title: ATAC-seq from heart right ventricle (ENCLB491BGA)

description:
https://www.encodeproject.org/experiments/ENCSR374ZRW/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR374ZRW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB491BGA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart right ventricle

value: PGD

value: 56 year

value: ENCBS963ZRX at ENCODE; https://www.encodeproject.org/ENCBS963ZRX/

value: Derived from ENCODE donor ENCDO907YUG; https://www.encodeproject.org/ENCDO907YUG/


title: ExpA-st10.5

status: Public on Oct 16 2022

type: SRA

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

country: Germany

institute: University Freiburg Medical Center

library_source: transcriptomic

data_processing:
Quality control was done using FastQC v0.11.5
paired-end reads were mapped to Xenopus laevis genome assembly v9.2 using RNA STAR v2.6.0b-1
featureCounts v1.6.3 was used to count uniquely mapped reads per gene
statistical analysis of differential gene expression was conducted in DEseq2 v1.22.1
Assembly: X. laevis v9.2 genome assembly
Supplementary files format and content: tabular results files dervied from DESeq2
DESeq2_result_*.tabular files with GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj columns

molecule: total RNA

organism: Xenopus laevis

source_name: epidermis, animal cap explant

growth_protocol: Explants were cut from the animal portion of stage 8 Xenopus laevis embryos in 1x Modified Barth's Saline (MBS), then they were maintained in the medium for at least 1 hour to heal. After healing of explants, they were transferred to 0.5x MBS containing 0.1% of Gentamycin and cultured in that medium until they reached the indicated stage.

extract_protocol:
Total RNA was extracted using the standard Trizol protocol.
500 ng total RNA per sample was used, poly-A selection and RNA-sequencing library preparation was done using non strand massively-parallel cDNA sequencing (mRNA-Seq) protocol from Illumina, the TruSeq RNA Library Preparation Kit v2, Set A (Illumina #RS-122-2301) according to manufacturer’s recommendation. Quality and integrity of RNA was assessed with the Fragment Analyzer from Advanced Analytical by using the standard sensitivity RNA Analysis Kit (Advanced Analytical #DNF-471). All samples selected for sequencing exhibited an RNA integrity number over 8. For accurate quantitation of cDNA libraries, the QuantiFluor™dsDNA System from Promega was used. The size of final cDNA libraries was determined using the dsDNA 905 Reagent Kit (Advanced Bioanalytical #DNF-905) exhibiting a sizing of 300 bp on average. Libraries were pooled and paired-end 100bp sequencing on a HiSeq4000 was conducted at the Vincent J. Coates Genomics Sequencing Lab, University of California at Berkeley.

treatment_protocol: Control embryos remained untreated.

tag: tissue

value: epidermis, animal cap explant

tag: age

value: embryonic stages 10.5

tag: genotype

value: wt

tag: treatment

value: control


title: WGBS from motor neuron (ENCLB201YCD)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR734EFX/
***************
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 PGP - iPSC
experiment encode accession: ENCSR734EFX
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB201YCD
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

source_name: Homo sapiens male adult (55 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

tag: biosample encode accession

tag: Sex

value: male

tag: health state

value: Healthy donor

tag: dev stage

value: adult

value: 55 year

tag: lab

value: Michael Snyder, Stanford

tag: source

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

tag: link

value: ENCBS599CHX at ENCODE; https://www.encodeproject.org/ENCBS599CHX/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: ExpA-st9

value: embryonic stages 9


title: ATAC-seq from left cardiac atrium (ENCLB102PYY)

description:
https://www.encodeproject.org/experiments/ENCSR330WUK/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human left cardiac atrium
experiment encode accession: ENCSR330WUK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB102PYY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (60 years) left cardiac atrium tissue, preserved by cryopreservation

value: left cardiac atrium

value: tissue

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

value: 60 year

value: Yiing Lin, MD, PhD

value: ENCBS068SOG at ENCODE; https://www.encodeproject.org/ENCBS068SOG/

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


title: ATAC-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB055ZSA)

description:
https://www.encodeproject.org/experiments/ENCSR335XRZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR335XRZ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-11-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB055ZSA
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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, 100 ng/mL Interleukin-12 subunit beta, anti-CD3 and anti-CD28 coated beads

value: primary cell

value: 36 year

value: StemExpress

tag: treatments

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

value: ENCBS123GMT at ENCODE; https://www.encodeproject.org/ENCBS123GMT/

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


title: DNase-seq from thymus (ENCLB377SKK)

description:
https://www.encodeproject.org/experiments/ENCSR794LIK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR794LIK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB377SKK

organism: Mus musculus

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

value: thymus

tag: description

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS425KHU at ENCODE; https://www.encodeproject.org/ENCBS425KHU/

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


title: ATAC-seq from heart right ventricle (ENCLB053OLW)

description:
https://www.encodeproject.org/experiments/ENCSR327DCG/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR327DCG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB053OLW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (46 years) heart right ventricle tissue, preserved by cryopreservation

value: heart right ventricle

value: tissue

value: Hypertrophic cardiomyopathy

value: 46 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS706EBL at ENCODE; https://www.encodeproject.org/ENCBS706EBL/

value: Derived from ENCODE donor ENCDO898MAD; https://www.encodeproject.org/ENCDO898MAD/


title: ATAC-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB500SEA)

description:
https://www.encodeproject.org/experiments/ENCSR335XRZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR335XRZ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-11-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB500SEA
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: primary cell

value: 36 year

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_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; 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: ENCBS049FOY at ENCODE; https://www.encodeproject.org/ENCBS049FOY/

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


title: DNase-seq from kidney (ENCLB525XQU)

description:
https://www.encodeproject.org/experiments/ENCSR788KLG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR788KLG
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB525XQU

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

value: kidney

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

value: female

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS862ZPS at ENCODE; https://www.encodeproject.org/ENCBS862ZPS/


title: ATAC-seq from left cardiac atrium (ENCLB058LCF)

description:
https://www.encodeproject.org/experiments/ENCSR330WUK/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human left cardiac atrium
experiment encode accession: ENCSR330WUK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB058LCF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: left cardiac atrium

value: tissue

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: ENCBS068SOG at ENCODE; https://www.encodeproject.org/ENCBS068SOG/

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


title: ATAC-seq from heart right ventricle (ENCLB730SSV)

description:
https://www.encodeproject.org/experiments/ENCSR327DCG/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR327DCG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB730SSV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart right ventricle

value: Hypertrophic cardiomyopathy

value: 46 year

value: Shin Lin

value: ENCBS706EBL at ENCODE; https://www.encodeproject.org/ENCBS706EBL/

value: Derived from ENCODE donor ENCDO898MAD; https://www.encodeproject.org/ENCDO898MAD/


title: DNase-seq from kidney (ENCLB980ITX)

description:
https://www.encodeproject.org/experiments/ENCSR291KQU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR291KQU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB980ITX

source_name: Mus musculus strain B6CASTF1/J female (9 months) kidney tissue

value: kidney

value: female

value: unknown

value: 9 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS439NGT at ENCODE; https://www.encodeproject.org/ENCBS439NGT/

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


title: ExpB-st9

value: epidermis, animal cap explant

value: embryonic stages 9

value: wt

value: control


title: ATAC-seq from bile duct (ENCLB204EEU)

description:
https://www.encodeproject.org/experiments/ENCSR325NFE/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on human bile duct
experiment encode accession: ENCSR325NFE
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB204EEU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female child (16 years) bile duct tissue, preserved by flash-freezing

value: bile duct

value: tissue

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

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS499YCO at ENCODE; https://www.encodeproject.org/ENCBS499YCO/

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


title: DNase-seq from left cerebral cortex (ENCLB606USZ)

description:
https://www.encodeproject.org/experiments/ENCSR386OBA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR386OBA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB606USZ

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

value: left cerebral cortex

value: B6Cast F1 DPN18-20months

value: female

value: adult

value: 18-20 month

value: Barbara Wold, Caltech

value: ENCBS096USK at ENCODE; https://www.encodeproject.org/ENCBS096USK/


title: DNase-seq from layer of hippocampus (ENCLB034YZD)

description:
https://www.encodeproject.org/experiments/ENCSR385DQL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR385DQL
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB034YZD

source_name: Mus musculus strain B6CASTF1/J male (18-20 months) layer of hippocampus tissue

value: layer of hippocampus

value: B6Cast F1 18 - 20 month male Hippocampus

value: male

value: not collected

value: The Jackson Laboratory

value: ENCBS217UPQ at ENCODE; https://www.encodeproject.org/ENCBS217UPQ/

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


title: DNase-seq from left cerebral cortex (ENCLB580LOC)

description:
https://www.encodeproject.org/experiments/ENCSR386OBA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR386OBA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB580LOC

value: tissue

value: ENCBS495TNP at ENCODE; https://www.encodeproject.org/ENCBS495TNP/


title: DNase-seq from naive B cell (ENCLB975DCD)

description:
https://www.encodeproject.org/experiments/ENCSR326TID/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR326TID
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB975DCD

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

value: naive B cell

value: primary cell

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

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS753EAQ at ENCODE; https://www.encodeproject.org/ENCBS753EAQ/

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


title: WGBS from motor neuron (ENCLB602ZNP)

description:
https://www.encodeproject.org/experiments/ENCSR734EFX/
***************
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 PGP - iPSC
experiment encode accession: ENCSR734EFX
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB602ZNP
fragmentation methods: shearing (Covaris generic)
size range: 450-650

value: motor neuron

value: in vitro differentiated cells

value: Healthy donor

value: adult

value: 55 year

value: Michael Snyder, Stanford

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

value: ENCBS538KXP at ENCODE; https://www.encodeproject.org/ENCBS538KXP/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: DNase-seq from HCT116 (ENCLB790OLP)

description:
https://www.encodeproject.org/experiments/ENCSR595CME/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR595CME
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB790OLP

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

value: cell line

value: male

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: ENCBS296AAV at ENCODE; https://www.encodeproject.org/ENCBS296AAV/

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


title: ATAC-seq from heart left ventricle (ENCLB003XSN)

description:
https://www.encodeproject.org/experiments/ENCSR593YFB/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR593YFB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB003XSN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (42 years) heart left ventricle tissue, preserved by cryopreservation

value: heart left ventricle

value: tissue

value: female

value: Dilated cardiomyopathy

value: 42 year

value: Shin Lin

value: ENCBS241ZPK at ENCODE; https://www.encodeproject.org/ENCBS241ZPK/

value: Derived from ENCODE donor ENCDO996EBJ; https://www.encodeproject.org/ENCDO996EBJ/


title: ATAC-seq from heart left ventricle (ENCLB316RLZ)

description:
https://www.encodeproject.org/experiments/ENCSR593YFB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR593YFB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB316RLZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: adult

value: Michael Snyder, Stanford


title: DNase-seq from kidney (ENCLB354VGG)

description:
https://www.encodeproject.org/experiments/ENCSR373ZJT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR373ZJT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB354VGG

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

value: kidney

value: male

value: postnatal

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS139OSR at ENCODE; https://www.encodeproject.org/ENCBS139OSR/

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


title: DNase-seq from kidney (ENCLB706MDT)

description:
https://www.encodeproject.org/experiments/ENCSR373ZJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373ZJT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB706MDT

value: tissue

value: ENCBS235AVO at ENCODE; https://www.encodeproject.org/ENCBS235AVO/


title: ATAC-seq from ovary (ENCLB338YUU)

description:
https://www.encodeproject.org/experiments/ENCSR571JFO/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human ovary
experiment encode accession: ENCSR571JFO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB338YUU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female child (16 years) ovary tissue, preserved by cryopreservation

value: ovary

value: female

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

value: child

value: 16 year

value: Yiing Lin, MD, PhD

value: ENCBS341EVB at ENCODE; https://www.encodeproject.org/ENCBS341EVB/

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


title: DNase-seq from urinary bladder (ENCLB129ZFS)

description:
https://www.encodeproject.org/experiments/ENCSR759ZVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR759ZVU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB129ZFS

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

value: urinary bladder

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: ENCBS663HSB at ENCODE; https://www.encodeproject.org/ENCBS663HSB/


title: DNase-seq from frontal cortex (ENCLB408ELA)

description:
https://www.encodeproject.org/experiments/ENCSR391LJN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR391LJN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB408ELA

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

value: frontal cortex

value: B6Cast F1 PND36 female Frontal Cortex

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS359RPC at ENCODE; https://www.encodeproject.org/ENCBS359RPC/


title: ATAC-seq from ovary (ENCLB759HCW)

description:
https://www.encodeproject.org/experiments/ENCSR571JFO/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human ovary
experiment encode accession: ENCSR571JFO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB759HCW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: ovary

value: tissue

value: female

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

value: child

value: Michael Snyder, Stanford


title: ATAC-seq from fallopian tube (ENCLB946DTY)

description:
https://www.encodeproject.org/experiments/ENCSR565DSD/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human fallopian tube
experiment encode accession: ENCSR565DSD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB946DTY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (61 years) fallopian tube tissue, preserved by flash-freezing

value: fallopian tube

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

value: 61 year

value: Yiing Lin, MD, PhD

value: ENCBS041TLB at ENCODE; https://www.encodeproject.org/ENCBS041TLB/

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


title: DNase-seq from right cerebral cortex (ENCLB382XIZ)

description:
https://www.encodeproject.org/experiments/ENCSR751LYJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR751LYJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB382XIZ

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

value: right cerebral cortex

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: ENCBS841VCR at ENCODE; https://www.encodeproject.org/ENCBS841VCR/

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


title: WGBS from motor neuron (ENCLB677ZQW)

description:
https://www.encodeproject.org/experiments/ENCSR310GNQ/
***************
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-29 - iPSC
experiment encode accession: ENCSR310GNQ
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB677ZQW
fragmentation methods: shearing (Covaris generic)
size range: 450-650

source_name: Homo sapiens male adult (47 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: Donor with Amyotrophic Lateral Sclerosis

value: 47 year

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

value: ENCBS199CPA at ENCODE; https://www.encodeproject.org/ENCBS199CPA/

value: Derived from ENCODE donor ENCDO908CUN; https://www.encodeproject.org/ENCDO908CUN/


title: WGBS from motor neuron (ENCLB396TQW)

description:
https://www.encodeproject.org/experiments/ENCSR310GNQ/
***************
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-29 - iPSC
experiment encode accession: ENCSR310GNQ
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB396TQW
fragmentation methods: shearing (Covaris generic)
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS928FQF at ENCODE; https://www.encodeproject.org/ENCBS928FQF/


title: DNase-seq from lung (ENCLB360XDJ)

description:
https://www.encodeproject.org/experiments/ENCSR756QHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR756QHG
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB360XDJ

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

value: lung

value: tissue

value: female

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS529ADM at ENCODE; https://www.encodeproject.org/ENCBS529ADM/


title: DNase-seq from right cerebral cortex (ENCLB926KKF)

description:
https://www.encodeproject.org/experiments/ENCSR751LYJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR751LYJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB926KKF

value: right cerebral cortex

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: ENCBS377OZR at ENCODE; https://www.encodeproject.org/ENCBS377OZR/


title: DNase-seq from HCT116 (ENCLB875FPP)

description:
https://www.encodeproject.org/experiments/ENCSR595CME/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR595CME
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB875FPP

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: ENCBS783IUR at ENCODE; https://www.encodeproject.org/ENCBS783IUR/

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


title: DNase-seq from frontal cortex (ENCLB854VAW)

description:
https://www.encodeproject.org/experiments/ENCSR391LJN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR391LJN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB854VAW

value: frontal cortex

value: tissue

value: B6Cast F1 PND36 female Frontal Cortex

value: female

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: ENCBS063LUJ at ENCODE; https://www.encodeproject.org/ENCBS063LUJ/

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


title: DNase-seq from ovary (ENCLB050RCU)

description:
https://www.encodeproject.org/experiments/ENCSR362ZRQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR362ZRQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB050RCU

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

value: ovary

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS273GQW at ENCODE; https://www.encodeproject.org/ENCBS273GQW/


title: ATAC-seq from fallopian tube (ENCLB901UJK)

description:
https://www.encodeproject.org/experiments/ENCSR565DSD/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human fallopian tube
experiment encode accession: ENCSR565DSD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB901UJK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: fallopian tube

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

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS041TLB at ENCODE; https://www.encodeproject.org/ENCBS041TLB/

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


title: DNase-seq from ovary (ENCLB535YZQ)

description:
https://www.encodeproject.org/experiments/ENCSR362ZRQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR362ZRQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB535YZQ

value: tissue

value: female

value: ENCBS361UPJ at ENCODE; https://www.encodeproject.org/ENCBS361UPJ/


title: DNase-seq from layer of hippocampus (ENCLB516CWE)

description:
https://www.encodeproject.org/experiments/ENCSR385DQL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR385DQL
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB516CWE

value: layer of hippocampus

value: B6Cast F1 18 - 20 month male Hippocampus

value: male

value: not collected

value: Barbara Wold, Caltech

value: ENCBS198CFI at ENCODE; https://www.encodeproject.org/ENCBS198CFI/

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


title: DNase-seq from T-cell (ENCLB759FJQ)

description:
https://www.encodeproject.org/experiments/ENCSR560MXA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR560MXA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB759FJQ

source_name: Homo sapiens female adult (21 years) T-cell primary cell

value: T-cell

value: primary cell

value: adult

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS860CTC at ENCODE; https://www.encodeproject.org/ENCBS860CTC/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: WGBS from motor neuron (ENCLB229KTN)

description:
https://www.encodeproject.org/experiments/ENCSR707MKB/
***************
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 - iNPC
experiment encode accession: ENCSR707MKB
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB229KTN
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: 49 year

value: Michael Snyder, Stanford

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

value: ENCBS624KMS at ENCODE; https://www.encodeproject.org/ENCBS624KMS/

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


title: WGBS from motor neuron (ENCLB567IQG)

description:
https://www.encodeproject.org/experiments/ENCSR707MKB/
***************
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 - iNPC
experiment encode accession: ENCSR707MKB
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB567IQG
fragmentation methods: shearing (Covaris generic)
size range: 450-650

value: male

value: ENCBS755WKM at ENCODE; https://www.encodeproject.org/ENCBS755WKM/


title: DNase-seq from left cerebral cortex (ENCLB058VUB)

description:
https://www.encodeproject.org/experiments/ENCSR357REQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR357REQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB058VUB

source_name: Mus musculus strain B6CASTF1/J female (14 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND14 Female 06 left cerebral cortex for Altius Stam biobank

value: female

value: not collected

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS788FXW at ENCODE; https://www.encodeproject.org/ENCBS788FXW/

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


title: ATAC-seq from bile duct (ENCLB542SDR)

description:
https://www.encodeproject.org/experiments/ENCSR325NFE/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human bile duct
experiment encode accession: ENCSR325NFE
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB542SDR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female child (16 years) bile duct tissue, preserved by flash-freezing

value: bile duct

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

value: child

value: 16 year

value: Yiing Lin, MD, PhD

value: ENCBS499YCO at ENCODE; https://www.encodeproject.org/ENCBS499YCO/

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


title: ATAC-seq from mucosa of urinary bladder (ENCLB134VYG)

description:
https://www.encodeproject.org/experiments/ENCSR548SSP/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human mucosa of urinary bladder
experiment encode accession: ENCSR548SSP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB134VYG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) mucosa of urinary bladder tissue, preserved by flash-freezing

value: mucosa of urinary bladder

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

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: ENCBS883TKQ at ENCODE; https://www.encodeproject.org/ENCBS883TKQ/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: DNase-seq from urinary bladder (ENCLB868HOX)

description:
https://www.encodeproject.org/experiments/ENCSR759ZVU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR759ZVU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB868HOX

value: urinary bladder

value: tissue

value: B6Cast F1 DPN18-20months

value: female

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS061HAV at ENCODE; https://www.encodeproject.org/ENCBS061HAV/


title: DNase-seq from left cerebral cortex (ENCLB283WPI)

description:
https://www.encodeproject.org/experiments/ENCSR357REQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR357REQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB283WPI

value: left cerebral cortex

value: B6Cast F1 PND14 Female 05 left cerebral cortex for Altius Stam biobank

value: not collected

value: 14 day

value: ENCBS167SOA at ENCODE; https://www.encodeproject.org/ENCBS167SOA/

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


title: DNase-seq from right cerebral cortex (ENCLB704ZLN)

description:
https://www.encodeproject.org/experiments/ENCSR740POH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR740POH
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB704ZLN

source_name: Mus musculus strain B6CASTF1/J male (14 days) right cerebral cortex tissue

value: right cerebral cortex

value: B6Cast F1 PND14 Male 06 right cerebral cortex for Altius Stam biobank

value: male

value: ENCBS619TUD at ENCODE; https://www.encodeproject.org/ENCBS619TUD/


title: ATAC-seq from mucosa of urinary bladder (ENCLB046RGL)

description:
https://www.encodeproject.org/experiments/ENCSR548SSP/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human mucosa of urinary bladder
experiment encode accession: ENCSR548SSP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB046RGL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: mucosa of urinary bladder

value: tissue

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

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS883TKQ at ENCODE; https://www.encodeproject.org/ENCBS883TKQ/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: DNase-seq from spleen (ENCLB405GXK)

description:
https://www.encodeproject.org/experiments/ENCSR736DMJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR736DMJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB405GXK

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

value: spleen

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

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS936CHA at ENCODE; https://www.encodeproject.org/ENCBS936CHA/


title: DNase-seq from kidney (ENCLB872QZJ)

description:
https://www.encodeproject.org/experiments/ENCSR352FCL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR352FCL
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB872QZJ

source_name: Mus musculus strain 5xFAD/CAST male (9 months) kidney tissue

value: kidney

value: male

value: unknown

value: 9 month

value: ENCBS105BQU at ENCODE; https://www.encodeproject.org/ENCBS105BQU/

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


title: DNase-seq from frontal cortex (ENCLB524WBM)

description:
https://www.encodeproject.org/experiments/ENCSR356UVK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR356UVK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB524WBM

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

value: frontal cortex

value: tissue

value: B6Cast F1 PND14 3x male Frontal Cortex

value: 14 day

value: ENCBS620KWH at ENCODE; https://www.encodeproject.org/ENCBS620KWH/

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


title: ATAC-seq from sciatic nerve (ENCLB768TWI)

description:
https://www.encodeproject.org/experiments/ENCSR533WFB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human sciatic nerve
experiment encode accession: ENCSR533WFB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB768TWI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: sciatic nerve

value: female

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

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS833LUO at ENCODE; https://www.encodeproject.org/ENCBS833LUO/

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


title: DNase-seq from frontal cortex (ENCLB092LKB)

description:
https://www.encodeproject.org/experiments/ENCSR356UVK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR356UVK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB092LKB

value: male

value: not collected

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS579IBG at ENCODE; https://www.encodeproject.org/ENCBS579IBG/


title: DNase-seq from HCT116 (ENCLB240QSD)

description:
https://www.encodeproject.org/experiments/ENCSR542UWN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR542UWN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB240QSD

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 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: ENCBS002PXM at ENCODE; https://www.encodeproject.org/ENCBS002PXM/

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


title: ATAC-seq from spleen (ENCLB630PWH)

description:
https://www.encodeproject.org/experiments/ENCSR182VGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human spleen
experiment encode accession: ENCSR182VGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB630PWH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) spleen tissue, preserved by cryopreservation

value: spleen

value: tissue

value: female

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

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: ENCBS393LZH at ENCODE; https://www.encodeproject.org/ENCBS393LZH/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: DNase-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB946NLZ)

description:
https://www.encodeproject.org/experiments/ENCSR534RXN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR534RXN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB946NLZ

source_name: Homo sapiens female adult (21 years) CD4-positive, CD25-positive, alpha-beta regulatory T primary cell

value: primary cell

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS155DPF at ENCODE; https://www.encodeproject.org/ENCBS155DPF/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: DNase-seq from frontal cortex (ENCLB565FCI)

description:
https://www.encodeproject.org/experiments/ENCSR338GYD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR338GYD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB565FCI

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

value: frontal cortex

value: B6Cast F1 PND25 female Frontal Cortex

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS346AOV at ENCODE; https://www.encodeproject.org/ENCBS346AOV/

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


title: DNase-seq from frontal cortex (ENCLB734VKM)

description:
https://www.encodeproject.org/experiments/ENCSR338GYD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR338GYD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB734VKM

value: tissue

value: female

value: ENCBS799EGA at ENCODE; https://www.encodeproject.org/ENCBS799EGA/


title: ATAC-seq from sciatic nerve (ENCLB656HHJ)

description:
https://www.encodeproject.org/experiments/ENCSR533WFB/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human sciatic nerve
experiment encode accession: ENCSR533WFB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB656HHJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: sciatic nerve

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

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS833LUO at ENCODE; https://www.encodeproject.org/ENCBS833LUO/

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


title: DNase-seq from layer of hippocampus (ENCLB959TFM)

description:
https://www.encodeproject.org/experiments/ENCSR348NWY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR348NWY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB959TFM

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

value: layer of hippocampus

value: B6Cast F1 PND25 female Hippocampus

value: not collected

value: ENCBS331UAU at ENCODE; https://www.encodeproject.org/ENCBS331UAU/


title: DNase-seq from frontal cortex (ENCLB682YUS)

description:
https://www.encodeproject.org/experiments/ENCSR325RZJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR325RZJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB682YUS

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

value: frontal cortex

value: B6Cast F1 2 month male Frontal Cortex

value: male

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS249YDU at ENCODE; https://www.encodeproject.org/ENCBS249YDU/


title: DNase-seq from HCT116 (ENCLB161GYV)

description:
https://www.encodeproject.org/experiments/ENCSR521WNU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR521WNU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB161GYV

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: adult

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: ENCBS016NYI at ENCODE; https://www.encodeproject.org/ENCBS016NYI/

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


title: DNase-seq from CD4-positive, alpha-beta memory T cell (ENCLB392MLU)

description:
https://www.encodeproject.org/experiments/ENCSR526TFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR526TFD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB392MLU

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

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

value: primary cell

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

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS224UJU at ENCODE; https://www.encodeproject.org/ENCBS224UJU/

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


title: DNase-seq from naive B cell (ENCLB443PSG)

description:
https://www.encodeproject.org/experiments/ENCSR184TUE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR184TUE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB443PSG

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

value: naive B cell

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

value: ENCBS860UYP at ENCODE; https://www.encodeproject.org/ENCBS860UYP/

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


title: DNase-seq from cerebellum (ENCLB650DQL)

description:
https://www.encodeproject.org/experiments/ENCSR335MHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR335MHR
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB650DQL

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

value: cerebellum

value: tissue

value: female

value: unknown

value: 11 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS437UZX at ENCODE; https://www.encodeproject.org/ENCBS437UZX/

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


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB757UUN)

description:
https://www.encodeproject.org/experiments/ENCSR181OGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR181OGW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB757UUN

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: ENCBS462QFO at ENCODE; https://www.encodeproject.org/ENCBS462QFO/

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


title: DNase-seq from spleen (ENCLB775PXJ)

description:
https://www.encodeproject.org/experiments/ENCSR597QYA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR597QYA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB775PXJ

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

value: spleen

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

value: 36 day

value: ENCBS990JDQ at ENCODE; https://www.encodeproject.org/ENCBS990JDQ/


title: DNase-seq from cerebellum (ENCLB044VXU)

description:
https://www.encodeproject.org/experiments/ENCSR336MBU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR336MBU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB044VXU

source_name: Mus musculus strain 5xFAD/CAST male (11-12 months) cerebellum tissue

value: cerebellum

value: tissue

value: male

value: unknown

value: 11-12 month

value: ENCBS989NWY at ENCODE; https://www.encodeproject.org/ENCBS989NWY/

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


title: WGBS from motor neuron (ENCLB387VFA)

description:
https://www.encodeproject.org/experiments/ENCSR519EKA/
***************
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-28 - iPSC
experiment encode accession: ENCSR519EKA
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB387VFA
fragmentation methods: shearing (Covaris generic)
size range: 450-650

source_name: Homo sapiens male adult (47 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: Donor with Amyotrophic Lateral Sclerosis

value: adult

value: 47 year

value: Michael Snyder, Stanford

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

value: ENCBS893TUZ at ENCODE; https://www.encodeproject.org/ENCBS893TUZ/

value: Derived from ENCODE donor ENCDO565NIZ; https://www.encodeproject.org/ENCDO565NIZ/


title: ATAC-seq from spleen (ENCLB256QPQ)

description:
https://www.encodeproject.org/experiments/ENCSR182VGJ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human spleen
experiment encode accession: ENCSR182VGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB256QPQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: spleen

value: female

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

value: 59 year

value: Yiing Lin, MD, PhD

value: ENCBS393LZH at ENCODE; https://www.encodeproject.org/ENCBS393LZH/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: DNase-seq from HCT116 (ENCLB477IQK)

description:
https://www.encodeproject.org/experiments/ENCSR980GWI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR980GWI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB477IQK

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS567QTT at ENCODE; https://www.encodeproject.org/ENCBS567QTT/

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


title: WGBS from motor neuron (ENCLB252YID)

description:
https://www.encodeproject.org/experiments/ENCSR519EKA/
***************
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-28 - iPSC
experiment encode accession: ENCSR519EKA
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB252YID
fragmentation methods: shearing (Covaris generic)
size range: 450-650

value: motor neuron

value: in vitro differentiated cells

value: Donor with Amyotrophic Lateral Sclerosis

value: adult

value: 47 year

value: Michael Snyder, Stanford

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

value: ENCBS603HOB at ENCODE; https://www.encodeproject.org/ENCBS603HOB/


title: DNase-seq from spleen (ENCLB416TVG)

description:
https://www.encodeproject.org/experiments/ENCSR597QYA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR597QYA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB416TVG

value: spleen

value: tissue

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

value: female

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS821ORP at ENCODE; https://www.encodeproject.org/ENCBS821ORP/

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


title: DNase-seq from layer of hippocampus (ENCLB760QYM)

description:
https://www.encodeproject.org/experiments/ENCSR348NWY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR348NWY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB760QYM

value: layer of hippocampus

value: B6Cast F1 PND25 female Hippocampus

value: 25 day

value: ENCBS574ZZC at ENCODE; https://www.encodeproject.org/ENCBS574ZZC/


title: DNase-seq from ovary (ENCLB396OMU)

description:
https://www.encodeproject.org/experiments/ENCSR591ILA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR591ILA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB396OMU

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

value: ovary

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

value: 14 day

value: ENCBS181AOU at ENCODE; https://www.encodeproject.org/ENCBS181AOU/


title: ATAC-seq from spleen (ENCLB157MNP)

description:
https://www.encodeproject.org/experiments/ENCSR979TCG/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human spleen
experiment encode accession: ENCSR979TCG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB157MNP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) spleen tissue, preserved by cryopreservation

value: spleen

value: tissue

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

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS923MCY at ENCODE; https://www.encodeproject.org/ENCBS923MCY/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: ATAC-seq from spleen (ENCLB503BNE)

description:
https://www.encodeproject.org/experiments/ENCSR979TCG/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human spleen
experiment encode accession: ENCSR979TCG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB503BNE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: female


title: DNase-seq from layer of hippocampus (ENCLB565OED)

description:
https://www.encodeproject.org/experiments/ENCSR581XCY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR581XCY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB565OED

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

value: layer of hippocampus

value: Stam pool I of 2 layer of hippocampus biosamples

value: male

value: unknown

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS805PPZ at ENCODE; https://www.encodeproject.org/ENCBS805PPZ/

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


title: ATAC-seq from bile duct (ENCLB218REE)

description:
https://www.encodeproject.org/experiments/ENCSR174MLD/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human bile duct
experiment encode accession: ENCSR174MLD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB218REE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: bile duct

value: tissue

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

value: 41 year

value: ENCBS897NAY at ENCODE; https://www.encodeproject.org/ENCBS897NAY/

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


title: ATAC-seq from bile duct (ENCLB955CWJ)

description:
https://www.encodeproject.org/experiments/ENCSR174MLD/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human bile duct
experiment encode accession: ENCSR174MLD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB955CWJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: adult

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD


title: DNase-seq from layer of hippocampus (ENCLB093CWZ)

description:
https://www.encodeproject.org/experiments/ENCSR315NES/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR315NES
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB093CWZ

source_name: Mus musculus strain B6CASTF1/J female (8-10 months) layer of hippocampus tissue

value: layer of hippocampus

value: Stam pool F of 2 layer of hippocampus biosamples

value: female

value: ENCBS581NAA at ENCODE; https://www.encodeproject.org/ENCBS581NAA/


title: DNase-seq from left cerebral cortex (ENCLB015YIH)

description:
https://www.encodeproject.org/experiments/ENCSR559CFZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR559CFZ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB015YIH

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

value: left cerebral cortex

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

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: ENCBS200FUK at ENCODE; https://www.encodeproject.org/ENCBS200FUK/


title: DNase-seq from layer of hippocampus (ENCLB427APZ)

description:
https://www.encodeproject.org/experiments/ENCSR581XCY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR581XCY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB427APZ

value: tissue

value: Stam pool L of 2 layer of hippocampus biosamples

value: male

value: unknown

value: 8-10 month

value: The Jackson Laboratory

value: ENCBS615CKD at ENCODE; https://www.encodeproject.org/ENCBS615CKD/

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


title: DNase-seq from spleen (ENCLB558CQR)

description:
https://www.encodeproject.org/experiments/ENCSR718NBH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR718NBH
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB558CQR

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

value: spleen

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

value: 14 day

value: ENCBS861CKV at ENCODE; https://www.encodeproject.org/ENCBS861CKV/


title: DNase-seq from right cerebral cortex (ENCLB592PXH)

description:
https://www.encodeproject.org/experiments/ENCSR551ZTT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR551ZTT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB592PXH

source_name: Mus musculus strain B6CASTF1/J male (36 days) right cerebral cortex tissue

value: right cerebral cortex

value: B6Cast F1 PND36 Male 06 right cerebral cortex for Altius Stam biobank

value: 36 day

value: ENCBS952MWI at ENCODE; https://www.encodeproject.org/ENCBS952MWI/


title: DNase-seq from layer of hippocampus (ENCLB551UZF)

description:
https://www.encodeproject.org/experiments/ENCSR315NES/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR315NES
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB551UZF

value: layer of hippocampus

value: Stam pool C of 2 layer of hippocampus biosamples

value: female

value: Barbara Wold, Caltech

value: ENCBS101NOF at ENCODE; https://www.encodeproject.org/ENCBS101NOF/


title: DNase-seq from right cerebral cortex (ENCLB284PIW)

description:
https://www.encodeproject.org/experiments/ENCSR571UMX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR571UMX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB284PIW

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

value: tissue

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: ENCBS287ZLU at ENCODE; https://www.encodeproject.org/ENCBS287ZLU/


title: DNase-seq from right cerebral cortex (ENCLB422VSX)

description:
https://www.encodeproject.org/experiments/ENCSR571UMX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR571UMX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB422VSX

value: The Jackson Laboratory

value: ENCBS867AAY at ENCODE; https://www.encodeproject.org/ENCBS867AAY/

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


title: ATAC-seq from cardiac septum (ENCLB980EVJ)

description:
https://www.encodeproject.org/experiments/ENCSR167SYF/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human cardiac septum
experiment encode accession: ENCSR167SYF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB980EVJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (41 years) cardiac septum tissue, preserved by cryopreservation

value: cardiac septum

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

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS961YCS at ENCODE; https://www.encodeproject.org/ENCBS961YCS/

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


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB370WEY)

description:
https://www.encodeproject.org/experiments/ENCSR304CXS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR304CXS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB370WEY

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

value: primary cell

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

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS488XUS at ENCODE; https://www.encodeproject.org/ENCBS488XUS/

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


title: ATAC-seq from kidney (ENCLB534ZLU)

description:
https://www.encodeproject.org/experiments/ENCSR297VGU/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human kidney
experiment encode accession: ENCSR297VGU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB534ZLU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) kidney tissue, preserved by cryopreservation

value: kidney

value: tissue

value: female

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

value: adult

value: 47 year

value: ENCBS659VRN at ENCODE; https://www.encodeproject.org/ENCBS659VRN/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: ATAC-seq from kidney (ENCLB940EFI)

description:
https://www.encodeproject.org/experiments/ENCSR297VGU/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human kidney
experiment encode accession: ENCSR297VGU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB940EFI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD


title: DNase-seq from adrenal gland (ENCLB586DOF)

description:
https://www.encodeproject.org/experiments/ENCSR551FWJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR551FWJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB586DOF

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

value: adrenal gland

value: Stam pool J of 6 adrenal gland biosamples

value: male

value: unknown

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS497OCW at ENCODE; https://www.encodeproject.org/ENCBS497OCW/

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


title: DNase-seq from urinary bladder (ENCLB816NJE)

description:
https://www.encodeproject.org/experiments/ENCSR193XFZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR193XFZ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB816NJE

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

value: urinary bladder

value: tissue

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

value: female

value: not collected

value: 36 day

value: ENCBS189KWB at ENCODE; https://www.encodeproject.org/ENCBS189KWB/


title: ATAC-seq from central memory CD8-positive, alpha-beta T cell (ENCLB191ZEE)

description:
https://www.encodeproject.org/experiments/ENCSR165FYY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR165FYY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB191ZEE
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (36 years) central memory CD8-positive, alpha-beta T primary cell

value: primary cell

value: adult

value: 36 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS042RAQ at ENCODE; https://www.encodeproject.org/ENCBS042RAQ/

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


title: DNase-seq from urinary bladder (ENCLB479VGK)

description:
https://www.encodeproject.org/experiments/ENCSR193XFZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR193XFZ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB479VGK

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

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS479NLQ at ENCODE; https://www.encodeproject.org/ENCBS479NLQ/


title: ATAC-seq from central memory CD8-positive, alpha-beta T cell (ENCLB215UTX)

description:
https://www.encodeproject.org/experiments/ENCSR165FYY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR165FYY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB215UTX
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: male

value: ENCBS185KSL at ENCODE; https://www.encodeproject.org/ENCBS185KSL/


title: DNase-seq from layer of hippocampus (ENCLB393PHN)

description:
https://www.encodeproject.org/experiments/ENCSR544UYQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR544UYQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB393PHN

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

value: layer of hippocampus

value: tissue

value: B6Cast F1 2 month female Hippocampus

value: female

value: 2 month

value: ENCBS763HFB at ENCODE; https://www.encodeproject.org/ENCBS763HFB/

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


title: ATAC-seq from spleen (ENCLB458ZIS)

description:
https://www.encodeproject.org/experiments/ENCSR158KCS/
***************
biological replicate number: 1
technical replicate number: 1
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: ENCLB458ZIS
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: 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: ENCBS327LSG at ENCODE; https://www.encodeproject.org/ENCBS327LSG/

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


title: DNase-seq from layer of hippocampus (ENCLB537CNL)

description:
https://www.encodeproject.org/experiments/ENCSR544UYQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR544UYQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB537CNL

value: not collected

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS293BMI at ENCODE; https://www.encodeproject.org/ENCBS293BMI/


title: ATAC-seq from cardiac septum (ENCLB664DWB)

description:
https://www.encodeproject.org/experiments/ENCSR167SYF/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human cardiac septum
experiment encode accession: ENCSR167SYF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB664DWB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: cardiac septum

value: tissue

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

value: 41 year

value: ENCBS961YCS at ENCODE; https://www.encodeproject.org/ENCBS961YCS/

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


title: DNase-seq from HCT116 (ENCLB370FUH)

description:
https://www.encodeproject.org/experiments/ENCSR163KCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR163KCQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB370FUH

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

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS140VNG at ENCODE; https://www.encodeproject.org/ENCBS140VNG/

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


title: WGBS from motor neuron (ENCLB771WTH)

description:
https://www.encodeproject.org/experiments/ENCSR978LOX/
***************
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 - iPSC
experiment encode accession: ENCSR978LOX
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB771WTH
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: Healthy donor

value: child

value: 6 year

value: Michael Snyder, Stanford

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

value: ENCBS486ZCH at ENCODE; https://www.encodeproject.org/ENCBS486ZCH/

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


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB413ZUO)

description:
https://www.encodeproject.org/experiments/ENCSR302MYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR302MYX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB413ZUO

value: primary cell

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

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS112SIZ at ENCODE; https://www.encodeproject.org/ENCBS112SIZ/

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


title: DNase-seq from frontal cortex (ENCLB633KLM)

description:
https://www.encodeproject.org/experiments/ENCSR193OYD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR193OYD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB633KLM

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

value: frontal cortex

value: tissue

value: B6Cast F1 PND36 male Frontal Cortex

value: male

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS300SMS at ENCODE; https://www.encodeproject.org/ENCBS300SMS/

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


title: DNase-seq from kidney (ENCLB250WBY)

description:
https://www.encodeproject.org/experiments/ENCSR788KLG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR788KLG
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB250WBY

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

value: kidney

value: B6Cast F1 PND36 Female 05 kidney for Altius Stam core

value: female

value: ENCBS128RPN at ENCODE; https://www.encodeproject.org/ENCBS128RPN/


title: DNase-seq from CD8-positive, alpha-beta memory T cell (ENCLB656XQS)

description:
https://www.encodeproject.org/experiments/ENCSR295UXT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR295UXT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB656XQS

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

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

value: primary cell

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

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS211ZQL at ENCODE; https://www.encodeproject.org/ENCBS211ZQL/

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


title: DNase-seq from adrenal gland (ENCLB640BIW)

description:
https://www.encodeproject.org/experiments/ENCSR551FWJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR551FWJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB640BIW

value: adrenal gland

value: tissue

value: Stam pool G of 6 adrenal gland biosamples

value: male

value: unknown

value: 8-10 month

value: ENCBS688CXG at ENCODE; https://www.encodeproject.org/ENCBS688CXG/


title: ATAC-seq from aorta (ENCLB769HRF)

description:
https://www.encodeproject.org/experiments/ENCSR295TFY/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human aorta
experiment encode accession: ENCSR295TFY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB769HRF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: aorta

value: female

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

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS349YCX at ENCODE; https://www.encodeproject.org/ENCBS349YCX/

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


title: DNase-seq from heart (ENCLB616FHZ)

description:
https://www.encodeproject.org/experiments/ENCSR541MWB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR541MWB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB616FHZ

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

value: heart

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS539HSZ at ENCODE; https://www.encodeproject.org/ENCBS539HSZ/

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


title: ATAC-seq from aorta (ENCLB086YXP)

description:
https://www.encodeproject.org/experiments/ENCSR295TFY/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human aorta
experiment encode accession: ENCSR295TFY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB086YXP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: aorta

value: tissue


title: DNase-seq from left cerebral cortex (ENCLB997DSL)

description:
https://www.encodeproject.org/experiments/ENCSR538SKV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR538SKV
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB997DSL

source_name: Mus musculus strain 5xFAD/CAST male (11 months) left cerebral cortex tissue

value: left cerebral cortex

value: male

value: unknown

value: 11 month

value: ENCBS954UZH at ENCODE; https://www.encodeproject.org/ENCBS954UZH/

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


title: ATAC-seq from psoas muscle (ENCLB864HGI)

description:
https://www.encodeproject.org/experiments/ENCSR154UWN/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human psoas muscle
experiment encode accession: ENCSR154UWN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB864HGI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female child (16 years) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

value: female

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

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS438ULC at ENCODE; https://www.encodeproject.org/ENCBS438ULC/

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


title: DNase-seq from cerebellum (ENCLB040TVG)

description:
https://www.encodeproject.org/experiments/ENCSR176CFX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR176CFX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB040TVG

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

value: cerebellum

value: B6Cast F1 PND36 Female 05 cerebellum for Altius Stam core

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS679DFS at ENCODE; https://www.encodeproject.org/ENCBS679DFS/

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


title: DNase-seq from heart (ENCLB414ALI)

description:
https://www.encodeproject.org/experiments/ENCSR541MWB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541MWB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB414ALI

value: heart

value: tissue

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: ENCBS440AHR at ENCODE; https://www.encodeproject.org/ENCBS440AHR/


title: WGBS from motor neuron (ENCLB789HCY)

description:
https://www.encodeproject.org/experiments/ENCSR978LOX/
***************
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 - iPSC
experiment encode accession: ENCSR978LOX
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB789HCY
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: ENCBS300FSG at ENCODE; https://www.encodeproject.org/ENCBS300FSG/

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


title: DNase-seq from frontal cortex (ENCLB738DQG)

description:
https://www.encodeproject.org/experiments/ENCSR193OYD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR193OYD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB738DQG

value: frontal cortex

value: B6Cast F1 PND36 male Frontal Cortex

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS682SCB at ENCODE; https://www.encodeproject.org/ENCBS682SCB/

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


title: DNase-seq from layer of hippocampus (ENCLB786TUV)

description:
https://www.encodeproject.org/experiments/ENCSR154CWQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR154CWQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB786TUV

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

value: layer of hippocampus

value: tissue

value: female

value: unknown

value: 9-10 month

value: ENCBS558DJW at ENCODE; https://www.encodeproject.org/ENCBS558DJW/


title: DNase-seq from cerebellum (ENCLB156BZF)

description:
https://www.encodeproject.org/experiments/ENCSR176CFX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR176CFX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB156BZF

value: cerebellum

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

value: ENCBS209BGT at ENCODE; https://www.encodeproject.org/ENCBS209BGT/


title: DNase-seq from layer of hippocampus (ENCLB621YUJ)

description:
https://www.encodeproject.org/experiments/ENCSR529QVB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR529QVB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB621YUJ

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

value: male

value: 9-11 month

value: ENCBS572EPH at ENCODE; https://www.encodeproject.org/ENCBS572EPH/

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


title: DNase-seq from lung (ENCLB707IQQ)

description:
https://www.encodeproject.org/experiments/ENCSR293SQC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR293SQC
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB707IQQ

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

value: lung

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

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: ENCBS306YPM at ENCODE; https://www.encodeproject.org/ENCBS306YPM/


title: DNase-seq from cerebellum (ENCLB642XAQ)

description:
https://www.encodeproject.org/experiments/ENCSR181OOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR181OOF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-08-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB642XAQ
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

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

value: tissue

value: B6Cast F1 PND4 3x Males 06 cerebellum for Altius Stam core

value: 4 day

value: The Jackson Laboratory

value: ENCBS716FWV at ENCODE; https://www.encodeproject.org/ENCBS716FWV/

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


title: ATAC-seq from psoas muscle (ENCLB080PUU)

description:
https://www.encodeproject.org/experiments/ENCSR154UWN/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human psoas muscle
experiment encode accession: ENCSR154UWN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB080PUU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: psoas muscle

value: female

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

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS438ULC at ENCODE; https://www.encodeproject.org/ENCBS438ULC/

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


title: DNase-seq from right cerebral cortex (ENCLB883LGS)

description:
https://www.encodeproject.org/experiments/ENCSR293BBH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR293BBH
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB883LGS

source_name: Mus musculus strain B6CASTF1/J female (36 days) right cerebral cortex tissue

value: right cerebral cortex

value: B6Cast F1 PND36 Female 06 right cerebral cortex for Altius Stam biobank

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: ENCBS858WRI at ENCODE; https://www.encodeproject.org/ENCBS858WRI/


title: DNase-seq from lung (ENCLB943NUW)

description:
https://www.encodeproject.org/experiments/ENCSR285LPX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR285LPX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB943NUW

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

value: lung

value: tissue

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

value: 10 day

value: The Jackson Laboratory

value: ENCBS946OEN at ENCODE; https://www.encodeproject.org/ENCBS946OEN/


title: DNase-seq from HCT116 (ENCLB698FEC)

description:
https://www.encodeproject.org/experiments/ENCSR702VYW/
***************
biological replicate number: 1
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: ENCLB698FEC

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

value: cell line

value: male

value: colorectal carcinoma

value: adult

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: ENCBS197XQV at ENCODE; https://www.encodeproject.org/ENCBS197XQV/

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