title: WGBS from motor neuron (ENCLB266MMU)

description:
https://www.encodeproject.org/experiments/ENCSR149NZN/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control CS14 - iNPC
experiment encode accession: ENCSR149NZN
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB266MMU
fragmentation methods: shearing (Covaris generic)
size range: 450-650

source_name: Homo sapiens female adult motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: female

value: Healthy donor

value: not collected

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS480PZD at ENCODE; https://www.encodeproject.org/ENCBS480PZD/

value: Derived from ENCODE donor ENCDO689YDN; https://www.encodeproject.org/ENCDO689YDN/


title: WGBS from motor neuron (ENCLB903FBM)

status: Public on Oct 16 2022

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/ENCSR149NZN/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control CS14 - iNPC
experiment encode accession: ENCSR149NZN
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB903FBM
fragmentation methods: shearing (Covaris generic)
size range: 450-650

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

tag: biosample encode accession

tag: Sex

tag: health state

tag: dev stage

value: adult

tag: age

tag: lab

tag: source

tag: link

value: ENCBS194LHN at ENCODE; https://www.encodeproject.org/ENCBS194LHN/


title: DNase-seq from HCT116 (ENCLB024FIA)

description:
https://www.encodeproject.org/experiments/ENCSR694YJR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR694YJR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB024FIA

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14

tag: line

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS811OFM at ENCODE; https://www.encodeproject.org/ENCBS811OFM/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: DNase-seq from frontal cortex (ENCLB004IXJ)

description:
https://www.encodeproject.org/experiments/ENCSR280ZEI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR280ZEI
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB004IXJ

organism: Mus musculus

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

value: frontal cortex

value: tissue

tag: description

value: B6Cast F1 2 month female Frontal Cortex

value: female

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS211MYI at ENCODE; https://www.encodeproject.org/ENCBS211MYI/

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


title: ATAC-seq from uterus (ENCLB017DBL)

description:
https://www.encodeproject.org/experiments/ENCSR705RZX/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human uterus
experiment encode accession: ENCSR705RZX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB017DBL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (46 years) uterus tissue, preserved by flash-freezing

value: uterus

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

value: adult

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS062YRE at ENCODE; https://www.encodeproject.org/ENCBS062YRE/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: ATAC-seq from uterus (ENCLB186VLL)

description:
https://www.encodeproject.org/experiments/ENCSR705RZX/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human uterus
experiment encode accession: ENCSR705RZX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB186VLL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000


title: DNase-seq from kidney (ENCLB898TNH)

description:
https://www.encodeproject.org/experiments/ENCSR170FAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR170FAP
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB898TNH

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

value: kidney

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

value: not collected

value: ENCBS766QZO at ENCODE; https://www.encodeproject.org/ENCBS766QZO/


title: DNase-seq from kidney (ENCLB498GHO)

description:
https://www.encodeproject.org/experiments/ENCSR170FAP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR170FAP
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB498GHO

value: tissue

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

value: female

value: 2 month

value: ENCBS872JUR at ENCODE; https://www.encodeproject.org/ENCBS872JUR/


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB904BOH)

description:
https://www.encodeproject.org/experiments/ENCSR291HMM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR291HMM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-08-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB904BOH

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

value: primary cell

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

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS170TKF at ENCODE; https://www.encodeproject.org/ENCBS170TKF/

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


title: ATAC-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB046DDV)

description:
https://www.encodeproject.org/experiments/ENCSR260LAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR260LAN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB046DDV
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (48 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: male

value: adult

value: 48 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS711DUV at ENCODE; https://www.encodeproject.org/ENCBS711DUV/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/


title: ATAC-seq from spleen (ENCLB699QKK)

description:
https://www.encodeproject.org/experiments/ENCSR158KCS/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human spleen
experiment encode accession: ENCSR158KCS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB699QKK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (61 years) spleen tissue, preserved by cryopreservation

value: spleen

value: tissue

value: female

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

value: 61 year

value: Yiing Lin, MD, PhD

value: ENCBS327LSG at ENCODE; https://www.encodeproject.org/ENCBS327LSG/

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


title: ATAC-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB556JML)

description:
https://www.encodeproject.org/experiments/ENCSR260LAN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR260LAN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB556JML
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: primary cell

value: ENCBS119LOF at ENCODE; https://www.encodeproject.org/ENCBS119LOF/


title: DNase-seq from left cerebral cortex (ENCLB198XSJ)

description:
https://www.encodeproject.org/experiments/ENCSR282IXW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR282IXW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB198XSJ

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

value: left cerebral cortex

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

value: not collected

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS289HDE at ENCODE; https://www.encodeproject.org/ENCBS289HDE/

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


title: DNase-seq from HCT116 (ENCLB631XVL)

description:
https://www.encodeproject.org/experiments/ENCSR694YJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR694YJR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB631XVL

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS357JIV at ENCODE; https://www.encodeproject.org/ENCBS357JIV/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: DNase-seq from HCT116 (ENCLB705ZCT)

description:
https://www.encodeproject.org/experiments/ENCSR702VYW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR702VYW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB705ZCT

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS865XEF at ENCODE; https://www.encodeproject.org/ENCBS865XEF/


title: DNase-seq from activated naive CD8-positive, alpha-beta T cell (ENCLB915KPB)

description:
https://www.encodeproject.org/experiments/ENCSR518YYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR518YYX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB915KPB

source_name: Homo sapiens male adult (30 years) activated naive CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS710PTW at ENCODE; https://www.encodeproject.org/ENCBS710PTW/

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


title: DNase-seq from left cerebral cortex (ENCLB807WBR)

description:
https://www.encodeproject.org/experiments/ENCSR282IXW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR282IXW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB807WBR

value: left cerebral cortex

value: tissue

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

value: female

value: not collected

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS280BBL at ENCODE; https://www.encodeproject.org/ENCBS280BBL/

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


title: DNase-seq from frontal cortex (ENCLB635CHW)

description:
https://www.encodeproject.org/experiments/ENCSR280ZEI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR280ZEI
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB635CHW

value: frontal cortex

value: B6Cast F1 2 month female Frontal Cortex

value: 2 month

value: ENCBS162XDT at ENCODE; https://www.encodeproject.org/ENCBS162XDT/


title: ATAC-seq from spleen (ENCLB601IZR)

description:
https://www.encodeproject.org/experiments/ENCSR694OWY/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human spleen
experiment encode accession: ENCSR694OWY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB601IZR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (26 years) spleen tissue, preserved by cryopreservation

value: spleen

value: male

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

value: adult

value: 26 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS936ARS at ENCODE; https://www.encodeproject.org/ENCBS936ARS/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: ATAC-seq from spleen (ENCLB325LIQ)

description:
https://www.encodeproject.org/experiments/ENCSR694OWY/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human spleen
experiment encode accession: ENCSR694OWY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB325LIQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: tissue


title: DNase-seq from lung (ENCLB884SBI)

description:
https://www.encodeproject.org/experiments/ENCSR702AVR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR702AVR
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB884SBI

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

value: lung

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

value: not collected

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS389AHI at ENCODE; https://www.encodeproject.org/ENCBS389AHI/


title: DNase-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB352ZWM)

description:
https://www.encodeproject.org/experiments/ENCSR515PDV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR515PDV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB352ZWM

source_name: Homo sapiens male adult (50 years) activated naive CD4-positive, alpha-beta T primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: primary cell

value: 50 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS518DQO at ENCODE; https://www.encodeproject.org/ENCBS518DQO/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: ATAC-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB939IOU)

description:
https://www.encodeproject.org/experiments/ENCSR513EVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR513EVP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-11-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB939IOU
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (42 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

value: male

value: adult

value: 42 year

value: AllCells

value: ENCBS749TWP at ENCODE; https://www.encodeproject.org/ENCBS749TWP/

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


title: DNase-seq from layer of hippocampus (ENCLB335HDU)

description:
https://www.encodeproject.org/experiments/ENCSR270DJQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR270DJQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB335HDU

source_name: Mus musculus strain B6CASTF1/J male (2 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: B6Cast F1 2 month male Hippocampus

value: not collected

value: 2 month

value: ENCBS945OLV at ENCODE; https://www.encodeproject.org/ENCBS945OLV/

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


title: DNase-seq from immature natural killer cell (ENCLB984ZXD)

description:
https://www.encodeproject.org/experiments/ENCSR696ZDW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR696ZDW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB984ZXD

source_name: Homo sapiens immature natural killer primary cell, preserved by cryopreservation

value: immature natural killer cell

value: primary cell

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS024BVP at ENCODE; https://www.encodeproject.org/ENCBS024BVP/

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


title: DNase-seq from urinary bladder (ENCLB383SQW)

description:
https://www.encodeproject.org/experiments/ENCSR690LVC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR690LVC
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB383SQW

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

value: urinary bladder

value: B6Cast F1 PND36 Male 06 urinary bladder for Altius Stam biobank

value: male

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS240XQJ at ENCODE; https://www.encodeproject.org/ENCBS240XQJ/


title: DNase-seq from layer of hippocampus (ENCLB151MAR)

description:
https://www.encodeproject.org/experiments/ENCSR270DJQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR270DJQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB151MAR

value: layer of hippocampus

value: tissue

value: B6Cast F1 2 month male Hippocampus

value: not collected

value: 2 month

value: ENCBS970QYI at ENCODE; https://www.encodeproject.org/ENCBS970QYI/


title: DNase-seq from left cerebral cortex (ENCLB982SPH)

description:
https://www.encodeproject.org/experiments/ENCSR255QUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR255QUX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB982SPH

source_name: Mus musculus strain B6CASTF1/J female postnatal (8-10 months) left cerebral cortex tissue

value: left cerebral cortex

value: female

value: postnatal

value: 8-10 month

value: ENCBS132ACH at ENCODE; https://www.encodeproject.org/ENCBS132ACH/

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


title: DNase-seq from urinary bladder (ENCLB407OOQ)

description:
https://www.encodeproject.org/experiments/ENCSR690LVC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR690LVC
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB407OOQ

value: urinary bladder

value: B6Cast F1 PND36 Male 05 urinary bladder for Altius Stam biobank

value: male

value: ENCBS391RQF at ENCODE; https://www.encodeproject.org/ENCBS391RQF/


title: DNase-seq from right cerebral cortex (ENCLB900UJA)

description:
https://www.encodeproject.org/experiments/ENCSR690IQA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR690IQA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB900UJA

source_name: Mus musculus strain B6CASTF1/J male (25 days) right cerebral cortex tissue

value: right cerebral cortex

value: B6Cast F1 PND25 Male 05 right cerebral cortex for Altius Stam biobank

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS175MTC at ENCODE; https://www.encodeproject.org/ENCBS175MTC/


title: DNase-seq from layer of hippocampus (ENCLB126DDL)

description:
https://www.encodeproject.org/experiments/ENCSR254KUF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR254KUF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB126DDL

source_name: Mus musculus strain B6CASTF1/J female (36 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: B6Cast F1 PND36 female Hippocampus

value: not collected

value: 36 day

value: ENCBS408XMD at ENCODE; https://www.encodeproject.org/ENCBS408XMD/


title: WGBS from motor neuron (ENCLB911ZVW)

description:
https://www.encodeproject.org/experiments/ENCSR509LMK/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control CS14 - iPSC
experiment encode accession: ENCSR509LMK
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB911ZVW
fragmentation methods: shearing (Covaris generic)
size range: 450-650

source_name: Homo sapiens female adult motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: female

value: Healthy donor

value: adult

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS901RNT at ENCODE; https://www.encodeproject.org/ENCBS901RNT/

value: Derived from ENCODE donor ENCDO689YDN; https://www.encodeproject.org/ENCDO689YDN/


title: DNase-seq from Caco-2 (ENCLB131CGI)

description:
https://www.encodeproject.org/experiments/ENCSR255STJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR255STJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB131CGI

source_name: Homo sapiens Caco-2 cell line

value: cell line

value: male

value: colorectal adenocarcinoma

value: 72 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS514GJK at ENCODE; https://www.encodeproject.org/ENCBS514GJK/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: ATAC-seq from T-helper 17 cell (ENCLB519YNY)

description:
https://www.encodeproject.org/experiments/ENCSR248ZAC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR248ZAC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-11-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB519YNY
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (42 years) T-helper 17 primary cell

value: T-helper 17 cell

value: primary cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS190MHX at ENCODE; https://www.encodeproject.org/ENCBS190MHX/

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


title: DNase-seq from layer of hippocampus (ENCLB633MDI)

description:
https://www.encodeproject.org/experiments/ENCSR247PTA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR247PTA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB633MDI

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

value: layer of hippocampus

value: tissue

value: B6Cast F1 PND14 3x female Hippocampus

value: female

value: not collected

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS173NQB at ENCODE; https://www.encodeproject.org/ENCBS173NQB/

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


title: DNase-seq from frontal cortex (ENCLB181NSA)

description:
https://www.encodeproject.org/experiments/ENCSR687OIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR687OIL
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB181NSA

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

value: frontal cortex

value: B6Cast F1 PND10 3x female Frontal Cortex

value: 10 day

value: ENCBS773DNE at ENCODE; https://www.encodeproject.org/ENCBS773DNE/


title: DNase-seq from layer of hippocampus (ENCLB057DGN)

description:
https://www.encodeproject.org/experiments/ENCSR247PTA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR247PTA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB057DGN

value: ENCBS332TLS at ENCODE; https://www.encodeproject.org/ENCBS332TLS/


title: ATAC-seq from upper lobe of left lung (ENCLB362GXM)

description:
https://www.encodeproject.org/experiments/ENCSR242QRV/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human upper lobe of left lung
experiment encode accession: ENCSR242QRV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB362GXM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (61 years) upper lobe of left lung tissue, preserved by cryopreservation

value: upper lobe of left lung

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

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS080DZD at ENCODE; https://www.encodeproject.org/ENCBS080DZD/

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


title: DNase-seq from frontal cortex (ENCLB603REX)

description:
https://www.encodeproject.org/experiments/ENCSR687OIL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR687OIL
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB603REX

value: tissue

value: female

value: not collected

value: Barbara Wold, Caltech

value: ENCBS180RYP at ENCODE; https://www.encodeproject.org/ENCBS180RYP/


title: WGBS from motor neuron (ENCLB467MJJ)

description:
https://www.encodeproject.org/experiments/ENCSR675UVC/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control SMA - iNPC
experiment encode accession: ENCSR675UVC
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB467MJJ
fragmentation methods: shearing (Covaris generic)
size range: 450-650

source_name: Homo sapiens male child (6 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: male

value: Healthy donor

value: child

value: 6 year

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS654DEO at ENCODE; https://www.encodeproject.org/ENCBS654DEO/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: DNase-seq from gastrocnemius (ENCLB463FEM)

description:
https://www.encodeproject.org/experiments/ENCSR976MHB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR976MHB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB463FEM

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

value: gastrocnemius

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

value: 2 month

value: The Jackson Laboratory

value: ENCBS022VHM at ENCODE; https://www.encodeproject.org/ENCBS022VHM/

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


title: DNase-seq from gastrocnemius (ENCLB986UPE)

description:
https://www.encodeproject.org/experiments/ENCSR976MHB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR976MHB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB986UPE

value: tissue

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

value: not collected

value: Barbara Wold, Caltech

value: ENCBS902TVO at ENCODE; https://www.encodeproject.org/ENCBS902TVO/


title: DNase-seq from CD4-positive, alpha-beta memory T cell (ENCLB789SUH)

description:
https://www.encodeproject.org/experiments/ENCSR977UMU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR977UMU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB789SUH

source_name: Homo sapiens embryo (59 days) liver tissue

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

value: primary cell

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

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

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS000UPK at ENCODE; https://www.encodeproject.org/ENCBS000UPK/

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


title: WGBS from motor neuron (ENCLB512EKL)

description:
https://www.encodeproject.org/experiments/ENCSR675UVC/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control SMA - iNPC
experiment encode accession: ENCSR675UVC
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB512EKL
fragmentation methods: shearing (Covaris generic)
size range: 450-650

value: motor neuron

value: in vitro differentiated cells

value: male

value: Healthy donor

value: child

value: 6 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS111PXK at ENCODE; https://www.encodeproject.org/ENCBS111PXK/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: DNase-seq from spleen (ENCLB524QFZ)

description:
https://www.encodeproject.org/experiments/ENCSR146PAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146PAW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB524QFZ

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

value: spleen

value: tissue

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

value: female

value: not collected

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS058LVQ at ENCODE; https://www.encodeproject.org/ENCBS058LVQ/

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


title: DNase-seq from spleen (ENCLB063WDG)

description:
https://www.encodeproject.org/experiments/ENCSR145GGC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR145GGC
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB063WDG

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

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

value: male

value: ENCBS990MFX at ENCODE; https://www.encodeproject.org/ENCBS990MFX/


title: DNase-seq from spleen (ENCLB097XDY)

description:
https://www.encodeproject.org/experiments/ENCSR145GGC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR145GGC
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB097XDY

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

value: ENCBS089ZYQ at ENCODE; https://www.encodeproject.org/ENCBS089ZYQ/


title: WGBS from motor neuron (ENCLB805ZXC)

description:
https://www.encodeproject.org/experiments/ENCSR509LMK/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control CS14 - iPSC
experiment encode accession: ENCSR509LMK
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB805ZXC
fragmentation methods: shearing (Covaris generic)
size range: 450-650

value: motor neuron

value: in vitro differentiated cells

value: Healthy donor

value: adult

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS835SNQ at ENCODE; https://www.encodeproject.org/ENCBS835SNQ/

value: Derived from ENCODE donor ENCDO689YDN; https://www.encodeproject.org/ENCDO689YDN/


title: DNase-seq from natural killer cell (ENCLB749AKE)

description:
https://www.encodeproject.org/experiments/ENCSR975LGK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR975LGK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB749AKE

source_name: Homo sapiens male adult (33 years) natural killer primary cell

value: natural killer cell

value: primary cell

value: 33 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS830NBW at ENCODE; https://www.encodeproject.org/ENCBS830NBW/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: DNase-seq from thymus (ENCLB403FCL)

description:
https://www.encodeproject.org/experiments/ENCSR133BTF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR133BTF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB403FCL

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

value: thymus

value: tissue

value: B6Cast F1 PND36 Female 06 thymus for Altius Stam biobank

value: female

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS409ZSQ at ENCODE; https://www.encodeproject.org/ENCBS409ZSQ/

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


title: DNase-seq from HCT116 (ENCLB215DLG)

description:
https://www.encodeproject.org/experiments/ENCSR690ADK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR690ADK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB215DLG

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS166GZO at ENCODE; https://www.encodeproject.org/ENCBS166GZO/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: ATAC-seq from upper lobe of left lung (ENCLB769BKX)

description:
https://www.encodeproject.org/experiments/ENCSR242QRV/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human upper lobe of left lung
experiment encode accession: ENCSR242QRV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB769BKX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: upper lobe of left lung

value: tissue

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

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS080DZD at ENCODE; https://www.encodeproject.org/ENCBS080DZD/

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


title: DNase-seq from Caco-2 (ENCLB351LZG)

description:
https://www.encodeproject.org/experiments/ENCSR255STJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR255STJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB351LZG

value: cell line

value: colorectal adenocarcinoma

value: 72 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS361NQA at ENCODE; https://www.encodeproject.org/ENCBS361NQA/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB579YOA)

description:
https://www.encodeproject.org/experiments/ENCSR969QKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR969QKG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB579YOA

source_name: Homo sapiens male adult (48 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: male

value: adult

value: 48 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS311MIB at ENCODE; https://www.encodeproject.org/ENCBS311MIB/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/


title: DNase-seq from layer of hippocampus (ENCLB560ZCL)

description:
https://www.encodeproject.org/experiments/ENCSR235KWU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR235KWU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB560ZCL

source_name: Mus musculus strain B6CASTF1/J male (25 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: B6Cast F1 PND25 male Hippocampus

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS226OKY at ENCODE; https://www.encodeproject.org/ENCBS226OKY/

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


title: ATAC-seq from fallopian tube (ENCLB033AEY)

description:
https://www.encodeproject.org/experiments/ENCSR238VHV/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human fallopian tube
experiment encode accession: ENCSR238VHV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB033AEY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (46 years) fallopian tube tissue, preserved by flash-freezing

value: fallopian tube

value: female

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

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS517PRL at ENCODE; https://www.encodeproject.org/ENCBS517PRL/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: ATAC-seq from fallopian tube (ENCLB012EOB)

description:
https://www.encodeproject.org/experiments/ENCSR238VHV/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human fallopian tube
experiment encode accession: ENCSR238VHV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB012EOB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: adult


title: DNase-seq from thymus (ENCLB315SIW)

description:
https://www.encodeproject.org/experiments/ENCSR133BTF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133BTF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB315SIW

value: thymus

value: tissue

value: B6Cast F1 PND36 Female 05 thymus for Altius Stam biobank

value: 36 day

value: ENCBS017TVO at ENCODE; https://www.encodeproject.org/ENCBS017TVO/


title: DNase-seq from right cerebral cortex (ENCLB970TPZ)

description:
https://www.encodeproject.org/experiments/ENCSR952RWH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR952RWH
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB970TPZ

source_name: Mus musculus strain B6CASTF1/J female (4 days) right cerebral cortex tissue

value: right cerebral cortex

value: B6Cast F1 PND4 Female 06 right cerebral cortex for Altius Stam biobank

value: not collected

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS144TZA at ENCODE; https://www.encodeproject.org/ENCBS144TZA/


title: DNase-seq from HCT116 (ENCLB444XAX)

description:
https://www.encodeproject.org/experiments/ENCSR129EWE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR129EWE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB444XAX

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS827ZQR at ENCODE; https://www.encodeproject.org/ENCBS827ZQR/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: DNase-seq from heart (ENCLB589XQQ)

description:
https://www.encodeproject.org/experiments/ENCSR147AIN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR147AIN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB589XQQ

source_name: Mus musculus strain B6CASTF1/J male postnatal (8-10 months) heart tissue

value: heart

value: tissue

value: postnatal

value: 8-10 month

value: ENCBS682ZFE at ENCODE; https://www.encodeproject.org/ENCBS682ZFE/

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


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB220GHC)

description:
https://www.encodeproject.org/experiments/ENCSR953OBW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR953OBW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-08-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB220GHC

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS840GDX at ENCODE; https://www.encodeproject.org/ENCBS840GDX/

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


title: DNase-seq from chondrocyte (ENCLB376KEB)

description:
https://www.encodeproject.org/experiments/ENCSR970DQR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR970DQR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB376KEB

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

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: female

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS360ANT at ENCODE; https://www.encodeproject.org/ENCBS360ANT/

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


title: DNase-seq from ovary (ENCLB554XEY)

description:
https://www.encodeproject.org/experiments/ENCSR232ELD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR232ELD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB554XEY

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

value: ovary

value: tissue

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

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS162ARS at ENCODE; https://www.encodeproject.org/ENCBS162ARS/

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


title: DNase-seq from heart (ENCLB077TJA)

description:
https://www.encodeproject.org/experiments/ENCSR944NVO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR944NVO
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB077TJA

source_name: Mus musculus strain B6CASTF1/J female (11 months) heart tissue

value: heart

value: unknown

value: 11 month

value: ENCBS936UFV at ENCODE; https://www.encodeproject.org/ENCBS936UFV/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB857JSL)

description:
https://www.encodeproject.org/experiments/ENCSR125OEJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR125OEJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB857JSL

source_name: Homo sapiens male adult (50 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: male

value: adult

value: 50 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS331IRO at ENCODE; https://www.encodeproject.org/ENCBS331IRO/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: DNase-seq from HCT116 (ENCLB760LJC)

description:
https://www.encodeproject.org/experiments/ENCSR975SCL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR975SCL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB760LJC

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS524SGS at ENCODE; https://www.encodeproject.org/ENCBS524SGS/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: DNase-seq from gastrocnemius (ENCLB681PGA)

description:
https://www.encodeproject.org/experiments/ENCSR115SWG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR115SWG
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB681PGA

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

value: gastrocnemius

value: tissue

value: B6Cast F1 PND36 Male 05 gastrocnemius for Altius Stam core

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS041BWV at ENCODE; https://www.encodeproject.org/ENCBS041BWV/

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


title: ATAC-seq from liver (ENCLB832VES)

description:
https://www.encodeproject.org/experiments/ENCSR124NNL/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human liver
experiment encode accession: ENCSR124NNL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB832VES
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (67 years) liver tissue, preserved by flash-freezing

value: liver

value: male

value: Cirrhosis, alpha-1 antitrypsin deficiency

value: adult

value: 67 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS924ALU at ENCODE; https://www.encodeproject.org/ENCBS924ALU/

value: Derived from ENCODE donor ENCDO747MSG; https://www.encodeproject.org/ENCDO747MSG/


title: DNase-seq from central memory CD4-positive, alpha-beta T cell (ENCLB376PFZ)

description:
https://www.encodeproject.org/experiments/ENCSR234FTX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR234FTX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-05-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB376PFZ

source_name: Homo sapiens male adult (42 years) central memory CD4-positive, alpha-beta T primary cell

value: primary cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS803LGZ at ENCODE; https://www.encodeproject.org/ENCBS803LGZ/

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


title: DNase-seq from H1 (ENCLB886KXP)

description:
https://www.encodeproject.org/experiments/ENCSR951BNY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR951BNY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB886KXP

source_name: Homo sapiens H1 cell line

value: cell line

value: healthy

value: embryonic

value: not collected

value: Job Dekker

value: ENCBS948AMI at ENCODE; https://www.encodeproject.org/ENCBS948AMI/

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


title: DNase-seq from gastrocnemius (ENCLB248ARK)

description:
https://www.encodeproject.org/experiments/ENCSR119IUE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR119IUE
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB248ARK

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

value: gastrocnemius

value: tissue

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

value: female

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS796XMS at ENCODE; https://www.encodeproject.org/ENCBS796XMS/

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


title: DNase-seq from layer of hippocampus (ENCLB100ZTW)

description:
https://www.encodeproject.org/experiments/ENCSR235KWU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR235KWU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB100ZTW

value: layer of hippocampus

value: B6Cast F1 PND25 male Hippocampus

value: male

value: 25 day

value: ENCBS706MON at ENCODE; https://www.encodeproject.org/ENCBS706MON/


title: ATAC-seq from liver (ENCLB368EBL)

description:
https://www.encodeproject.org/experiments/ENCSR124NNL/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human liver
experiment encode accession: ENCSR124NNL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB368EBL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: liver

value: Cirrhosis, alpha-1 antitrypsin deficiency

value: adult

value: 67 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS924ALU at ENCODE; https://www.encodeproject.org/ENCBS924ALU/

value: Derived from ENCODE donor ENCDO747MSG; https://www.encodeproject.org/ENCDO747MSG/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB088LMA)

description:
https://www.encodeproject.org/experiments/ENCSR232NLA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR232NLA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB088LMA

source_name: Homo sapiens male adult (35 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS622GQP at ENCODE; https://www.encodeproject.org/ENCBS622GQP/

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


title: DNase-seq from cerebellum (ENCLB286IUU)

description:
https://www.encodeproject.org/experiments/ENCSR934ECT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR934ECT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB286IUU

source_name: Mus musculus strain B6CASTF1/J male (8-10 months) cerebellum tissue

value: cerebellum

value: tissue

value: Stam pool K of 2 cerebellum biosamples

value: male

value: unknown

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS579QDL at ENCODE; https://www.encodeproject.org/ENCBS579QDL/

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


title: DNase-seq from urinary bladder (ENCLB771OYC)

description:
https://www.encodeproject.org/experiments/ENCSR105BDM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105BDM
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB771OYC

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

value: urinary bladder

value: B6Cast F1 PND25 Female 05 urinary bladder for Altius Stam biobank

value: female

value: not collected

value: 25 day

value: ENCBS458FEC at ENCODE; https://www.encodeproject.org/ENCBS458FEC/


title: DNase-seq from left cerebral cortex (ENCLB316TLS)

description:
https://www.encodeproject.org/experiments/ENCSR106PXP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR106PXP
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB316TLS

source_name: Mus musculus strain B6CASTF1/J male (25 days) left cerebral cortex tissue

value: left cerebral cortex

value: B6Cast F1 PND25 Male 06 left cerebral cortex for Altius Stam biobank

value: ENCBS751XOU at ENCODE; https://www.encodeproject.org/ENCBS751XOU/


title: DNase-seq from T-helper 2 cell (ENCLB663XGC)

description:
https://www.encodeproject.org/experiments/ENCSR223XND/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR223XND
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB663XGC

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

value: T-helper 2 cell

value: primary cell

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS375UMH at ENCODE; https://www.encodeproject.org/ENCBS375UMH/

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


title: DNase-seq from gastrocnemius (ENCLB957RDZ)

description:
https://www.encodeproject.org/experiments/ENCSR498SCU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR498SCU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB957RDZ

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

value: gastrocnemius

value: tissue

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

value: male

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS203TGZ at ENCODE; https://www.encodeproject.org/ENCBS203TGZ/

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


title: ATAC-seq from left ventricle myocardium inferior (ENCLB193OET)

description:
https://www.encodeproject.org/experiments/ENCSR946MAI/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human left ventricle myocardium inferior
experiment encode accession: ENCSR946MAI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB193OET
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (60 years) left ventricle myocardium inferior tissue, preserved by cryopreservation

value: left ventricle myocardium inferior

value: Inferior wall of left ventricle.

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS112FLS at ENCODE; https://www.encodeproject.org/ENCBS112FLS/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: ATAC-seq from heart left ventricle (ENCLB793HBH)

description:
https://www.encodeproject.org/experiments/ENCSR225FZH/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR225FZH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB793HBH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (55 years) heart left ventricle tissue

value: heart left ventricle

value: ischemic (EF 25% LVEDD 6.9; RV normal size, moderate dysfunction)

value: adult

value: 55 year

value: Shin Lin

value: ENCBS456UEC at ENCODE; https://www.encodeproject.org/ENCBS456UEC/

value: Derived from ENCODE donor ENCDO439CAZ; https://www.encodeproject.org/ENCDO439CAZ/


title: DNase-seq from left cerebral cortex (ENCLB279INW)

description:
https://www.encodeproject.org/experiments/ENCSR106PXP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR106PXP
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB279INW

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND25 Male 05 left cerebral cortex for Altius Stam biobank

value: male

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS188MXH at ENCODE; https://www.encodeproject.org/ENCBS188MXH/


title: DNase-seq from memory B cell (ENCLB184CJR)

description:
https://www.encodeproject.org/experiments/ENCSR229BGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR229BGG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB184CJR

source_name: Homo sapiens male adult (40 years) memory B primary cell

value: memory B cell

value: primary cell

value: 40 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS784URX at ENCODE; https://www.encodeproject.org/ENCBS784URX/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: ATAC-seq from heart left ventricle (ENCLB898KJX)

description:
https://www.encodeproject.org/experiments/ENCSR225FZH/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR225FZH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB898KJX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart left ventricle

value: ischemic (EF 25% LVEDD 6.9; RV normal size, moderate dysfunction)

value: adult

value: 55 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS456UEC at ENCODE; https://www.encodeproject.org/ENCBS456UEC/

value: Derived from ENCODE donor ENCDO439CAZ; https://www.encodeproject.org/ENCDO439CAZ/


title: DNase-seq from gastrocnemius (ENCLB004BCV)

description:
https://www.encodeproject.org/experiments/ENCSR115SWG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR115SWG
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB004BCV

value: gastrocnemius

value: tissue

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

value: male

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS748SUN at ENCODE; https://www.encodeproject.org/ENCBS748SUN/

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


title: DNase-seq from cerebellum (ENCLB620PCG)

description:
https://www.encodeproject.org/experiments/ENCSR502NYH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR502NYH
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB620PCG

source_name: Mus musculus strain 5xFAD/CAST male (9-11 months) cerebellum tissue

value: cerebellum

value: unknown

value: 9-11 month

value: ENCBS684OHZ at ENCODE; https://www.encodeproject.org/ENCBS684OHZ/

value: Derived from ENCODE donor ENCDO996MUL; https://www.encodeproject.org/ENCDO996MUL/


title: Enamel knot in mouse tooth germ 2

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

library_source: transcriptomic

data_processing:
TotalOmics Transcriptome (Reference-based, Quant): STAR-RSEM-TCC method
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v.2.8 (parameter- Quality limit: Phred quality score 20, reads shorter than 50 bp were removed)
Trimmed sequence reads were mapped to GrCM38/mm10 and ASM813125v1 using aligner STAR v.2.7.1a (ENCODE standard options with “-quantMode TranscriptomeSAM”)
RPKM/FPKM and TPM values were performed using RSEM v.1.3.1
Assembly: mm10, ASM813125v1
Supplementary files format and content: tab-delimited text files include RPKM/FPKM values for each Sample

molecule: total RNA

source_name: epithelial cells

extract_protocol:
Tooth germ were dissected from the mandibles of mouse and gerbil. Tooth germs were fixed with 4% PFA, then frozen-sectioned with cryostat. Then, enamel knot region from mouse and gerbil tooth germs were seperated with laser microdissection. RNA was extracted using TRIzol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell type

value: epithelial cells

tag: genotype

value: WT

tag: developmental stage

value: embryonic day 13


title: Enamel knot in mouse tooth germ 1


title: ATAC-seq from left ventricle myocardium inferior (ENCLB650JCD)

description:
https://www.encodeproject.org/experiments/ENCSR946MAI/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human left ventricle myocardium inferior
experiment encode accession: ENCSR946MAI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB650JCD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: left ventricle myocardium inferior

value: tissue

value: Inferior wall of left ventricle.

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS112FLS at ENCODE; https://www.encodeproject.org/ENCBS112FLS/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: DNase-seq from thymus (ENCLB315CFT)

description:
https://www.encodeproject.org/experiments/ENCSR090RLB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR090RLB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB315CFT

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

value: thymus

value: B6Cast F1 PND25 Female 05 thymus for Altius Stam biobank

value: female

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS356AHT at ENCODE; https://www.encodeproject.org/ENCBS356AHT/

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


title: DNase-seq from thymus (ENCLB212YEB)

description:
https://www.encodeproject.org/experiments/ENCSR090RLB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR090RLB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB212YEB

value: tissue

value: B6Cast F1 PND25 Female 06 thymus for Altius Stam biobank

value: ENCBS306MYU at ENCODE; https://www.encodeproject.org/ENCBS306MYU/


title: DNase-seq from heart (ENCLB267VLS)

description:
https://www.encodeproject.org/experiments/ENCSR104ZBW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR104ZBW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB267VLS

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

value: heart

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

value: 36 day

value: ENCBS108MJF at ENCODE; https://www.encodeproject.org/ENCBS108MJF/


title: ATAC-seq from lower lobe of right lung (ENCLB823EZG)

description:
https://www.encodeproject.org/experiments/ENCSR923VTG/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human lower lobe of right lung
experiment encode accession: ENCSR923VTG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB823EZG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (60 years) lower lobe of right lung tissue, preserved by cryopreservation

value: lower lobe of right lung

value: male

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS595DKG at ENCODE; https://www.encodeproject.org/ENCBS595DKG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: DNase-seq from left cerebral cortex (ENCLB601EUE)

description:
https://www.encodeproject.org/experiments/ENCSR098GIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR098GIZ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB601EUE

source_name: Mus musculus strain B6CASTF1/J female (9 months) left cerebral cortex tissue

value: left cerebral cortex

value: female

value: unknown

value: 9 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS682AVR at ENCODE; https://www.encodeproject.org/ENCBS682AVR/

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


title: Liver, Carbon tetrachloride, 48 hours, Rep3

city: Cambridge

first: Kristin

last: Knouse

state: MA

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

description: Sample 12

data_processing:
Base calls were performed by the instrument control software and further processed using the Offline Base Caller version 1.9.4 (Illumina).
Samples were mapped with STAR version 2.6.1a to the mouse genome release mm10, using a gtf file from ENSEMBL version GRCm38.91, and setting the maximum intron length (“alignIntronMax”) parameter to 50000. We ran featureCounts version 1.6 to assign reads to genes using the same gft file and setting “-s” parameter to 2.
We normalized gene counts with DESeq2 version 1.22.2.  FPKMs were calculated using the function fpkm within the DESeq2 package. The FPKMs values for the three replicates were averaged, and protein coding genes were selected based on the annotation in the gtf file.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet providing average FPKM across three replicates for each time point for each gene

molecule: polyA RNA

source_name: Liver

extract_protocol:
For all time points, livers from three male C57BL/6J mice were harvested, flushed with PBS, immediately immersed in RNAlater (Qiagen), incubated at room temperature for 24 hours, and stored at -20 °C until future use. To isolate RNA, 30 mg of each tissue was removed from RNAlater and homogenized in 700 µL of QIAzol lysis reagent (Qiagen) using the TissueRuptor homogenizer (Qiagen). RNA was purified using the miRNeasy Kit (Qiagen) according to kit instructions and eluted in 30 µL of nuclease-free water.
RNA sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (KAPA Biosystems) according to manufacturer instructions. Briefly, 0.1-1 ug of total RNA was enriched for polyadenylated sequences using oligo-dT magnetic bead capture. The enriched mRNA fraction was then fragmented and first-strand cDNA generated using random primers. Strand specificity was achieved during second-strand cDNA synthesis by replacing dTTP with dUTP to quench the second strand during amplification. The resulting cDNA was A-tailed and ligated with indexed adapters. The library was amplified using a DNA polymerase that cannot incorporate past dUTPs to quench the second strand during PCR. The libraries were quantified using a KAPA qPCR Library Quantification Kit (KAPA Biosystems) as per manufacturer instructions.

treatment_protocol: Partial hepatectomies were performed as described in Knouse et al. Cell 2018. Carbon tetrachloride was injected intraperitoneally at a dose of 2 µL/gram of 25% carbon tetrachloride diluted in corn oil.

tag: tissue

value: Liver

tag: treatment

value: Carbon tetrachloride


title: DNase-seq from spleen (ENCLB191OQH)

description:
https://www.encodeproject.org/experiments/ENCSR097TGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR097TGW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB191OQH

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

value: spleen

value: tissue

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: ENCBS851XBM at ENCODE; https://www.encodeproject.org/ENCBS851XBM/


title: Liver, Carbon tetrachloride, 24 hours, Rep3

description: Sample 11


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB039OYJ)

description:
https://www.encodeproject.org/experiments/ENCSR938OKL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR938OKL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB039OYJ

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

value: primary cell

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

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS977UPT at ENCODE; https://www.encodeproject.org/ENCBS977UPT/

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


title: DNase-seq from A673 (ENCLB958NRI)

description:
https://www.encodeproject.org/experiments/ENCSR114QAK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR114QAK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-08-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB958NRI

source_name: Homo sapiens A673 cell line

value: cell line

value: female

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS008FJR at ENCODE; https://www.encodeproject.org/ENCBS008FJR/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: DNase-seq from gastrocnemius (ENCLB372SEM)

description:
https://www.encodeproject.org/experiments/ENCSR092QSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR092QSI
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB372SEM

source_name: Mus musculus strain B6CASTF1/J male postnatal (8-10 months) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: male

value: postnatal

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS833OIM at ENCODE; https://www.encodeproject.org/ENCBS833OIM/

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


title: Liver, Carbon tetrachloride, 6 hours, Rep3

description: Sample 9

value: Liver

value: Carbon tetrachloride


title: WGBS from motor neuron (ENCLB128RQU)

description:
https://www.encodeproject.org/experiments/ENCSR222DHK/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: ALS-52 - iPSC
experiment encode accession: ENCSR222DHK
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB128RQU
fragmentation methods: shearing (Covaris generic)
size range: 450-650

source_name: Homo sapiens male adult (49 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: Donor with Amyotrophic Lateral Sclerosis

value: adult

value: 49 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS929JII at ENCODE; https://www.encodeproject.org/ENCBS929JII/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: DNase-seq from endodermal cell (ENCLB143ZWP)

description:
https://www.encodeproject.org/experiments/ENCSR940CXU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR940CXU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB143ZWP

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

value: endodermal cell

value: male

value: healthy

value: embryonic

value: not collected

value: Job Dekker, UMass

value: René Maehr

value: ENCBS543YDE at ENCODE; https://www.encodeproject.org/ENCBS543YDE/

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


title: DNase-seq from cerebellum (ENCLB749LBY)

description:
https://www.encodeproject.org/experiments/ENCSR088WAL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR088WAL
assay title: DNase-seq
assembly: mm10
encode release date: 2022-07-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB749LBY

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

value: cerebellum

value: tissue

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

value: female

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS242ZYV at ENCODE; https://www.encodeproject.org/ENCBS242ZYV/

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


title: DNase-seq from ovary (ENCLB502HSF)

description:
https://www.encodeproject.org/experiments/ENCSR087SUF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR087SUF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB502HSF

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

value: ovary

value: B6Cast F1 PND36 Female 05 ovary for Altius Stam biobank

value: 36 day

value: ENCBS998GPG at ENCODE; https://www.encodeproject.org/ENCBS998GPG/


title: DNase-seq from activated B cell (ENCLB557KXE)

description:
https://www.encodeproject.org/experiments/ENCSR109DTU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR109DTU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB557KXE

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

value: activated B cell

value: primary cell

value: male

value: adult

value: 22 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS175FVF at ENCODE; https://www.encodeproject.org/ENCBS175FVF/

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


title: Liver, Partial hepatectomy, 12 hours, Rep3

description: Sample 6

value: Liver

value: Partial hepatectomy


title: Liver, Carbon tetrachloride, 12 hours, Rep3

description: Sample 10

value: Carbon tetrachloride


title: WGBS from motor neuron (ENCLB545KAC)

description:
https://www.encodeproject.org/experiments/ENCSR222DHK/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: ALS-52 - iPSC
experiment encode accession: ENCSR222DHK
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB545KAC
fragmentation methods: shearing (Covaris generic)
size range: 450-650

value: motor neuron

value: in vitro differentiated cells

value: Donor with Amyotrophic Lateral Sclerosis

value: 49 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS840HUK at ENCODE; https://www.encodeproject.org/ENCBS840HUK/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: DNase-seq from left cerebral cortex (ENCLB711MXT)

description:
https://www.encodeproject.org/experiments/ENCSR084EBB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR084EBB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB711MXT

source_name: Mus musculus strain B6CASTF1/J female (4 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND4 Female 06 left cerebral cortex for Altius Stam biobank

value: female

value: not collected

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS770GTI at ENCODE; https://www.encodeproject.org/ENCBS770GTI/

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


title: Liver, Partial hepatectomy, 48 hours, Rep3

description: Sample 8

value: Liver

value: Partial hepatectomy


title: ATAC-seq from lower lobe of right lung (ENCLB430WSU)

description:
https://www.encodeproject.org/experiments/ENCSR923VTG/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human lower lobe of right lung
experiment encode accession: ENCSR923VTG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB430WSU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: lower lobe of right lung

value: male

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: Yiing Lin, MD, PhD

value: ENCBS595DKG at ENCODE; https://www.encodeproject.org/ENCBS595DKG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: Liver, Partial hepatectomy, 24 hours, Rep3

description: Sample 7


title: ATAC-seq from heart right ventricle (ENCLB577YGP)

description:
https://www.encodeproject.org/experiments/ENCSR491VKV/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR491VKV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB577YGP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (73 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: ischemic (EF 35%, LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 73 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS405JXY at ENCODE; https://www.encodeproject.org/ENCBS405JXY/

value: Derived from ENCODE donor ENCDO804CLC; https://www.encodeproject.org/ENCDO804CLC/


title: Liver, Partial hepatectomy, 6 hours, Rep3

description: Sample 5

value: Liver

value: Partial hepatectomy


title: DNase-seq from frontal cortex (ENCLB768BDW)

description:
https://www.encodeproject.org/experiments/ENCSR671GNH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR671GNH
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB768BDW

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

value: frontal cortex

value: B6Cast F1 PND25 male Frontal Cortex

value: male

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS742EDO at ENCODE; https://www.encodeproject.org/ENCBS742EDO/

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


title: Liver, 8 weeks, Rep3

description: Sample 4


title: ATAC-seq from heart right ventricle (ENCLB681YMJ)

description:
https://www.encodeproject.org/experiments/ENCSR491VKV/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR491VKV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB681YMJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart right ventricle

value: tissue

value: ischemic (EF 35%, LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: adult


title: DNase-seq from HCT116 (ENCLB455KXT)

description:
https://www.encodeproject.org/experiments/ENCSR498JAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR498JAW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB455KXT

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS137WSD at ENCODE; https://www.encodeproject.org/ENCBS137WSD/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Liver, Postnatal day 15, Rep3

description: Sample 2

value: Liver


title: Liver, Postnatal day 2, Rep3

description: Sample 1


title: Liver, Carbon tetrachloride, 6 hours, Rep2

description: Sample 9

value: Carbon tetrachloride


title: DNase-seq from urinary bladder (ENCLB291LCS)

description:
https://www.encodeproject.org/experiments/ENCSR885XDO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR885XDO
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB291LCS

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

value: urinary bladder

value: B6Cast F1 DPN18-20months

value: male

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS419DSC at ENCODE; https://www.encodeproject.org/ENCBS419DSC/


title: ATAC-seq from posterior vena cava (ENCLB570DMY)

description:
https://www.encodeproject.org/experiments/ENCSR913FZQ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human posterior vena cava
experiment encode accession: ENCSR913FZQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB570DMY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female child (16 years) posterior vena cava tissue, preserved by flash-freezing

value: posterior vena cava

value: tissue

value: female

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

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS382WLT at ENCODE; https://www.encodeproject.org/ENCBS382WLT/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: DNase-seq from left cerebral cortex (ENCLB014UBE)

description:
https://www.encodeproject.org/experiments/ENCSR084EBB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR084EBB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB014UBE

value: left cerebral cortex

value: B6Cast F1 PND4 Female 05 left cerebral cortex for Altius Stam biobank

value: not collected

value: 4 day

value: ENCBS593PMU at ENCODE; https://www.encodeproject.org/ENCBS593PMU/

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


title: Liver, Partial hepatectomy, 24 hours, Rep2

description: Sample 7

value: Liver

value: Partial hepatectomy


title: DNase-seq from gastrocnemius (ENCLB998HNH)

description:
https://www.encodeproject.org/experiments/ENCSR073YXT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR073YXT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB998HNH

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

value: gastrocnemius

value: tissue

value: B6Cast F1 PND36 Female 06 gastrocnemius for Altius Stam core

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS313QCX at ENCODE; https://www.encodeproject.org/ENCBS313QCX/


title: Liver, Carbon tetrachloride, 24 hours, Rep2

description: Sample 11

source_name: Liver

value: Carbon tetrachloride


title: Liver, Carbon tetrachloride, 12 hours, Rep2

description: Sample 10


title: DNase-seq from adrenal gland (ENCLB816BWG)

description:
https://www.encodeproject.org/experiments/ENCSR667KPL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR667KPL
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB816BWG

source_name: Mus musculus strain B6CASTF1/J female (8-10 months) adrenal gland tissue

value: adrenal gland

value: Stam pool A of 6 adrenal gland biosamples

value: female

value: unknown

value: 8-10 month

value: ENCBS642YJZ at ENCODE; https://www.encodeproject.org/ENCBS642YJZ/


title: DNase-seq from cerebellum (ENCLB918XOS)

description:
https://www.encodeproject.org/experiments/ENCSR671GDA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR671GDA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB918XOS

source_name: Mus musculus strain B6CASTF1/J female (9-10 months) cerebellum tissue

value: cerebellum

value: 9-10 month

value: ENCBS525ZQK at ENCODE; https://www.encodeproject.org/ENCBS525ZQK/

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


title: Liver, Partial hepatectomy, 6 hours, Rep2

description: Sample 5

value: Liver

value: Partial hepatectomy


title: Liver, 8 weeks, Rep2

description: Sample 4


title: DNase-seq from ovary (ENCLB095SOC)

description:
https://www.encodeproject.org/experiments/ENCSR087SUF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR087SUF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB095SOC

value: ovary

value: tissue

value: B6Cast F1 PND36 Female 06 ovary for Altius Stam biobank

value: not collected

value: 36 day

value: ENCBS352ROO at ENCODE; https://www.encodeproject.org/ENCBS352ROO/


title: Liver, Partial hepatectomy, 12 hours, Rep2

description: Sample 6


title: DNase-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB035LAY)

description:
https://www.encodeproject.org/experiments/ENCSR917BSW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR917BSW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB035LAY

source_name: Homo sapiens male adult (36 years) stimulated activated effector memory CD8-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-12 subunit alpha, anti-CD3 and anti-CD28 coated beads, 100 ng/mL Interleukin-12 subunit beta

value: primary cell

value: male

value: adult

value: 36 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS469YJQ at ENCODE; https://www.encodeproject.org/ENCBS469YJQ/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: ATAC-seq from posterior vena cava (ENCLB333YOD)

description:
https://www.encodeproject.org/experiments/ENCSR913FZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human posterior vena cava
experiment encode accession: ENCSR913FZQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB333YOD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: posterior vena cava

value: female

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

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS382WLT at ENCODE; https://www.encodeproject.org/ENCBS382WLT/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/