title: DNase-seq from HCT116 (ENCLB689WLQ)

description:
https://www.encodeproject.org/experiments/ENCSR498JAW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR498JAW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB689WLQ

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: ENCBS467OOU at ENCODE; https://www.encodeproject.org/ENCBS467OOU/

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


title: ATAC-seq from heart left ventricle (ENCLB672QMY)

status: Public on Oct 16 2022

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR899YEP/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR899YEP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB672QMY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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 (61 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

tag: biosample encode accession

tag: Sex

tag: health state

value: nonischemic (EF 11% LVEDD 7.7; RV severe dilation, severe dysfunction)

tag: dev stage

value: adult

tag: age

value: 61 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Shin Lin

tag: link

value: ENCBS517ZWK at ENCODE; https://www.encodeproject.org/ENCBS517ZWK/

value: Derived from ENCODE donor ENCDO808ASZ; https://www.encodeproject.org/ENCDO808ASZ/


title: Liver, Postnatal day 26, Rep2

city: Cambridge

first: Kristin

last: Knouse

state: MA

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

description: Sample 3

library_source: transcriptomic

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

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

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

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

tag: tissue

value: Liver

tag: genotype

tag: treatment


title: Liver, Postnatal day 15, Rep2

description: Sample 2


title: Liver, Carbon tetrachloride, 48 hours, Rep2

description: Sample 12

value: Carbon tetrachloride


title: DNase-seq from thymus (ENCLB809EOC)

description:
https://www.encodeproject.org/experiments/ENCSR068MCK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR068MCK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB809EOC

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

value: thymus

tag: description

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

value: male

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS911BWB at ENCODE; https://www.encodeproject.org/ENCBS911BWB/

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


title: Liver, Postnatal day 26, Rep3

description: Sample 3


title: DNase-seq from adrenal gland (ENCLB147MJO)

description:
https://www.encodeproject.org/experiments/ENCSR655MEK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR655MEK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB147MJO

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

value: adrenal gland

value: tissue

value: Stam pool D of 6 adrenal gland biosamples

value: female

value: 8-10 month

value: ENCBS238RCY at ENCODE; https://www.encodeproject.org/ENCBS238RCY/


title: ATAC-seq from heart left ventricle (ENCLB478GDB)

description:
https://www.encodeproject.org/experiments/ENCSR899YEP/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR899YEP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB478GDB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart left ventricle

value: nonischemic (EF 11% LVEDD 7.7; RV severe dilation, severe dysfunction)

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS517ZWK at ENCODE; https://www.encodeproject.org/ENCBS517ZWK/

value: Derived from ENCODE donor ENCDO808ASZ; https://www.encodeproject.org/ENCDO808ASZ/


title: ATAC-seq from upper lobe of left lung (ENCLB053BFO)

description:
https://www.encodeproject.org/experiments/ENCSR895SEG/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human upper lobe of left lung
experiment encode accession: ENCSR895SEG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB053BFO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: upper lobe of left lung

value: male

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

value: 60 year

value: Yiing Lin, MD, PhD

value: ENCBS891MLV at ENCODE; https://www.encodeproject.org/ENCBS891MLV/

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


title: Liver, Postnatal day 2, Rep2

description: Sample 1

value: Liver


title: DNase-seq from H1 (ENCLB177TNR)

description:
https://www.encodeproject.org/experiments/ENCSR951BNY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR951BNY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB177TNR
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens H1 cell line

tag: line

value: cell line

value: healthy

value: embryonic

value: not collected

value: John Stamatoyannopoulos, UW

value: Job Dekker

value: ENCBS474GKG at ENCODE; https://www.encodeproject.org/ENCBS474GKG/

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


title: ATAC-seq from upper lobe of left lung (ENCLB700SYL)

description:
https://www.encodeproject.org/experiments/ENCSR895SEG/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human upper lobe of left lung
experiment encode accession: ENCSR895SEG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB700SYL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: tissue

value: adult

value: Michael Snyder, Stanford


title: Liver, Partial hepatectomy, 48 hours, Rep2

description: Sample 8

value: Partial hepatectomy


title: DNase-seq from spleen (ENCLB039TBF)

description:
https://www.encodeproject.org/experiments/ENCSR876YAF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR876YAF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB039TBF

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

value: spleen

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

value: female

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS898ZWC at ENCODE; https://www.encodeproject.org/ENCBS898ZWC/

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


title: Liver, Carbon tetrachloride, 24 hours, Rep1

description: Sample 11

value: Liver

value: Carbon tetrachloride


title: Liver, Carbon tetrachloride, 48 hours, Rep1

description: Sample 12


title: DNase-seq from excitatory neuron (ENCLB678QDX)

description:
https://www.encodeproject.org/experiments/ENCSR109RIQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR109RIQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB678QDX

source_name: Homo sapiens male adult (53 years) excitatory neuron in vitro differentiated cells nuclear fraction

value: excitatory neuron

value: in vitro differentiated cells

value: male

value: 53 year

value: John Stamatoyannopoulos, UW

tag: subcellular fraction term name

value: nucleus

value: AllCells

value: ENCBS761ZFJ at ENCODE; https://www.encodeproject.org/ENCBS761ZFJ/

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


title: DNase-seq from HCT116 (ENCLB788ARZ)

description:
https://www.encodeproject.org/experiments/ENCSR477IQW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR477IQW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB788ARZ

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

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS184IVK at ENCODE; https://www.encodeproject.org/ENCBS184IVK/

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


title: DNase-seq from excitatory neuron (ENCLB690RWW)

description:
https://www.encodeproject.org/experiments/ENCSR109RIQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR109RIQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB690RWW

source_name: Homo sapiens male adult (53 years) excitatory neuron in vitro differentiated cells

value: excitatory neuron

value: ENCBS800IAL at ENCODE; https://www.encodeproject.org/ENCBS800IAL/


title: Liver, Carbon tetrachloride, 12 hours, Rep1

description: Sample 10

value: Liver

value: Carbon tetrachloride


title: DNase-seq from HCT116 (ENCLB556KTV)

description:
https://www.encodeproject.org/experiments/ENCSR477IQW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR477IQW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB556KTV

value: male

value: ENCBS026CTI at ENCODE; https://www.encodeproject.org/ENCBS026CTI/


title: DNase-seq from kidney (ENCLB915UQS)

description:
https://www.encodeproject.org/experiments/ENCSR060ALG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR060ALG
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB915UQS

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

value: kidney

value: tissue

value: female

value: postnatal

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS692TFI at ENCODE; https://www.encodeproject.org/ENCBS692TFI/

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


title: ATAC-seq from ovary (ENCLB576FGF)

description:
https://www.encodeproject.org/experiments/ENCSR476WNA/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human ovary
experiment encode accession: ENCSR476WNA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB576FGF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: ovary

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

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS246QPU at ENCODE; https://www.encodeproject.org/ENCBS246QPU/

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


title: Liver, Carbon tetrachloride, 6 hours, Rep1

description: Sample 9

value: Liver

value: Carbon tetrachloride


title: Liver, Partial hepatectomy, 48 hours, Rep1

description: Sample 8

value: Partial hepatectomy


title: ATAC-seq from CD4-positive, alpha-beta T cell (ENCLB298OOA)

description:
https://www.encodeproject.org/experiments/ENCSR841LHT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR841LHT
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB298OOA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (20 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS354THN at ENCODE; https://www.encodeproject.org/ENCBS354THN/

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


title: ATAC-seq from ovary (ENCLB023XDE)

description:
https://www.encodeproject.org/experiments/ENCSR476WNA/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human ovary
experiment encode accession: ENCSR476WNA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-02-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB023XDE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: ovary

value: tissue

value: female

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

value: adult


title: DNase-seq from left cerebral cortex (ENCLB262OUW)

description:
https://www.encodeproject.org/experiments/ENCSR471DVS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR471DVS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB262OUW

source_name: Mus musculus strain 5xFAD/CAST male (9 months) left cerebral cortex tissue

value: left cerebral cortex

value: unknown

value: 9 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS156LPB at ENCODE; https://www.encodeproject.org/ENCBS156LPB/

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


title: DNase-seq from chondrocyte (ENCLB304BFY)

description:
https://www.encodeproject.org/experiments/ENCSR970DQR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR970DQR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB304BFY
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS994JQF at ENCODE; https://www.encodeproject.org/ENCBS994JQF/

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


title: DNase-seq from frontal cortex (ENCLB599BZS)

description:
https://www.encodeproject.org/experiments/ENCSR061TLH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR061TLH
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB599BZS

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

value: frontal cortex

value: tissue

value: B6Cast F1 PND10 3x male Frontal Cortex

value: male

value: not collected

value: 10 day

value: ENCBS030EDW at ENCODE; https://www.encodeproject.org/ENCBS030EDW/

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


title: DNase-seq from thymus (ENCLB027DHB)

description:
https://www.encodeproject.org/experiments/ENCSR049ACM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR049ACM
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB027DHB

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

value: thymus

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

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS488SXJ at ENCODE; https://www.encodeproject.org/ENCBS488SXJ/


title: DNase-seq from osteocyte (ENCLB414TBU)

description:
https://www.encodeproject.org/experiments/ENCSR818HHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR818HHN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB414TBU
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: osteocyte

value: in vitro differentiated cells

value: female

value: healthy

value: embryonic

value: 5 day

value: John Stamatoyannopoulos, UW

value: SESCC

value: ENCBS076BKW at ENCODE; https://www.encodeproject.org/ENCBS076BKW/


title: Liver, Partial hepatectomy, 24 hours, Rep1

description: Sample 7

source_name: Liver

value: Liver

value: Partial hepatectomy


title: DNase-seq from HCT116 (ENCLB920LUE)

description:
https://www.encodeproject.org/experiments/ENCSR878VJL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR878VJL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB920LUE

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

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS324LVI at ENCODE; https://www.encodeproject.org/ENCBS324LVI/

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


title: DNase-seq from kidney (ENCLB001GLZ)

description:
https://www.encodeproject.org/experiments/ENCSR060ALG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR060ALG
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB001GLZ

value: kidney

value: tissue

value: female

value: postnatal

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS953GVN at ENCODE; https://www.encodeproject.org/ENCBS953GVN/

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


title: DNase-seq from inflammatory macrophage (ENCLB872ZTQ)

description:
https://www.encodeproject.org/experiments/ENCSR803BLT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR803BLT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB872ZTQ
instrument models: Illumina HiSeq 4000,Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens male adult (21 years) inflammatory macrophage primary cell treated with lipopolysaccharide for 1 hour

value: inflammatory macrophage

value: primary cell

value: male

value: 21 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

tag: treatments

value: treatment_term_id:CHEBI:16412; treatment_term_name:lipopolysaccharide; treatment_type:chemical; duration:1; duration_units:hour;

value: ENCBS832VLJ at ENCODE; https://www.encodeproject.org/ENCBS832VLJ/

value: Derived from ENCODE donor ENCDO733YAB; https://www.encodeproject.org/ENCDO733YAB/


title: Liver, Partial hepatectomy, 12 hours, Rep1

description: Sample 6

value: Liver

value: Partial hepatectomy


title: DNase-seq from layer of hippocampus (ENCLB647ZAN)

description:
https://www.encodeproject.org/experiments/ENCSR459CXJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR459CXJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB647ZAN

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

value: layer of hippocampus

value: tissue

value: B6Cast F1 PND36 male Hippocampus

value: not collected

value: 36 day

value: ENCBS324HPA at ENCODE; https://www.encodeproject.org/ENCBS324HPA/


title: Liver, Partial hepatectomy, 6 hours, Rep1

description: Sample 5


title: DNase-seq from right cerebral cortex (ENCLB221JAP)

description:
https://www.encodeproject.org/experiments/ENCSR224FBA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR224FBA
assay title: DNase-seq
assembly: mm10
encode release date: 2022-07-21
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB221JAP

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

value: right cerebral cortex

value: B6Cast F1 PND4 Male 05 right cerebral cortex for Altius Stam biobank

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS721RMD at ENCODE; https://www.encodeproject.org/ENCBS721RMD/

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


title: DNase-seq from cerebellum (ENCLB489DYN)

description:
https://www.encodeproject.org/experiments/ENCSR181OOF/
***************
biological replicate number: 2
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: ENCLB489DYN

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

value: cerebellum

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

value: male

value: ENCBS561TMO at ENCODE; https://www.encodeproject.org/ENCBS561TMO/


title: DNase-seq from urinary bladder (ENCLB891AVL)

description:
https://www.encodeproject.org/experiments/ENCSR453OSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR453OSR
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB891AVL

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

value: urinary bladder

value: B6Cast F1 PND4 Male 05 urinary bladder for Altius Stam biobank

value: ENCBS844IWB at ENCODE; https://www.encodeproject.org/ENCBS844IWB/


title: DNase-seq from HCT116 (ENCLB712BHM)

description:
https://www.encodeproject.org/experiments/ENCSR878VJL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR878VJL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB712BHM

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS806VMA at ENCODE; https://www.encodeproject.org/ENCBS806VMA/

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


title: Liver, 8 weeks, Rep1

description: Sample 4

value: Liver


title: Liver, Postnatal day 26, Rep1

description: Sample 3


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB648SVI)

description:
https://www.encodeproject.org/experiments/ENCSR068KDQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR068KDQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB648SVI

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS372AWJ at ENCODE; https://www.encodeproject.org/ENCBS372AWJ/

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


title: DNase-seq from thymus (ENCLB353RTK)

description:
https://www.encodeproject.org/experiments/ENCSR049ACM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR049ACM
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB353RTK

value: thymus

value: tissue

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

value: male

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS653QYD at ENCODE; https://www.encodeproject.org/ENCBS653QYD/

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


title: DNase-seq from left cerebral cortex (ENCLB977IKY)

description:
https://www.encodeproject.org/experiments/ENCSR078JJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR078JJT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-07-21
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB977IKY

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

value: left cerebral cortex

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

value: 4 day

value: ENCBS167PTD at ENCODE; https://www.encodeproject.org/ENCBS167PTD/


title: DNase-seq from gastrocnemius (ENCLB197YHW)

description:
https://www.encodeproject.org/experiments/ENCSR862OIS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR862OIS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB197YHW

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

value: gastrocnemius

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

value: female

value: not collected

value: 2 month

value: ENCBS858UYH at ENCODE; https://www.encodeproject.org/ENCBS858UYH/


title: DNase-seq from T-helper 2 cell (ENCLB530RGC)

description:
https://www.encodeproject.org/experiments/ENCSR655LUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR655LUX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-05-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB530RGC

source_name: Homo sapiens male adult (38 years) T-helper 2 primary cell

value: T-helper 2 cell

value: primary cell

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS579RSJ at ENCODE; https://www.encodeproject.org/ENCBS579RSJ/

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


title: DNase-seq from gastrocnemius (ENCLB331QRH)

description:
https://www.encodeproject.org/experiments/ENCSR498SCU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR498SCU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB331QRH
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: tissue

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

value: male

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS992QJM at ENCODE; https://www.encodeproject.org/ENCBS992QJM/

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


title: DNase-seq from spleen (ENCLB862JRG)

description:
https://www.encodeproject.org/experiments/ENCSR039FQF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR039FQF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB862JRG

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

value: spleen

value: B6Cast F1 DPN18-20months

value: 18-20 month

value: ENCBS434QFK at ENCODE; https://www.encodeproject.org/ENCBS434QFK/


title: ATAC-seq from ovary (ENCLB859BDE)

description:
https://www.encodeproject.org/experiments/ENCSR872MAO/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human ovary
experiment encode accession: ENCSR872MAO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB859BDE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: ovary

value: female

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

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS083CPL at ENCODE; https://www.encodeproject.org/ENCBS083CPL/

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


title: Liver, Postnatal day 15, Rep1

description: Sample 2

value: Liver


title: DNase-seq from gastrocnemius (ENCLB802BXF)

description:
https://www.encodeproject.org/experiments/ENCSR862OIS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR862OIS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB802BXF

value: gastrocnemius

value: tissue

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

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS577OXE at ENCODE; https://www.encodeproject.org/ENCBS577OXE/


title: DNase-seq from adrenal gland (ENCLB222RQJ)

description:
https://www.encodeproject.org/experiments/ENCSR822RKU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR822RKU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-03-12
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB222RQJ
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: adrenal gland

value: B6Cast F1 PND4 3x Males 05 adrenal gland for Altius Stam core

value: male

value: 4 day

value: ENCBS110XTZ at ENCODE; https://www.encodeproject.org/ENCBS110XTZ/

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


title: ATAC-seq from ovary (ENCLB922HRA)

description:
https://www.encodeproject.org/experiments/ENCSR872MAO/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human ovary
experiment encode accession: ENCSR872MAO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB922HRA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: ovary

value: female

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

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS083CPL at ENCODE; https://www.encodeproject.org/ENCBS083CPL/


title: DNase-seq from layer of hippocampus (ENCLB312SJL)

description:
https://www.encodeproject.org/experiments/ENCSR648GZU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR648GZU
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB312SJL

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

value: layer of hippocampus

value: tissue

value: B6Cast F1 18 - 20 month female Hippocampus

value: not collected

value: 18-20 month

value: Barbara Wold, Caltech

value: ENCBS557IAD at ENCODE; https://www.encodeproject.org/ENCBS557IAD/


title: DNase-seq from kidney (ENCLB571HYW)

description:
https://www.encodeproject.org/experiments/ENCSR605PMM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR605PMM
assay title: DNase-seq
assembly: mm10
encode release date: 2022-05-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB571HYW
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: kidney

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

value: male

value: 14 day

value: The Jackson Laboratory

value: ENCBS013RUL at ENCODE; https://www.encodeproject.org/ENCBS013RUL/


title: Liver, Postnatal day 2, Rep1

description: Sample 1

source_name: Liver

value: Liver


title: DNase-seq from inflammatory macrophage (ENCLB847HOO)

description:
https://www.encodeproject.org/experiments/ENCSR593WXK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR593WXK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB847HOO
instrument models: Illumina NextSeq 500,Illumina HiSeq 4000,Illumina HiSeq 2500

source_name: Homo sapiens male adult (21 years) inflammatory macrophage primary cell

value: inflammatory macrophage

value: primary cell

value: adult

value: 21 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS298AWT at ENCODE; https://www.encodeproject.org/ENCBS298AWT/

value: Derived from ENCODE donor ENCDO733YAB; https://www.encodeproject.org/ENCDO733YAB/


title: DNase-seq from central memory CD4-positive, alpha-beta T cell (ENCLB971LLI)

description:
https://www.encodeproject.org/experiments/ENCSR467YCD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR467YCD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-05-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB971LLI

source_name: Homo sapiens male adult (38 years) central memory CD4-positive, alpha-beta T primary cell

value: 38 year

value: AllCells

value: ENCBS362AFQ at ENCODE; https://www.encodeproject.org/ENCBS362AFQ/

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


title: DNase-seq from CD14-positive monocyte (ENCLB534ETE)

description:
https://www.encodeproject.org/experiments/ENCSR464ETX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR464ETX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB534ETE
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000,Illumina HiSeq 4000,Illumina NextSeq 500

source_name: Homo sapiens male adult (21 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: male

value: ENCBS087UPP at ENCODE; https://www.encodeproject.org/ENCBS087UPP/


title: DNase-seq from gastrocnemius (ENCLB413GUJ)

description:
https://www.encodeproject.org/experiments/ENCSR641XZF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR641XZF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-03-12
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB413GUJ

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

value: gastrocnemius

value: tissue

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

value: female

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS664QFU at ENCODE; https://www.encodeproject.org/ENCBS664QFU/

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


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB803TLM)

description:
https://www.encodeproject.org/experiments/ENCSR875IVR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR875IVR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB803TLM

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: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS635DXW at ENCODE; https://www.encodeproject.org/ENCBS635DXW/

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


title: DNase-seq from immature natural killer cell (ENCLB838HGA)

description:
https://www.encodeproject.org/experiments/ENCSR654LST/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR654LST
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB838HGA

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

value: immature natural killer cell

value: healthy

value: ENCBS880JPN at ENCODE; https://www.encodeproject.org/ENCBS880JPN/

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


title: ATAC-seq from K562 (ENCLB044PVF)

description:
https://www.encodeproject.org/experiments/ENCSR956DNB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on K562 cells stained for GATA1 and sorted for highest 15% of expression
experiment encode accession: ENCSR956DNB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Will Greenleaf, Stanford
library encode accession: ENCLB044PVF
size range: 180-1000

source_name: Homo sapiens K562 cell line, preserved by flash-freezing

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: ENCBS498BIZ at ENCODE; https://www.encodeproject.org/ENCBS498BIZ/

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


title: DNase-seq from HCT116 (ENCLB819CDY)

description:
https://www.encodeproject.org/experiments/ENCSR867ITQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR867ITQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB819CDY

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

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: ENCBS474PRW at ENCODE; https://www.encodeproject.org/ENCBS474PRW/

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


title: DNase-seq from cerebellum (ENCLB141YZS)

description:
https://www.encodeproject.org/experiments/ENCSR639CNY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639CNY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB141YZS

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

value: cerebellum

value: tissue

value: Stam pool B of 2 cerebellum biosamples

value: unknown

value: 8-10 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS796RXY at ENCODE; https://www.encodeproject.org/ENCBS796RXY/

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


title: ATAC-seq from K562 (ENCLB310BBE)

description:
https://www.encodeproject.org/experiments/ENCSR956DNB/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on K562 cells stained for GATA1 and sorted for highest 15% of expression
experiment encode accession: ENCSR956DNB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Will Greenleaf, Stanford
library encode accession: ENCLB310BBE
size range: 180-1000

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: ENCBS488XZO at ENCODE; https://www.encodeproject.org/ENCBS488XZO/

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


title: DNase-seq from HCT116 (ENCLB937RRX)

description:
https://www.encodeproject.org/experiments/ENCSR867ITQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR867ITQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB937RRX

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: ENCBS474PRW at ENCODE; https://www.encodeproject.org/ENCBS474PRW/

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


title: ATAC-seq from K562 (ENCLB263WRG)

description:
https://www.encodeproject.org/experiments/ENCSR859USB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on K562 cells stained for GATA1 and sorted for lowest 15% of expression
experiment encode accession: ENCSR859USB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Will Greenleaf, Stanford
library encode accession: ENCLB263WRG
size range: 180-1000

value: cell line

value: ENCBS473EKR at ENCODE; https://www.encodeproject.org/ENCBS473EKR/


title: DNase-seq from urinary bladder (ENCLB651UIC)

description:
https://www.encodeproject.org/experiments/ENCSR854UWF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR854UWF
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB651UIC

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

value: urinary bladder

value: tissue

value: B6Cast F1 PND 2 months Female 05 urinary bladder for Altius Stam biobank

value: female

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS416TTV at ENCODE; https://www.encodeproject.org/ENCBS416TTV/

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


title: ATAC-seq from K562 (ENCLB483GFH)

description:
https://www.encodeproject.org/experiments/ENCSR859USB/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on K562 cells stained for GATA1 and sorted for lowest 15% of expression
experiment encode accession: ENCSR859USB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Will Greenleaf, Stanford
library encode accession: ENCLB483GFH
size range: 180-1000

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: ATCC

value: ENCBS159JJR at ENCODE; https://www.encodeproject.org/ENCBS159JJR/

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


title: DNase-seq from cerebellum (ENCLB206JGK)

description:
https://www.encodeproject.org/experiments/ENCSR934ECT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR934ECT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB206JGK

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

value: cerebellum

value: Stam pool H of 2 cerebellum biosamples

value: male

value: unknown

value: 8-10 month

value: ENCBS901TDV at ENCODE; https://www.encodeproject.org/ENCBS901TDV/


title: rpopho_2

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description: 150 x 150 cycle paired end sequence

data_processing:
Libraries are fed into Novaseq6000 machines according to activity and expected data volume. A paired-end 150 bp sequencing strategy was used and all samples were sequenced to at least 6 Gb.
XPRESSpipe v0.6.3 was used to process sequence files, with the following command: xpresspipe peRNAseq ... -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGATGACTATCTCGTATGCCGTCTTCTGCTTG --sjdbOverhang 149 --quantification_method htseq --remove_rrna. See supplementary files for XPRESSpipe dependencies and settings used.
Assembly: Ensembl Saccharomyces_cerevisiae release-106
Supplementary files format and content: Tab-delimited text file - processed count data

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae (BY)

growth_protocol: Grown in indicated media overnight and harvested between OD=0.2-0.4, with a total OD of 5 per sample.

extract_protocol:
Direct-zol RNA Miniprep
After the QC procedures, mRNA from eukaryotic organisms is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library is ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to I ng/gl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).

treatment_protocol: Treatment is indicated above

tag: cell type

value: yeast cells

value: rpo41pho85 deletion

value: no treatment


title: rpopho_3

description: 150 x 150 cycle paired end sequence


title: rpopho_1

description: 150 x 150 cycle paired end sequence


title: rpo41_3

description: 150 x 150 cycle paired end sequence

value: rpo41 deletion


title: rpo41_1

description: 150 x 150 cycle paired end sequence


title: ATAC-seq from bile duct (ENCLB360GAG)

description:
https://www.encodeproject.org/experiments/ENCSR653ZWW/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human bile duct
experiment encode accession: ENCSR653ZWW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB360GAG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) bile duct tissue, preserved by flash-freezing

value: bile duct

value: tissue

value: female

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

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS830GZJ at ENCODE; https://www.encodeproject.org/ENCBS830GZJ/

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


title: DNase-seq from gastrocnemius (ENCLB088YFT)

description:
https://www.encodeproject.org/experiments/ENCSR854SEB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR854SEB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB088YFT

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

value: gastrocnemius

value: postnatal

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS835IZT at ENCODE; https://www.encodeproject.org/ENCBS835IZT/

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


title: Sample_RV1_WT_1_IGO_13684_B_9

city: New York City

first: Dan

last: Li

state: NY

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
Reads quality were analyzed by FastQC (version 0.11.9) and mapped to Human genome (GRCh38) using STAR_2.5.3a. The BAM file quality were analyzed with qualimap bamqc and RNA-seq quality was analyzed with qualimap rnaseq (QualiMap v.2.2.2-dev). The counts per gene were quantified with STAR --quantMode GeneCounts
Assembly: GRCh38
Supplementary files format and content: comma-separated read counts

source_name: ETV4WT, replicate 1, RNAseq

extract_protocol:
PC3 and 22Rv1 prostate cell lines were infected with Lentivirus with mutated ETV4: ETV4AAA-IRES-eGFP, wild type ETV4: ETV4WT-IRES-eGFP, and control vector IRES-eGFP by MSCV-IRES-GFP vector ((Addgene #20672)). After 1 week Lentivirus infection and transgene overexpression, live cells were sorted out by flow cytometry as DAPI negative and EGFP positive. Total RNA were extracted and library was built and sequenced by Poly A enrichment Whole transcriptome sequencing, NextSeq 500 Illumina sequencing instrument according to manufacturer’s specifications. For each sample, 40~50 million reads were acquired.
Cells were directly processed with 10X genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 according to manufacturer’s specifications. For each sample, 200 million reads were acquired on NovaSeq platform S4 flow cell.

tag: cell line

value: prostate

value: 1 week after ETV4WT-IRES-eGFP overexpression


title: DNase-seq from left cerebral cortex (ENCLB261GDN)

description:
https://www.encodeproject.org/experiments/ENCSR636QXK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR636QXK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB261GDN

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

value: left cerebral cortex

tag: biosample encode accession

value: male

value: 8-10 month

value: ENCBS166ATN at ENCODE; https://www.encodeproject.org/ENCBS166ATN/


title: DNase-seq from cerebellum (ENCLB137KND)

description:
https://www.encodeproject.org/experiments/ENCSR639CNY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR639CNY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB137KND

value: cerebellum

value: tissue

value: Stam pool E of 2 cerebellum biosamples

tag: Sex

value: female

value: unknown

value: ENCBS776BLV at ENCODE; https://www.encodeproject.org/ENCBS776BLV/


title: Sample_RV1_WT_2_IGO_13684_B_10

source_name: ETV4WT, replicate 2, RNAseq


title: ATAC-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB724RTZ)

description:
https://www.encodeproject.org/experiments/ENCSR863TVR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR863TVR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB724RTZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (33 years) stimulated activated naive CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours

value: primary cell

value: adult

value: 33 year

value: Michael Snyder, Stanford

value: StemExpress

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS929IQW at ENCODE; https://www.encodeproject.org/ENCBS929IQW/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: pho85_3

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: pho85 deletion

value: no treatment


title: pho85_2

description: 150 x 150 cycle paired end sequence


title: DNase-seq from heart (ENCLB949IBO)

description:
https://www.encodeproject.org/experiments/ENCSR441MWY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR441MWY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB949IBO

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

value: heart

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

value: not collected

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS703WZZ at ENCODE; https://www.encodeproject.org/ENCBS703WZZ/

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


title: DNase-seq from left cerebral cortex (ENCLB212UZO)

description:
https://www.encodeproject.org/experiments/ENCSR636QXK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR636QXK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB212UZO

value: left cerebral cortex

value: tissue

value: male

value: postnatal

value: 8-10 month

value: ENCBS697AZL at ENCODE; https://www.encodeproject.org/ENCBS697AZL/


title: Sample_RV1_EGFP_1_IGO_13684_B_7

source_name: EGFP, replicate 1, RNAseq

value: prostate

value: 1 week after IRES-eGFP overexpression

value: MSCV-IRES-eGFP


title: rpo41_2

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: rpo41 deletion

value: no treatment


title: DNase-seq from lung (ENCLB292KHV)

description:
https://www.encodeproject.org/experiments/ENCSR427LHI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR427LHI
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB292KHV

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

value: lung

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

value: not collected

value: 36 day

value: ENCBS206JEJ at ENCODE; https://www.encodeproject.org/ENCBS206JEJ/


title: Sample_RV1_AAA_2_IGO_13684_B_12

source_name: ETV4AAA, replicate 2, RNAseq

value: 1 week after ETV4AAA-IRES-eGFP overexpression


title: DNase-seq from lung (ENCLB161TYX)

description:
https://www.encodeproject.org/experiments/ENCSR427LHI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR427LHI
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB161TYX

value: tissue

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

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS517MLV at ENCODE; https://www.encodeproject.org/ENCBS517MLV/

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


title: DNase-seq from CD4-positive, alpha-beta memory T cell (ENCLB190FLZ)

description:
https://www.encodeproject.org/experiments/ENCSR862ZDV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR862ZDV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB190FLZ

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

tag: health state

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS353CMJ at ENCODE; https://www.encodeproject.org/ENCBS353CMJ/

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


title: ATAC-seq from heart left ventricle (ENCLB587ENF)

description:
https://www.encodeproject.org/experiments/ENCSR451JSB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR451JSB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB587ENF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (56 years) heart left ventricle tissue

value: heart left ventricle

value: female

value: PGD

tag: dev stage

value: adult

value: 56 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS593MGA at ENCODE; https://www.encodeproject.org/ENCBS593MGA/

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


title: ATAC-seq from bile duct (ENCLB731KFD)

description:
https://www.encodeproject.org/experiments/ENCSR653ZWW/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human bile duct
experiment encode accession: ENCSR653ZWW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB731KFD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: bile duct

value: tissue

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

tag: age

value: 47 year

value: Yiing Lin, MD, PhD

value: ENCBS830GZJ at ENCODE; https://www.encodeproject.org/ENCBS830GZJ/

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


title: bar1_aF_2

description: 150 x 150 cycle paired end sequence

source_name: Saccharomyces cerevisiae (W303)

value: yeast cells

value: bar1 deletion W303

value: treat with alpha factor


title: bar1_aF_3

description: 150 x 150 cycle paired end sequence


title: Sample_PC3_WT_2_IGO_13684_B_4

value: prostate

value: 1 week after ETV4WT-IRES-eGFP overexpression


title: ATAC-seq from heart left ventricle (ENCLB017QKX)

description:
https://www.encodeproject.org/experiments/ENCSR451JSB/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR451JSB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB017QKX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart left ventricle

value: female

value: PGD

value: adult

value: 56 year

tag: lab


title: Sample_RV1_EGFP_2_IGO_13684_B_8

source_name: EGFP, replicate 2, RNAseq

value: 1 week after IRES-eGFP overexpression

value: MSCV-IRES-eGFP


title: DNase-seq from left cerebral cortex (ENCLB664ZVN)

description:
https://www.encodeproject.org/experiments/ENCSR029GTO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR029GTO
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB664ZVN

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

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND 2 months Male 06 left cerebral cortex for Altius Stam biobank

value: male

value: not collected

value: 2 month

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

value: ENCBS176AFW at ENCODE; https://www.encodeproject.org/ENCBS176AFW/

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


title: Sample_PC3_WT_1_IGO_13684_B_3

value: prostate

value: 1 week after ETV4WT-IRES-eGFP overexpression


title: DNase-seq from left cerebral cortex (ENCLB691XEL)

description:
https://www.encodeproject.org/experiments/ENCSR029GTO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR029GTO
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB691XEL

value: B6Cast F1 PND 2 months Male 05 left cerebral cortex for Altius Stam biobank

tag: link

value: ENCBS537NSS at ENCODE; https://www.encodeproject.org/ENCBS537NSS/


title: ATAC-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB591UEE)

description:
https://www.encodeproject.org/experiments/ENCSR863TVR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR863TVR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB591UEE
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: primary cell

value: adult

value: 33 year

value: Michael Snyder, Stanford

value: StemExpress

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS940BAI at ENCODE; https://www.encodeproject.org/ENCBS940BAI/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: ATAC-seq from T-cell (ENCLB564ZBJ)

description:
https://www.encodeproject.org/experiments/ENCSR032MEH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR032MEH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB564ZBJ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (43 years) T-cell primary cell

value: T-cell

value: male

value: 43 year

value: ENCBS412VQV at ENCODE; https://www.encodeproject.org/ENCBS412VQV/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: ATAC-seq from T-cell (ENCLB418IJB)

description:
https://www.encodeproject.org/experiments/ENCSR032MEH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR032MEH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB418IJB
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: ENCBS791KYH at ENCODE; https://www.encodeproject.org/ENCBS791KYH/


title: bar1_aF_1

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: bar1 deletion W303

value: treat with alpha factor


title: DNase-seq from layer of hippocampus (ENCLB446PMI)

description:
https://www.encodeproject.org/experiments/ENCSR021NVL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR021NVL
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB446PMI

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

value: layer of hippocampus

value: tissue

value: unknown

value: 11-12 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS768VWT at ENCODE; https://www.encodeproject.org/ENCBS768VWT/

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


title: bar1_3

description: 150 x 150 cycle paired end sequence

value: no treatment


title: pho85_1

description: 150 x 150 cycle paired end sequence

source_name: Saccharomyces cerevisiae (BY)

value: pho85 deletion


title: DNase-seq from right cerebral cortex (ENCLB052JDK)

description:
https://www.encodeproject.org/experiments/ENCSR415MMR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR415MMR
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB052JDK

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

value: right cerebral cortex

value: B6Cast F1 PND 2 months Female 05 right cerebral cortex for Altius Stam biobank

value: female

value: not collected

value: 2 month

value: ENCBS246ONY at ENCODE; https://www.encodeproject.org/ENCBS246ONY/

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


title: Sample_PC3_EGFP_2_IGO_13684_B_2

tag: tissue

value: prostate

value: 1 week after IRES-eGFP overexpression

value: MSCV-IRES-eGFP


title: DNase-seq from CD4-positive, alpha-beta memory T cell (ENCLB764JVL)

description:
https://www.encodeproject.org/experiments/ENCSR437PXY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR437PXY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB764JVL

source_name: Homo sapiens with multiple sclerosis; 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: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS015CUU at ENCODE; https://www.encodeproject.org/ENCBS015CUU/

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


title: ATAC-seq from heart left ventricle (ENCLB647WLR)

description:
https://www.encodeproject.org/experiments/ENCSR848TMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR848TMJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB647WLR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (69 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: male

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS862FYW at ENCODE; https://www.encodeproject.org/ENCBS862FYW/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: DNase-seq from thymus (ENCLB007UZM)

description:
https://www.encodeproject.org/experiments/ENCSR830IOW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR830IOW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB007UZM

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

value: thymus

value: B6Cast F1 DPN18-20months

value: female

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS307CAT at ENCODE; https://www.encodeproject.org/ENCBS307CAT/

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


title: bar1_2

description: 150 x 150 cycle paired end sequence

value: yeast cells

tag: genotype

value: bar1 deletion W303

value: no treatment


title: Sample_PC3_AAA_2_IGO_13684_B_6

value: prostate

tag: treatment

value: 1 week after ETV4AAA-IRES-eGFP overexpression


title: bar1_1

description: 150 x 150 cycle paired end sequence


title: ATAC-seq from heart left ventricle (ENCLB695WXJ)

description:
https://www.encodeproject.org/experiments/ENCSR848TMJ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR848TMJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB695WXJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart left ventricle

value: tissue

value: male

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: adult

value: 69 year

value: Michael Snyder, Stanford


title: WT_noURA_3

description: 150 x 150 cycle paired end sequence

value: wild-type

value: grow with no uracil for 4hr


title: Sample_RV1_AAA_1_IGO_13684_B_11

source_name: ETV4AAA, replicate 1, RNAseq


title: DNase-seq from thymus (ENCLB816EDE)

description:
https://www.encodeproject.org/experiments/ENCSR830IOW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR830IOW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB816EDE

value: thymus

tag: description

value: B6Cast F1 DPN18-20months

value: female

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS053SGQ at ENCODE; https://www.encodeproject.org/ENCBS053SGQ/


title: Sample_PC3_AAA_1_IGO_13684_B_5

value: prostate

value: 1 week after ETV4AAA-IRES-eGFP overexpression


title: WT_noURA_2

description: 150 x 150 cycle paired end sequence

value: yeast cells


title: DNase-seq from adrenal gland (ENCLB912DUN)

description:
https://www.encodeproject.org/experiments/ENCSR632BLV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR632BLV
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB912DUN

source_name: Mus musculus strain 5xFAD/CAST male (9-13 months) adrenal gland tissue

value: adrenal gland

value: tissue

value: male

value: unknown

value: 9-13 month

value: ENCBS817CNT at ENCODE; https://www.encodeproject.org/ENCBS817CNT/

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


title: ATAC-seq from jejunum (ENCLB191ZAJ)

description:
https://www.encodeproject.org/experiments/ENCSR415LEB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human jejunum
experiment encode accession: ENCSR415LEB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB191ZAJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) jejunum tissue, preserved by flash-freezing

value: jejunum

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

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS753MYQ at ENCODE; https://www.encodeproject.org/ENCBS753MYQ/

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


title: DNase-seq from adrenal gland (ENCLB693LMT)

description:
https://www.encodeproject.org/experiments/ENCSR632BLV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR632BLV
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB693LMT

source_name: Mus musculus strain 5xFAD/CAST male (9-12 months) adrenal gland tissue

value: 9-12 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS836XYC at ENCODE; https://www.encodeproject.org/ENCBS836XYC/


title: LIM1 KD 3-3

city: Toon

first: Hiroaki

last: Kato

department: Obsterics and Gynecology

country: Japan

institute: Ehime university hospital

description:
50BSH20232
cultured cells (passage 8)
DK21246_12

data_processing:
Sequence data were mapped on the human genome (hg19) using Hisat2 and analyzed by R.
Assembly: hg19

source_name: HEC50B LIM1 shRNA3

growth_protocol: Cells was cultured in DMEM supplemented with 10% FBS and 1% antibiotics at 37°C in a humidified atomosphere of 5% CO2.

extract_protocol:
Total RNA was extracted with Isogen (Nippon gene, Japan) and RNeasy spin column kit (Qiagen, USA). 1 µg of RNA samples with RNA integrity number (RIN) greater than 9 were used for library prepairation.
RNA-Seq libraries were prepared using the Illumina NextSeq 500/550 High Output Kit v2.5 (Illumina, San Diego CA)  according to the manufacturer's instructions.

treatment_protocol: Cells was infected by lentivirus to transfect LIM1 shRNA and control vectors. To establish stable sublines, selection was performed by 10 μg/ml puromycin treatment.

value: human endometrial cancer (G3) cell line

tag: transfection

value: LIM1 shRNA3


title: WT_noURA_1

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: wild-type

value: grow with no uracil for 4hr


title: ATAC-seq from jejunum (ENCLB982INL)

description:
https://www.encodeproject.org/experiments/ENCSR415LEB/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human jejunum
experiment encode accession: ENCSR415LEB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB982INL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: jejunum

value: tissue

value: female


title: LIM1 KD 3-2

description:
50BSH20231
cultured cells (passage 8)
DK21246_11


title: DNase-seq from heart (ENCLB241IWD)

description:
https://www.encodeproject.org/experiments/ENCSR021LAC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR021LAC
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB241IWD

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

value: heart

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

value: not collected

value: 14 day

value: ENCBS723SYB at ENCODE; https://www.encodeproject.org/ENCBS723SYB/

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


title: ATAC-seq from posterior vena cava (ENCLB416EEI)

description:
https://www.encodeproject.org/experiments/ENCSR213DBU/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on human posterior vena cava
experiment encode accession: ENCSR213DBU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB416EEI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (26 years) posterior vena cava tissue, preserved by flash-freezing

value: posterior vena cava

value: male

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

value: adult

value: 26 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS994SJY at ENCODE; https://www.encodeproject.org/ENCBS994SJY/

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


title: WT_noPi_3

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: wild-type

value: grow with no phosphate for 4hr


title: LIM1 KD 3-1

description:
50BSH20230
cultured cells (passage 8)
DK21246_10

value: human endometrial cancer (G3) cell line

value: LIM1 shRNA3


title: Sample_PC3_EGFP_1_IGO_13684_B_1

source_name: EGFP, replicate 1, RNAseq

value: prostate

value: 1 week after IRES-eGFP overexpression

value: MSCV-IRES-eGFP


title: WT_noPi_2

description: 150 x 150 cycle paired end sequence


title: LIM1 KD 2-3

description:
50BSH20229
cultured cells (passage 8)
DK21246_09

source_name: HEC50B LIM1 shRNA2

value: LIM1 shRNA2


title: DNase-seq from heart (ENCLB696EOO)

description:
https://www.encodeproject.org/experiments/ENCSR021LAC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR021LAC
assay title: DNase-seq
assembly: mm10
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB696EOO

value: heart

value: tissue

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

value: female

value: not collected

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS038ZFJ at ENCODE; https://www.encodeproject.org/ENCBS038ZFJ/

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


title: DNase-seq from lung (ENCLB949KJV)

description:
https://www.encodeproject.org/experiments/ENCSR408JZW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR408JZW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB949KJV

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

value: lung

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: ENCBS211BWR at ENCODE; https://www.encodeproject.org/ENCBS211BWR/


title: ATAC-seq from right cardiac atrium (ENCLB656IED)

description:
https://www.encodeproject.org/experiments/ENCSR822BAD/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right cardiac atrium
experiment encode accession: ENCSR822BAD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB656IED
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (46 years) right cardiac atrium tissue, preserved by cryopreservation

value: right cardiac atrium

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

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS328NIN at ENCODE; https://www.encodeproject.org/ENCBS328NIN/

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


title: DNase-seq from lung (ENCLB819ARX)

description:
https://www.encodeproject.org/experiments/ENCSR408JZW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR408JZW
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB819ARX

value: tissue

value: Barbara Wold, Caltech

value: ENCBS585WXB at ENCODE; https://www.encodeproject.org/ENCBS585WXB/


title: LIM1 KD 2-2

description:
50BSH20228
cultured cells (passage 8)
DK21246_08

value: human endometrial cancer (G3) cell line

value: LIM1 shRNA2


title: WT_noPi_1

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: wild-type

value: grow with no phosphate for 4hr


title: ATAC-seq from posterior vena cava (ENCLB338EOC)

description:
https://www.encodeproject.org/experiments/ENCSR213DBU/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human posterior vena cava
experiment encode accession: ENCSR213DBU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB338EOC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: posterior vena cava

value: male

value: adult

value: 26 year

value: ENCBS994SJY at ENCODE; https://www.encodeproject.org/ENCBS994SJY/

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


title: WT_SD_2

description: 150 x 150 cycle paired end sequence

value: no treatment (ctrl for no ura)


title: DNase-seq from activated T-helper 1 cell (ENCLB749EOW)

description:
https://www.encodeproject.org/experiments/ENCSR636DIR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR636DIR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB749EOW

source_name: Homo sapiens male adult (35 years) activated T-helper 1 primary cell treated with 1 ug/mL Interleukin-4 antibody, 30 ng/mL Interleukin-12 subunit alpha, 30 ng/mL Interleukin-12 subunit beta, anti-CD3 and anti-CD28 coated beads

value: activated T-helper 1 cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS885JGI at ENCODE; https://www.encodeproject.org/ENCBS885JGI/

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


title: LIM1 KD 1-3

description:
50BSH20226
cultured cells (passage 8)
DK21246_06

source_name: HEC50B LIM1 shRNA1

value: human endometrial cancer (G3) cell line

value: LIM1 shRNA1


title: WT_SD_1

description: 150 x 150 cycle paired end sequence

source_name: Saccharomyces cerevisiae (BY)

value: yeast cells

value: wild-type


title: DNase-seq from lung (ENCLB294MFW)

description:
https://www.encodeproject.org/experiments/ENCSR211TTY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR211TTY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB294MFW

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

value: lung

value: tissue

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

value: female

value: not collected

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS217GGG at ENCODE; https://www.encodeproject.org/ENCBS217GGG/

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


title: DNase-seq from lung (ENCLB009YOQ)

description:
https://www.encodeproject.org/experiments/ENCSR211TTY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR211TTY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB009YOQ

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

value: ENCBS307ZKZ at ENCODE; https://www.encodeproject.org/ENCBS307ZKZ/


title: LIM1 KD 1-2

description:
50BSH20225
cultured cells (passage 8)
DK21246_05


title: ATAC-seq from sciatic nerve (ENCLB233YUN)

description:
https://www.encodeproject.org/experiments/ENCSR619LHF/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on human sciatic nerve
experiment encode accession: ENCSR619LHF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB233YUN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) sciatic nerve tissue, preserved by flash-freezing

value: sciatic nerve

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

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS182LUZ at ENCODE; https://www.encodeproject.org/ENCBS182LUZ/

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


title: DNase-seq from adrenal gland (ENCLB705BNH)

description:
https://www.encodeproject.org/experiments/ENCSR406JCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR406JCQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB705BNH

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

value: adrenal gland

value: tissue

value: B6Cast F1 DPN18-20months

value: female

value: 18-20 month

value: ENCBS772VQG at ENCODE; https://www.encodeproject.org/ENCBS772VQG/


title: WT_Pi_3

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: wild-type

value: grow with phosphate for 4hr


title: LIM1 KD 1-1

description:
50BSH20224
cultured cells (passage 8)
DK21246_04

value: human endometrial cancer (G3) cell line

value: LIM1 shRNA1


title: DNase-seq from natural killer cell (ENCLB720MIA)

description:
https://www.encodeproject.org/experiments/ENCSR409ZBD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR409ZBD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB720MIA

source_name: Homo sapiens male adult (47 years) natural killer primary cell treated with 100 ng/mL Interleukin-12 subunit alpha, 100 ng/mL Interleukin-15, 100 ng/mL Interleukin-12 subunit beta, 100 ng/mL Interleukin-18

value: natural killer cell

value: primary cell

value: male

value: adult

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; 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_id:UniProtKB:Q14116; treatment_term_name:Interleukin-18; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS412KSR at ENCODE; https://www.encodeproject.org/ENCBS412KSR/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: Control 3

description:
50BSH20223
cultured cells (passage 8)
DK21246_03

source_name: HEC50B control shRNA

value: control shRNA


title: WT_Pi_2

description: 150 x 150 cycle paired end sequence


title: WT_SD_3

description: 150 x 150 cycle paired end sequence

value: no treatment (ctrl for no ura)


title: ATAC-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB689UIH)

description:
https://www.encodeproject.org/experiments/ENCSR019XCN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR019XCN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB689UIH
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: 36 year

value: Michael Snyder, Stanford

value: ENCBS493MBH at ENCODE; https://www.encodeproject.org/ENCBS493MBH/

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


title: DNase-seq from heart (ENCLB159FFA)

description:
https://www.encodeproject.org/experiments/ENCSR613LJB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR613LJB
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB159FFA

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

value: heart

value: tissue

value: unknown

value: 9 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS851XAM at ENCODE; https://www.encodeproject.org/ENCBS851XAM/

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


title: LIM1 KD 2-1

description:
50BSH20227
cultured cells (passage 8)
DK21246_07

value: human endometrial cancer (G3) cell line

value: LIM1 shRNA2


title: DNase-seq from kidney (ENCLB573OXP)

description:
https://www.encodeproject.org/experiments/ENCSR018FXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR018FXD
assay title: DNase-seq
assembly: mm10
encode release date: 2022-09-29
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB573OXP

source_name: Mus musculus strain 5xFAD/CAST female (11 months) kidney tissue

value: kidney

value: female

value: 11 month

value: ENCBS168MFN at ENCODE; https://www.encodeproject.org/ENCBS168MFN/


title: ATAC-seq from right cardiac atrium (ENCLB497UUG)

description:
https://www.encodeproject.org/experiments/ENCSR822BAD/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on human right cardiac atrium
experiment encode accession: ENCSR822BAD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB497UUG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: right cardiac atrium

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

value: adult

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS328NIN at ENCODE; https://www.encodeproject.org/ENCBS328NIN/

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


title: Control 2

description:
50BSH20222
cultured cells (passage 8)
DK21246_02

value: control shRNA


title: WT_Pi_1

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: wild-type

value: grow with phosphate for 4hr


title: WT_no_treatment_3

description: 150 x 150 cycle paired end sequence

value: no treatment (ctrl for pho85, rpo41)


title: Control 1

description:
50BSH20221
cultured cells (passage 8)
DK21246_01

value: human endometrial cancer (G3) cell line


title: DNase-seq from frontal cortex (ENCLB594KVJ)

description:
https://www.encodeproject.org/experiments/ENCSR611CEJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR611CEJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB594KVJ

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

value: frontal cortex

value: tissue

value: B6Cast F1 PND14 3x female Frontal Cortex

value: female

value: not collected

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS511HRX at ENCODE; https://www.encodeproject.org/ENCBS511HRX/

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


title: DNase-seq from frontal cortex (ENCLB681YXG)

description:
https://www.encodeproject.org/experiments/ENCSR611CEJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR611CEJ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-04-07
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB681YXG

value: ENCBS589QKH at ENCODE; https://www.encodeproject.org/ENCBS589QKH/


title: DNase-seq from mammary epithelial cell (ENCLB178KQJ)

description:
https://www.encodeproject.org/experiments/ENCSR817ALC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR817ALC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-03-12
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB178KQJ

source_name: Homo sapiens female adult (19 years) mammary epithelial primary cell

value: mammary epithelial cell

value: primary cell

value: adult

value: 19 year

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS872AAB at ENCODE; https://www.encodeproject.org/ENCBS872AAB/

value: Derived from ENCODE donor ENCDO955XOD; https://www.encodeproject.org/ENCDO955XOD/


title: WT_no_treatment_2

description: 150 x 150 cycle paired end sequence

value: yeast cells

value: wild-type

value: no treatment (ctrl for pho85, rpo41)


title: ATAC-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB948JOT)

description:
https://www.encodeproject.org/experiments/ENCSR019XCN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR019XCN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB948JOT
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: male

value: 36 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS946YNV at ENCODE; https://www.encodeproject.org/ENCBS946YNV/

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