATAC-seq from activated T-cell (ENCLB361LTS)

description:
https://www.encodeproject.org/experiments/ENCSR993XED/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR993XED
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB361LTS
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (38 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours

value: activated T-cell

value: primary cell

value: male

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:4; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour;

value: ENCBS242OKS at ENCODE; https://www.encodeproject.org/ENCBS242OKS/

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


title: Sample 1 Prostate Tumor


title: DNase-seq from thymus (ENCLB499FPB)

description:
https://www.encodeproject.org/experiments/ENCSR315TVO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR315TVO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB499FPB

value: thymus

value: tissue

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

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS828IKW at ENCODE; https://www.encodeproject.org/ENCBS828IKW/

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


title: KYSE150_2_8

city: Dallas

first: Adwait Amod

last: Sathe

state: Texas

address: 5323 Harry Hines Blvd.

department: McDermott Center of Human Growth and Development

institute: UT Southwestern Medical Center

data_processing:
Paired-end 75 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to mouse genome using bowtie2 (v2.3.3.1)
Duplicates were marked using picard-tools (v2.2.1) and blacklist regions were removed using bedtools (v2.7.1)
TN5 shifting of bam files was performed using the open-source Perl script "ATAC_BAM_shiftrt_gappedAlign.pl"
peaks were called using MACS version 2.1.0.20160309 with the following setting: Q-value < 0.05 and using the random background
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using HOMER. Scores represent normalized counts per 10 million.

source_name: Esophageal squamous carcinoma cell line

growth_protocol: HET-1A cells were cultured in BEBM medium with all the additives as ATCC recommends. KYSE-30 and KYSE-150 cells were grown in RPMI/F12 + 5% FBS + 1% antibiotic-antimycotic.

extract_protocol:
ATAC-seq libraries were prepared using the ATAC-seq inventor’s original protocol. Cells were harvested for ATAC-seq by centrifugation and re-suspended in cold PBS. 50,000 cells were immediately lysed using cold lysis buffer, and isolated nuclei from the cells were incubated in the Tn5-mediated transposase reaction mix for 30 min at 37 °C.
Following purification, the fragmented DNA library from each cell line was barcoded by PCR using customized Illumina sequencing primers. After primer dimers were cleaned up with AMPure XP beads (Beckman Coulter, CA), libraries were validated by Bioanalyzer and quantified by qRT-PCR.

value: esophagus

tag: cell line

value: esophageal squamous cell carcinoma (ESCC) cell line KYSE-150


title: TF ChIP-seq from A549 (ENCLB851EAU)

description:
https://www.encodeproject.org/experiments/ENCSR913JBH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TP63 ChIP-seq on human A549
experiment encode accession: ENCSR913JBH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR779AKU, ENCSR997RBV
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB851EAU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: male

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS820YKP at ENCODE; https://www.encodeproject.org/ENCBS820YKP/

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


title: TF ChIP-seq from HepG2 (ENCLB781QXT)

description:
https://www.encodeproject.org/experiments/ENCSR695WOH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR695WOH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042HRU
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB781QXT
fragmentation methods: sonication (generic)

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

tag: health state

value: hepatocellular carcinoma

value: ENCBS537XHZ at ENCODE; https://www.encodeproject.org/ENCBS537XHZ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/