title: total RNA-seq from heart (ENCLB173AKT)

description:
https://www.encodeproject.org/experiments/ENCSR465PBJ/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND 18-20 months Female heart
experiment encode accession: ENCSR465PBJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB173AKT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: tissue

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS281CBG at ENCODE; https://www.encodeproject.org/ENCBS281CBG/

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


title: DNase-seq from head of caudate nucleus (ENCLB214IMH)

status: Public on Nov 04 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR297WRG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR297WRG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB214IMH
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens female adult (90 or above years) head of caudate nucleus tissue

value: head of caudate nucleus

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

tag: age

value: 90 or above year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Rush University

tag: link

value: ENCBS323FAL at ENCODE; https://www.encodeproject.org/ENCBS323FAL/

value: Derived from ENCODE donor ENCDO948PMW; https://www.encodeproject.org/ENCDO948PMW/


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB000NKX)

description:
https://www.encodeproject.org/experiments/ENCSR122KBB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR122KBB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242OUP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB000NKX
fragmentation methods: none

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

tag: antibody

value: primary cell

tag: description

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

value: not collected

tag: health state

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: PSAT1_KO_SD_4

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

description: human colon cancer cells

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg19 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

molecule: polyA RNA

source_name: Colon

extract_protocol:
Total RNA was extracted from samples using the RNeasy Mini kit (Life Technologies). Samples were then subject to poly(A) selection using oligo-dT beads (Life Technologies).
TotalScript RNA-Seq Kit (Epicentre)

treatment_protocol: HCT116 cells containing empty vector (EV) were given complete or serine deficient medium and HCT116 cells with deletion of PSAT1 (PSAT1 KO)  were given serine deficient medium for 24 hrs and RNA seq was carried out.

tag: cell type

value: colon


title: total RNA-seq from heart (ENCLB856BQX)

description:
https://www.encodeproject.org/experiments/ENCSR767PMR/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND14 3x Males heart
experiment encode accession: ENCSR767PMR
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB856BQX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

molecule: total RNA

organism: Mus musculus

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

value: heart

value: tissue

value: B6Cast F1 PND14 3x Males 04 heart for Wold biobank

value: male

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS306HAS at ENCODE; https://www.encodeproject.org/ENCBS306HAS/

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


title: DNase-seq from activated effector memory CD8-positive, alpha-beta T cell (ENCLB500ZJA)

description:
https://www.encodeproject.org/experiments/ENCSR133QIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133QIE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB500ZJA

source_name: Homo sapiens male adult (33 years) activated effector memory CD8-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-12 subunit alpha, anti-CD3 and anti-CD28 coated beads, 100 ng/mL Interleukin-12 subunit beta

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: StemExpress

tag: treatments

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

value: ENCBS462YWK at ENCODE; https://www.encodeproject.org/ENCBS462YWK/

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


title: PSAT1_KO_SD_3

description: human colon cancer cells

value: colon


title: R8560

city: Los Angeles

first: Richard

middle: Sungho

last: Ahn

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

data_processing:
Read quality was checked using FastQC 0.11.8
Reads aligned using STAR 2.7.2a
Count table generated using featureCounts 2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file containing a matrix of counts

source_name: Whole Blood

extract_protocol:
RNA was isolated from 1 mL RBC-lysed whole blood samples stored in RNAlater (500 μl). Globin RNA was removed using the GLOBINCLEAR kit.
Libraries were prepared for samples that passed quality control using the KAPA stranded mRNA kit.

tag: subject id

tag: timepoint

tag: cmv dnaemia


title: R8519


title: PSAT1_KO_SD_2

description: human colon cancer cells


title: total RNA-seq from left cerebral cortex (ENCLB326FOC)

description:
https://www.encodeproject.org/experiments/ENCSR764GMN/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND25 Male L. cortex
experiment encode accession: ENCSR764GMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB326FOC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND25 Male 03 left cerebral cortex for Wold biobank

value: unknown

value: 25 day

value: ENCBS770ANB at ENCODE; https://www.encodeproject.org/ENCBS770ANB/


title: R8251


title: total RNA-seq from heart (ENCLB916JUR)

description:
https://www.encodeproject.org/experiments/ENCSR767PMR/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND14 3x Males heart
experiment encode accession: ENCSR767PMR
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB916JUR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: B6Cast F1 PND14 3x Males 03 heart for Wold biobank

value: male

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS274KEH at ENCODE; https://www.encodeproject.org/ENCBS274KEH/


title: PSAT1_KO_SD_1

description: human colon cancer cells


title: total RNA-seq from left cerebral cortex (ENCLB189IJS)

description:
https://www.encodeproject.org/experiments/ENCSR764GMN/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND25 Male L. cortex
experiment encode accession: ENCSR764GMN
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB189IJS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6Cast F1 PND25 Male 04 left cerebral cortex for Wold biobank

value: ENCBS964RWE at ENCODE; https://www.encodeproject.org/ENCBS964RWE/

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


title: Histone ChIP-seq from motor neuron (ENCLB825FBM)

description:
https://www.encodeproject.org/experiments/ENCSR207VLY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR207VLY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR175HRD
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB825FBM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male child (6 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: child

value: 6 year

value: Michael Snyder, Stanford

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

value: Healthy donor

value: ENCBS409BIE at ENCODE; https://www.encodeproject.org/ENCBS409BIE/

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


title: ATAC-seq from activated naive B cell (ENCLB088FAZ)

description:
https://www.encodeproject.org/experiments/ENCSR379NMT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR379NMT
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB088FAZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: activated naive B cell

value: primary cell

value: male

value: adult

value: 40 year

value: StemExpress

value: ENCBS012FWY at ENCODE; https://www.encodeproject.org/ENCBS012FWY/

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


title: EV_SD_4_S46

description: human colon cancer cells

value: colon


title: R8786


title: R7894


title: total RNA-seq from layer of hippocampus (ENCLB925OEH)

description:
https://www.encodeproject.org/experiments/ENCSR576HNP/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6Cast F1 18 - 20 months male
experiment encode accession: ENCSR576HNP
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB925OEH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: layer of hippocampus

value: tissue

value: hippocampus_B6Cast F1_18 - 20 months_male_6_ENC4_cDNA515

value: unknown

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS168YXE at ENCODE; https://www.encodeproject.org/ENCBS168YXE/

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


title: EV_SD_3_S45

description: human colon cancer cells


title: TF ChIP-seq from WTC11 (ENCLB931IUW)

description:
https://www.encodeproject.org/experiments/ENCSR288NNJ/
***************
biological replicate number: 1
technical replicate number: 2
description: eGFP-ZNF416 ChIP-seq on human WTC11
experiment encode accession: ENCSR288NNJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR654GXW
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB931IUW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF416

tag: line

value: cell line

value: 30 year

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS501IGG at ENCODE; https://www.encodeproject.org/ENCBS501IGG/

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


title: TF ChIP-seq from WTC11 (ENCLB019WQI)

description:
https://www.encodeproject.org/experiments/ENCSR288NNJ/
***************
biological replicate number: 2
technical replicate number: 2
description: eGFP-ZNF416 ChIP-seq on human WTC11
experiment encode accession: ENCSR288NNJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR654GXW
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB019WQI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: adult

value: ENCBS366VMA at ENCODE; https://www.encodeproject.org/ENCBS366VMA/


title: total RNA-seq from layer of hippocampus (ENCLB904CNC)

description:
https://www.encodeproject.org/experiments/ENCSR576HNP/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6Cast F1 18 - 20 months male
experiment encode accession: ENCSR576HNP
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB904CNC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

value: tissue

value: hippocampus_B6Cast F1_18 - 20 months_male_7_ENC4_cDNA516

value: ENCBS226ECT at ENCODE; https://www.encodeproject.org/ENCBS226ECT/


title: total RNA-seq from left cerebral cortex (ENCLB806CBZ)

description:
https://www.encodeproject.org/experiments/ENCSR712PLG/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND 18-20 months Female L. cortex
experiment encode accession: ENCSR712PLG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB806CBZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: left cerebral cortex

value: B6Cast F1 DPN18-20months

value: female

value: 18-20 month

value: Barbara Wold, Caltech

value: ENCBS833RXG at ENCODE; https://www.encodeproject.org/ENCBS833RXG/


title: R7617


title: EV_SD_1_S43

description: human colon cancer cells

value: colon


title: ATAC-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB700SDZ)

description:
https://www.encodeproject.org/experiments/ENCSR373NFA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373NFA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB700SDZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: primary cell

value: 50 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS404KSW at ENCODE; https://www.encodeproject.org/ENCBS404KSW/

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


title: R7267


title: EV_Comp_4_S42

description: human colon cancer cells


title: ATAC-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB277BZZ)

description:
https://www.encodeproject.org/experiments/ENCSR373NFA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR373NFA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB277BZZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: male

value: adult

value: ENCBS879GSE at ENCODE; https://www.encodeproject.org/ENCBS879GSE/


title: total RNA-seq from left cerebral cortex (ENCLB023SHR)

description:
https://www.encodeproject.org/experiments/ENCSR712PLG/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND 18-20 months Female L. cortex
experiment encode accession: ENCSR712PLG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB023SHR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: The Jackson Laboratory

value: ENCBS774TTB at ENCODE; https://www.encodeproject.org/ENCBS774TTB/

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


title: R7296


title: total RNA-seq from left cerebral cortex (ENCLB669APY)

description:
https://www.encodeproject.org/experiments/ENCSR757VTG/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND4 Female L. cortex
experiment encode accession: ENCSR757VTG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB669APY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: left cerebral cortex

value: B6Cast F1 PND4 Female 04 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 4 day

value: ENCBS567ZSA at ENCODE; https://www.encodeproject.org/ENCBS567ZSA/


title: ATAC-seq from CD8-positive naive resting alpha-beta T cell (ENCLB008RFX)

description:
https://www.encodeproject.org/experiments/ENCSR283LPH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR283LPH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB008RFX
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: primary cell

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

tag: subcellular fraction term name

value: nucleus

value: ENCBS276ZZS at ENCODE; https://www.encodeproject.org/ENCBS276ZZS/

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


title: R7213


title: total RNA-seq from left cerebral cortex (ENCLB305DYS)

description:
https://www.encodeproject.org/experiments/ENCSR757VTG/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND4 Female L. cortex
experiment encode accession: ENCSR757VTG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB305DYS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: B6Cast F1 PND4 Female 03 left cerebral cortex for Wold biobank

tag: biosample encode accession

value: Barbara Wold, Caltech

value: ENCBS151XIY at ENCODE; https://www.encodeproject.org/ENCBS151XIY/


title: R6931


title: EV_Comp_2_S40

description: human colon cancer cells

value: colon


title: R7691


title: total RNA-seq from heart (ENCLB907ZBF)

description:
https://www.encodeproject.org/experiments/ENCSR573TZD/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND14 3x Females heart
experiment encode accession: ENCSR573TZD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB907ZBF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: heart

value: B6Cast F1 PND14 Female 04 heart for Wold biobank

tag: Sex

value: 14 day

value: The Jackson Laboratory

value: ENCBS807VSF at ENCODE; https://www.encodeproject.org/ENCBS807VSF/

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


title: ATAC-seq from activated regulatory T cell (ENCLB173XRP)

description:
https://www.encodeproject.org/experiments/ENCSR094QFZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR094QFZ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB173XRP
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (38 years) activated regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

value: activated regulatory T cell

value: primary cell

value: male

tag: dev stage

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS119ZDR at ENCODE; https://www.encodeproject.org/ENCBS119ZDR/

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


title: R6902


title: EV_SD_2_S44

description: human colon cancer cells


title: EV_Comp_1_S39

description: human colon cancer cells


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB393SOC)

description:
https://www.encodeproject.org/experiments/ENCSR367WVH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR367WVH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB393SOC

source_name: Homo sapiens male adult (33 years) CD8-positive naive resting alpha-beta T primary cell

tag: age

value: 33 year

value: StemExpress

value: ENCBS689LKA at ENCODE; https://www.encodeproject.org/ENCBS689LKA/

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


title: total RNA-seq from heart (ENCLB638CEY)

description:
https://www.encodeproject.org/experiments/ENCSR573TZD/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND14 3x Females heart
experiment encode accession: ENCSR573TZD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB638CEY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: tissue

value: B6Cast F1 PND14 3x Females 03 heart for Wold biobank

value: female

value: unknown

value: 14 day

tag: lab

value: Barbara Wold, Caltech

value: ENCBS976RBP at ENCODE; https://www.encodeproject.org/ENCBS976RBP/


title: DNase-seq from kidney (ENCLB067KIV)

description:
https://www.encodeproject.org/experiments/ENCSR692ASO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR692ASO
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB067KIV
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: kidney

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

value: male

value: 4 day

tag: source

value: The Jackson Laboratory

value: ENCBS442IFD at ENCODE; https://www.encodeproject.org/ENCBS442IFD/

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


title: total RNA-seq from left cerebral cortex (ENCLB672EDA)

description:
https://www.encodeproject.org/experiments/ENCSR864IYS/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND36 Male L. cortex
experiment encode accession: ENCSR864IYS
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB672EDA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: left cerebral cortex

value: B6Cast F1 PND36 Male 03 left cerebral cortex for Wold biobank

value: 36 day

tag: link

value: ENCBS994YKJ at ENCODE; https://www.encodeproject.org/ENCBS994YKJ/


title: DNase-seq from cerebellum (ENCLB214SEF)

description:
https://www.encodeproject.org/experiments/ENCSR913LCG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR913LCG
assay title: DNase-seq
assembly: mm10
encode release date: 2021-08-24
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB214SEF
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: cerebellum

value: tissue

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

value: ENCBS137PEC at ENCODE; https://www.encodeproject.org/ENCBS137PEC/


title: R6361


title: total RNA-seq from left cerebral cortex (ENCLB509ICM)

description:
https://www.encodeproject.org/experiments/ENCSR864IYS/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND36 Male L. cortex
experiment encode accession: ENCSR864IYS
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB509ICM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6Cast F1 PND36 Male 04 left cerebral cortex for Wold biobank

value: unknown

value: Barbara Wold, Caltech

value: ENCBS452FVI at ENCODE; https://www.encodeproject.org/ENCBS452FVI/


title: TF ChIP-seq from HepG2 (ENCLB966HQN)

description:
https://www.encodeproject.org/experiments/ENCSR363XHT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR363XHT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615JHA
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB966HQN
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HES4

tag: antibody

value: cell line

value: male

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS204RRC at ENCODE; https://www.encodeproject.org/ENCBS204RRC/

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


title: R6861

source_name: Whole Blood


title: DNase-seq from adrenal gland (ENCLB070RAZ)

description:
https://www.encodeproject.org/experiments/ENCSR840HMW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR840HMW
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB070RAZ
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: adrenal gland

tag: description

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

value: female

value: 4 day

value: The Jackson Laboratory

value: ENCBS376DPA at ENCODE; https://www.encodeproject.org/ENCBS376DPA/

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


title: EV_Comp_3_S41

description: human colon cancer cells

source_name: Colon

value: colon


title: R6213


title: total RNA-seq from adrenal gland (ENCLB387VKY)

description:
https://www.encodeproject.org/experiments/ENCSR571OZD/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND14_3x Males 03_ENC4_cDNA446
experiment encode accession: ENCSR571OZD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB387VKY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: tissue

value: B6Cast F1 PND14 3x Males 04 adrenal gland for Wold core

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS361GTM at ENCODE; https://www.encodeproject.org/ENCBS361GTM/


title: Histone ChIP-seq from motor neuron (ENCLB719HWH)

description:
https://www.encodeproject.org/experiments/ENCSR358AOC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR358AOC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR663GIS
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB719HWH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (49 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: male

tag: health state

value: Donor with Amyotrophic Lateral Sclerosis

value: adult

value: 49 year

value: Michael Snyder, Stanford

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

value: ENCBS980NQQ at ENCODE; https://www.encodeproject.org/ENCBS980NQQ/

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


title: DNase-seq from adrenal gland (ENCLB139TST)

description:
https://www.encodeproject.org/experiments/ENCSR837TJD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR837TJD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB139TST
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: adrenal gland

value: tissue

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

value: female

value: The Jackson Laboratory

value: ENCBS010HTX at ENCODE; https://www.encodeproject.org/ENCBS010HTX/

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


title: TF ChIP-seq from HepG2 (ENCLB372DCP)

description:
https://www.encodeproject.org/experiments/ENCSR363XHT/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR363XHT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615JHA
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB372DCP
fragmentation methods: sonication (generic)

value: cell line

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS428IKH at ENCODE; https://www.encodeproject.org/ENCBS428IKH/

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


title: total RNA-seq from adrenal gland (ENCLB075KTZ)

description:
https://www.encodeproject.org/experiments/ENCSR571OZD/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND14_3x Males 03_ENC4_cDNA446
experiment encode accession: ENCSR571OZD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB075KTZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6Cast F1 PND14 3x Males 03 adrenal gland for Wold core

value: male

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS479RMT at ENCODE; https://www.encodeproject.org/ENCBS479RMT/


title: Histone ChIP-seq from motor neuron (ENCLB955QAC)

description:
https://www.encodeproject.org/experiments/ENCSR358AOC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR358AOC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR663GIS
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB955QAC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: Donor with Amyotrophic Lateral Sclerosis

value: adult

value: 49 year

value: Michael Snyder, Stanford

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

value: ENCBS855DRG at ENCODE; https://www.encodeproject.org/ENCBS855DRG/

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


title: R6064


title: DNase-seq from kidney (ENCLB158RFF)

description:
https://www.encodeproject.org/experiments/ENCSR984XSP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR984XSP
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB158RFF
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: kidney

value: tissue

value: B6Cast F1 PND10 3x Males 06 kidney for Altius Stam core

value: 10 day

value: The Jackson Laboratory

value: ENCBS242ELR at ENCODE; https://www.encodeproject.org/ENCBS242ELR/

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


title: R6180


title: total RNA-seq from adrenal gland (ENCLB511MXI)

description:
https://www.encodeproject.org/experiments/ENCSR652VMD/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND10_Male 03_ENC4_cDNA442
experiment encode accession: ENCSR652VMD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB511MXI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: adrenal gland

value: B6Cast F1 PND10 Male 04 adrenal gland for Wold core

value: male

value: unknown

value: Barbara Wold, Caltech

value: ENCBS368WXW at ENCODE; https://www.encodeproject.org/ENCBS368WXW/


title: Control ChIP-seq from A549 (ENCLB384CEP)

description:
https://www.encodeproject.org/experiments/ENCSR365RFY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR365RFY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB384CEP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF302

value: cell line

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS080VNN at ENCODE; https://www.encodeproject.org/ENCBS080VNN/

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


title: ATAC-seq from motor neuron (ENCLB370VUP)

description:
https://www.encodeproject.org/experiments/ENCSR065CER/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR065CER
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB370VUP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: Donor with Amyotrophic Lateral Sclerosis

value: 49 year

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

value: ENCBS855DRG at ENCODE; https://www.encodeproject.org/ENCBS855DRG/

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


title: Histone ChIP-seq from motor neuron (ENCLB370DWQ)

description:
https://www.encodeproject.org/experiments/ENCSR207VLY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on human motor neuron
experiment encode accession: ENCSR207VLY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR175HRD
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB370DWQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male child (6 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: male

value: child

value: 6 year

value: Healthy donor

value: ENCBS182GDQ at ENCODE; https://www.encodeproject.org/ENCBS182GDQ/

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


title: DNase-seq from cerebellum (ENCLB100YCA)

description:
https://www.encodeproject.org/experiments/ENCSR641YOC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR641YOC
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB100YCA
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: cerebellum

value: tissue

value: B6Cast F1 PND10 3x Females 05 cerebellum for Altius Stam core

value: female

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS184IDE at ENCODE; https://www.encodeproject.org/ENCBS184IDE/

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


title: R6707


title: total RNA-seq from gastrocnemius (ENCLB428JLV)

description:
https://www.encodeproject.org/experiments/ENCSR640PLU/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND36 Male
experiment encode accession: ENCSR640PLU
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB428JLV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: gastrocnemius

value: B6Cast F1 PND36 Male 03 gastrocnemius for Wold core

value: 36 day

value: ENCBS182MGW at ENCODE; https://www.encodeproject.org/ENCBS182MGW/


title: DNase-seq from gastrocnemius (ENCLB658RPS)

description:
https://www.encodeproject.org/experiments/ENCSR639OQQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR639OQQ
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB658RPS
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

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

value: male

value: 4 day

value: ENCBS958KUJ at ENCODE; https://www.encodeproject.org/ENCBS958KUJ/


title: R6042


title: R9373


title: R9318


title: total RNA-seq from gastrocnemius (ENCLB977QHR)

description:
https://www.encodeproject.org/experiments/ENCSR640PLU/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND36 Male
experiment encode accession: ENCSR640PLU
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB977QHR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: B6Cast F1 PND36 Male 04 gastrocnemius for Wold core

value: ENCBS458CJW at ENCODE; https://www.encodeproject.org/ENCBS458CJW/


title: total RNA-seq from adrenal gland (ENCLB098XAY)

description:
https://www.encodeproject.org/experiments/ENCSR442XRH/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND 18-20 months_Female 03 _ENC4_cDNA463
experiment encode accession: ENCSR442XRH
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB098XAY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: adrenal gland

value: adrenal gland_B6Cast F1 PND 18-20 months_Female 04 _ENC4_cDNA464

value: female

value: unknown

value: 18-20 month

value: ENCBS703MDQ at ENCODE; https://www.encodeproject.org/ENCBS703MDQ/


title: R9359


title: ATAC-seq from motor neuron (ENCLB308QMT)

description:
https://www.encodeproject.org/experiments/ENCSR065CER/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR065CER
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB308QMT
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: Donor with Amyotrophic Lateral Sclerosis

value: adult

value: 49 year

value: Michael Snyder, Stanford

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

value: ENCBS980NQQ at ENCODE; https://www.encodeproject.org/ENCBS980NQQ/

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


title: total RNA-seq from adrenal gland (ENCLB080LOG)

description:
https://www.encodeproject.org/experiments/ENCSR652VMD/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND10_Male 03_ENC4_cDNA442
experiment encode accession: ENCSR652VMD
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB080LOG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: B6Cast F1 PND10 Male 03 adrenal gland for Wold core

value: male

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS588OTO at ENCODE; https://www.encodeproject.org/ENCBS588OTO/

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


title: total RNA-seq from adrenal gland (ENCLB686WLX)

description:
https://www.encodeproject.org/experiments/ENCSR442XRH/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND 18-20 months_Female 03 _ENC4_cDNA463
experiment encode accession: ENCSR442XRH
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB686WLX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: female

value: unknown

value: 18-20 month

value: ENCBS180MQS at ENCODE; https://www.encodeproject.org/ENCBS180MQS/


title: DNase-seq from kidney (ENCLB258ZHJ)

description:
https://www.encodeproject.org/experiments/ENCSR634ZDI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR634ZDI
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB258ZHJ
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: kidney

value: B6Cast F1 PND4 3x Females 06 kidney for Altius Stam core

value: 4 day

value: ENCBS914VCE at ENCODE; https://www.encodeproject.org/ENCBS914VCE/


title: DNase-seq from cerebellum (ENCLB561FHZ)

description:
https://www.encodeproject.org/experiments/ENCSR594HUH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR594HUH
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB561FHZ
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: cerebellum

value: tissue

value: B6Cast F1 PND10 3x Males 05 cerebellum for Altius Stam core

value: ENCBS346ZTC at ENCODE; https://www.encodeproject.org/ENCBS346ZTC/


title: R9306


title: DNase-seq from adrenal gland (ENCLB448KRY)

description:
https://www.encodeproject.org/experiments/ENCSR428CWD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR428CWD
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB448KRY
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: B6Cast F1 PND25 Male 05 adrenal gland for Altius Stam core

value: male

value: 25 day

value: Barbara Wold, Caltech

value: ENCBS906QIR at ENCODE; https://www.encodeproject.org/ENCBS906QIR/


title: BruUV-seq from IMR-90 (ENCLB920GIB)

description:
https://www.encodeproject.org/experiments/ENCSR351BRO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR351BRO
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR103IHW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB920GIB
size range: 400-500

source_name: Homo sapiens IMR-90 cell line

value: cell line

value: female

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS994KKX at ENCODE; https://www.encodeproject.org/ENCBS994KKX/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: total RNA-seq from left cerebral cortex (ENCLB130SFP)

description:
https://www.encodeproject.org/experiments/ENCSR702MVT/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND14 3x Males L. cortex
experiment encode accession: ENCSR702MVT
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB130SFP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: left cerebral cortex

value: B6Cast F1 PND14 3x Males 03 left cerebral cortex for Wold biobank

value: unknown

value: 14 day

value: The Jackson Laboratory

value: ENCBS993UDC at ENCODE; https://www.encodeproject.org/ENCBS993UDC/

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


title: R9288

source_name: Whole Blood


title: DNase-seq from gastrocnemius (ENCLB994OEW)

description:
https://www.encodeproject.org/experiments/ENCSR391YHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR391YHC
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB994OEW
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: gastrocnemius

value: tissue

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

value: male

value: 25 day

value: Barbara Wold, Caltech

value: ENCBS166BEA at ENCODE; https://www.encodeproject.org/ENCBS166BEA/


title: WGBS from bone marrow (ENCLB710QQH)

description:
https://www.encodeproject.org/experiments/ENCSR442FIY/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse bone marrow
experiment encode accession: ENCSR442FIY
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB710QQH
fragmentation methods: shearing (Covaris S2)
size range: 180-500

source_name: Mus musculus strain B6NCrl mixed sex adult (54-61 days) bone marrow tissue

value: bone marrow

value: Bone marrow from 16 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS218HTH at ENCODE; https://www.encodeproject.org/ENCBS218HTH/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: DNase-seq from adrenal gland (ENCLB663CDA)

description:
https://www.encodeproject.org/experiments/ENCSR385MRA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR385MRA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB663CDA
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: adrenal gland

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

value: unknown

value: 36 day

value: The Jackson Laboratory

value: ENCBS406KMH at ENCODE; https://www.encodeproject.org/ENCBS406KMH/

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


title: R9169


title: WGBS from bone marrow (ENCLB415NJA)

description:
https://www.encodeproject.org/experiments/ENCSR442FIY/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse bone marrow
experiment encode accession: ENCSR442FIY
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB415NJA
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: tissue

value: ENCBS430NOM at ENCODE; https://www.encodeproject.org/ENCBS430NOM/


title: ATAC-seq from HCT116 (ENCLB695IVW)

description:
https://www.encodeproject.org/experiments/ENCSR182JAI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR182JAI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB695IVW
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

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: ENCBS994GFO at ENCODE; https://www.encodeproject.org/ENCBS994GFO/

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


title: TF ChIP-seq from WTC11 (ENCLB379LXQ)

description:
https://www.encodeproject.org/experiments/ENCSR181ELQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-OVOL2 ChIP-seq on human WTC11
experiment encode accession: ENCSR181ELQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB379LXQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens OVOL2

value: adult

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS838QPG at ENCODE; https://www.encodeproject.org/ENCBS838QPG/

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB427ENQ)

description:
https://www.encodeproject.org/experiments/ENCSR033XWU/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4+ T cells (CD3+CD4+)
experiment encode accession: ENCSR033XWU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB427ENQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS075SKQ at ENCODE; https://www.encodeproject.org/ENCBS075SKQ/

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


title: WGBS from bone marrow (ENCLB781EXP)

description:
https://www.encodeproject.org/experiments/ENCSR442FIY/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse bone marrow
experiment encode accession: ENCSR442FIY
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB781EXP
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: bone marrow

value: tissue

value: Bone marrow from 16 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS218HTH at ENCODE; https://www.encodeproject.org/ENCBS218HTH/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: R9057


title: DNase-seq from gastrocnemius (ENCLB769ORF)

description:
https://www.encodeproject.org/experiments/ENCSR566VOB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR566VOB
assay title: DNase-seq
assembly: mm10
encode release date: 2021-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB769ORF
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: gastrocnemius

value: B6Cast F1 PND10 3x Females 05 gastrocnemius for Altius Stam core

value: female

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS363ZDB at ENCODE; https://www.encodeproject.org/ENCBS363ZDB/

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


title: DNase-seq from gastrocnemius (ENCLB788IND)

description:
https://www.encodeproject.org/experiments/ENCSR104BED/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR104BED
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB788IND
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: tissue

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

value: 14 day

value: ENCBS803LTR at ENCODE; https://www.encodeproject.org/ENCBS803LTR/


title: BruUV-seq from IMR-90 (ENCLB170SXU)

description:
https://www.encodeproject.org/experiments/ENCSR351BRO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR351BRO
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR103IHW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB170SXU
size range: 400-500

value: cell line

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS658LYN at ENCODE; https://www.encodeproject.org/ENCBS658LYN/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: R8876


title: DNase-seq from adrenal gland (ENCLB229FWR)

description:
https://www.encodeproject.org/experiments/ENCSR205UJK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR205UJK
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB229FWR
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: adrenal gland

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

value: male

value: unknown

value: ENCBS578KCV at ENCODE; https://www.encodeproject.org/ENCBS578KCV/


title: DNase-seq from cerebellum (ENCLB550DHY)

description:
https://www.encodeproject.org/experiments/ENCSR197ZAV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR197ZAV
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB550DHY
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: cerebellum

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

value: female

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS778FPW at ENCODE; https://www.encodeproject.org/ENCBS778FPW/

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


title: R8679


title: ATAC-seq from HCT116 (ENCLB052JKL)

description:
https://www.encodeproject.org/experiments/ENCSR345XUN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR345XUN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB052JKL
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS815HME at ENCODE; https://www.encodeproject.org/ENCBS815HME/

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


title: R9309


title: TF ChIP-seq from WTC11 (ENCLB345PRW)

description:
https://www.encodeproject.org/experiments/ENCSR181ELQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-OVOL2 ChIP-seq on human WTC11
experiment encode accession: ENCSR181ELQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB345PRW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS549LXL at ENCODE; https://www.encodeproject.org/ENCBS549LXL/

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


title: total RNA-seq from left cerebral cortex (ENCLB500ETG)

description:
https://www.encodeproject.org/experiments/ENCSR702MVT/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND14 3x Males L. cortex
experiment encode accession: ENCSR702MVT
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB500ETG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND14 3x Males 04 left cerebral cortex for Wold biobank

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS233WUB at ENCODE; https://www.encodeproject.org/ENCBS233WUB/


title: ATAC-seq from HCT116 (ENCLB367HRY)

description:
https://www.encodeproject.org/experiments/ENCSR182JAI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR182JAI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB367HRY
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: cell line

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: colorectal carcinoma

value: ENCBS461KYG at ENCODE; https://www.encodeproject.org/ENCBS461KYG/


title: DNase-seq from cerebellum (ENCLB062QCJ)

description:
https://www.encodeproject.org/experiments/ENCSR197ZAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR197ZAV
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB062QCJ
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

value: cerebellum

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

value: female

value: ENCBS263HBU at ENCODE; https://www.encodeproject.org/ENCBS263HBU/

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


title: ATAC-seq from HCT116 (ENCLB449ZXS)

description:
https://www.encodeproject.org/experiments/ENCSR345XUN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR345XUN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB449ZXS
fragmentation methods: sonication (Bioruptor Pico)
size range: 150-1000

value: male

value: ENCBS916CCP at ENCODE; https://www.encodeproject.org/ENCBS916CCP/

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


title: total RNA-seq from heart (ENCLB106BAA)

description:
https://www.encodeproject.org/experiments/ENCSR621FZG/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND25 Female heart
experiment encode accession: ENCSR621FZG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB106BAA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: heart

value: tissue

value: B6Cast F1 PND25 Female 03 heart for Wold biobank

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS395IFQ at ENCODE; https://www.encodeproject.org/ENCBS395IFQ/


title: DNase-seq from posterior cingulate gyrus (ENCLB145FBA)

description:
https://www.encodeproject.org/experiments/ENCSR059ETS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059ETS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB145FBA
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Homo sapiens female adult (85 years) posterior cingulate gyrus tissue

value: posterior cingulate gyrus

value: adult

value: 85 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS303JLZ at ENCODE; https://www.encodeproject.org/ENCBS303JLZ/

value: Derived from ENCODE donor ENCDO741DAO; https://www.encodeproject.org/ENCDO741DAO/


title: DNase-seq from kidney (ENCLB809DLS)

description:
https://www.encodeproject.org/experiments/ENCSR162TZA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR162TZA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-08-24
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB809DLS
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: kidney

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

value: male

value: 36 day

value: ENCBS588AUH at ENCODE; https://www.encodeproject.org/ENCBS588AUH/

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


title: total RNA-seq from layer of hippocampus (ENCLB567ECK)

description:
https://www.encodeproject.org/experiments/ENCSR548BTE/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6CastF1 PND36 male
experiment encode accession: ENCSR548BTE
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB567ECK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: layer of hippocampus

value: tissue

value: unknown

value: ENCBS421GWA at ENCODE; https://www.encodeproject.org/ENCBS421GWA/


title: DNase-seq from cerebellum (ENCLB783LKZ)

description:
https://www.encodeproject.org/experiments/ENCSR026MFT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR026MFT
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB783LKZ
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: cerebellum

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

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS770WQZ at ENCODE; https://www.encodeproject.org/ENCBS770WQZ/


title: R8407

source_name: Whole Blood


title: R7970


title: ATAC-seq from activated regulatory T cell (ENCLB353JAI)

description:
https://www.encodeproject.org/experiments/ENCSR261PWP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR261PWP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB353JAI
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (42 years) activated regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

value: activated regulatory T cell

value: primary cell

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS552AXV at ENCODE; https://www.encodeproject.org/ENCBS552AXV/

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


title: total RNA-seq from layer of hippocampus (ENCLB351OLV)

description:
https://www.encodeproject.org/experiments/ENCSR548BTE/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6CastF1 PND36 male
experiment encode accession: ENCSR548BTE
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB351OLV
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

value: tissue

value: male

value: unknown

value: 36 day

value: ENCBS154RYV at ENCODE; https://www.encodeproject.org/ENCBS154RYV/

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


title: ATAC-seq from HCT116 (ENCLB822GCL)

description:
https://www.encodeproject.org/experiments/ENCSR059BAR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059BAR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB822GCL
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5 treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

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: colorectal carcinoma

value: ENCBS252ELL at ENCODE; https://www.encodeproject.org/ENCBS252ELL/

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


title: ATAC-seq from HCT116 (ENCLB550ZHF)

description:
https://www.encodeproject.org/experiments/ENCSR059BAR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR059BAR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB550ZHF
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: adult

value: ENCBS242YQT at ENCODE; https://www.encodeproject.org/ENCBS242YQT/


title: DNase-seq from kidney (ENCLB837JKX)

description:
https://www.encodeproject.org/experiments/ENCSR023EDS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR023EDS
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB837JKX
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: kidney

value: B6Cast F1 PND25 Male 06 kidney for Altius Stam core

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS502RZJ at ENCODE; https://www.encodeproject.org/ENCBS502RZJ/


title: DNase-seq from kidney (ENCLB373PLD)

description:
https://www.encodeproject.org/experiments/ENCSR023EDS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR023EDS
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB373PLD
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

value: tissue

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

value: male

value: unknown

value: ENCBS512HPV at ENCODE; https://www.encodeproject.org/ENCBS512HPV/

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


title: total RNA-seq from gastrocnemius (ENCLB324KOJ)

description:
https://www.encodeproject.org/experiments/ENCSR603KGM/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND14 3x Males
experiment encode accession: ENCSR603KGM
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB324KOJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: gastrocnemius

value: B6Cast F1 PND14 3x Males 04 gastrocnemius for Wold core

value: 14 day

value: ENCBS368GVV at ENCODE; https://www.encodeproject.org/ENCBS368GVV/


title: WGBS from bone marrow (ENCLB183MEU)

description:
https://www.encodeproject.org/experiments/ENCSR442FIY/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse bone marrow
experiment encode accession: ENCSR442FIY
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB183MEU
fragmentation methods: shearing (Covaris S2)
size range: 180-500

source_name: Mus musculus strain B6NCrl mixed sex adult (54-61 days) bone marrow tissue

value: bone marrow

value: Bone marrow from 16 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS430NOM at ENCODE; https://www.encodeproject.org/ENCBS430NOM/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: total RNA-seq from heart (ENCLB360OTY)

description:
https://www.encodeproject.org/experiments/ENCSR621FZG/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND25 Female heart
experiment encode accession: ENCSR621FZG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB360OTY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: tissue

value: B6Cast F1 PND25 Female 04 heart for Wold biobank

value: female

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS130WUG at ENCODE; https://www.encodeproject.org/ENCBS130WUG/


title: R7754


title: total RNA-seq from gastrocnemius (ENCLB106CPZ)

description:
https://www.encodeproject.org/experiments/ENCSR603KGM/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND14 3x Males
experiment encode accession: ENCSR603KGM
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB106CPZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: gastrocnemius

value: B6Cast F1 PND14 3x Males 03 gastrocnemius for Wold core

value: male

value: unknown

value: 14 day

value: ENCBS340HGO at ENCODE; https://www.encodeproject.org/ENCBS340HGO/

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


title: DNase-seq from kidney (ENCLB245JDO)

description:
https://www.encodeproject.org/experiments/ENCSR113CGA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR113CGA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB245JDO
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

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

value: kidney

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

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


title: R7652


title: ATAC-seq from HCT116 (ENCLB047INV)

description:
https://www.encodeproject.org/experiments/ENCSR260SWI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR260SWI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB047INV
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

value: ENCBS962OFA at ENCODE; https://www.encodeproject.org/ENCBS962OFA/

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


title: DNase-seq from kidney (ENCLB044PTH)

description:
https://www.encodeproject.org/experiments/ENCSR113CGA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR113CGA
assay title: DNase-seq
assembly: mm10
encode release date: 2021-06-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB044PTH
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

value: tissue

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

value: female

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS638XMD at ENCODE; https://www.encodeproject.org/ENCBS638XMD/


title: ATAC-seq from HCT116 (ENCLB715QBW)

description:
https://www.encodeproject.org/experiments/ENCSR260SWI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR260SWI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB715QBW
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: male

value: ENCBS390RMH at ENCODE; https://www.encodeproject.org/ENCBS390RMH/


title: R8579


title: total RNA-seq from gastrocnemius (ENCLB264QAY)

description:
https://www.encodeproject.org/experiments/ENCSR432KHK/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND25 Male
experiment encode accession: ENCSR432KHK
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB264QAY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: gastrocnemius

value: B6Cast F1 PND25 Male 04 gastrocnemius for Wold core

value: unknown

value: 25 day

value: ENCBS737XNU at ENCODE; https://www.encodeproject.org/ENCBS737XNU/

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


title: R7454


title: total RNA-seq from gastrocnemius (ENCLB972WOO)

description:
https://www.encodeproject.org/experiments/ENCSR432KHK/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND25 Male
experiment encode accession: ENCSR432KHK
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB972WOO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6Cast F1 PND25 Male 03 gastrocnemius for Wold core

value: ENCBS404WDD at ENCODE; https://www.encodeproject.org/ENCBS404WDD/


title: R7775


title: RNAseq-HL-E125-WT

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

data_processing: Single-end reads were mapped to the mm9 reference genome using STAR mapper version 2.5.2a with default settings. Further processing was done according to (Paliou et al. 2019). BigWig files were visualized in the UCSC genome browser. Counting was done using R version 3.6.2 and differential expression was analyzed through the “DEseq2” R package. The DEseq2 R package was also used to produce heatmaps by subtracting from each gene value per condition, given by vst, the mean value of all conditions. Genes were picked according to adjusted p-value, all being significantly differentially expressed between conditions. Pitx1 fold enrichment between WT GFP+ and GFP- populations was calculated normalizing the total normalized read count per million. Significance in the fold enrichment was calculated using a Student’s t.test (type 2, 1 tail), inputting the normalized counts from each condition (2 normalized counts per genetic background). Expression heatmaps were generated for satellite and mesenchymal markers as defined in Supplementary table S1. Moreover, genes with expression less or equal to 1 RPKM in all 8 samples (GFP+ wildtype: replicate 1 and 2; GFP- wildtype: replicate 1 and 2, GFP+ mutant: replicate 1 and 2; GFP- mutant: replicate 1 and 2) were removed from the analysis. For the GFP- specific heatmap, we additionally removed all genes with less or equal to 1 RPKM in all 4 GFP- samples. The colour of the expression heatmap corresponds to the z-score transformed RPKM values, using the mean and standard deviation per gene based on all 8 samples. Log2FC was calculated by averaging replicates RPKM for each datasets and dividing Pitx1GFP and Pitx1GFP;ΔPen values.

source_name: Embryonic Limb Bud

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted according to GFP status.

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C, supernatant was discarded and cells frozen at -80°C. Total RNA from 1,5 x10^5 cells was isolated using the RNeasy Micro Kit (QIAGEN, ID:74004) following manufacturer’s instructions and then stored frozen at -80°C. Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 5 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell for an average of 35 mio reads / library. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: tissue

value: Embryonic Limb Bud

tag: cell population

value: whole limb

tag: genotype

value: wildtype


title: R7325

tag: subject id

tag: timepoint


title: ATAC-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB810KMZ)

description:
https://www.encodeproject.org/experiments/ENCSR174SUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR174SUM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB810KMZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: primary cell

value: adult

value: 48 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS763XZW at ENCODE; https://www.encodeproject.org/ENCBS763XZW/

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


title: ATAC-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB380SWI)

description:
https://www.encodeproject.org/experiments/ENCSR174SUM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR174SUM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB380SWI
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: male

value: ENCBS623HHL at ENCODE; https://www.encodeproject.org/ENCBS623HHL/


title: total RNA-seq from layer of hippocampus (ENCLB340EBO)

description:
https://www.encodeproject.org/experiments/ENCSR421HSE/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6CastF1 PND14 3x male
experiment encode accession: ENCSR421HSE
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB340EBO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: layer of hippocampus

value: tissue

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS299AJA at ENCODE; https://www.encodeproject.org/ENCBS299AJA/


title: R7433

tag: cmv dnaemia


title: ATAC-seq from activated effector memory CD8-positive, alpha-beta T cell (ENCLB774LNE)

description:
https://www.encodeproject.org/experiments/ENCSR335LHS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR335LHS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB774LNE
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (33 years) activated effector memory CD8-positive, alpha-beta T primary cell

value: 33 year

value: ENCBS371TCO at ENCODE; https://www.encodeproject.org/ENCBS371TCO/

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


title: R7204


title: R7082


title: RNAseq-HL-E125-WT-GFPhigh

value: Embryonic Limb Bud

value: GFP++


title: total RNA-seq from left cerebral cortex (ENCLB130HBI)

description:
https://www.encodeproject.org/experiments/ENCSR516DAX/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND10 Male L. cortex
experiment encode accession: ENCSR516DAX
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB130HBI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: left cerebral cortex

value: B6Cast F1 PND10 Male 04 left cerebral cortex for Wold biobank

value: 10 day

value: ENCBS919NNU at ENCODE; https://www.encodeproject.org/ENCBS919NNU/

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


title: R6989


title: ATAC-seq from activated effector memory CD8-positive, alpha-beta T cell (ENCLB355CYJ)

description:
https://www.encodeproject.org/experiments/ENCSR335LHS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR335LHS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB355CYJ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: primary cell

value: male

value: adult

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS257CBK at ENCODE; https://www.encodeproject.org/ENCBS257CBK/


title: RNAseq-HL-E125-WT-GFPinterm

value: GFP+-


title: total RNA-seq from left cerebral cortex (ENCLB365RSW)

description:
https://www.encodeproject.org/experiments/ENCSR516DAX/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND10 Male L. cortex
experiment encode accession: ENCSR516DAX
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB365RSW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: B6Cast F1 PND10 Male 03 left cerebral cortex for Wold biobank

value: unknown

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS941MMJ at ENCODE; https://www.encodeproject.org/ENCBS941MMJ/


title: RNAseq-HL-E125-WT-GFP

value: Embryonic Limb Bud

value: whole limb


title: Control ChIP-seq from WTC11 (ENCLB288HKO)

description:
https://www.encodeproject.org/experiments/ENCSR049LUW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR049LUW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB288HKO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line

tag: line

value: cell line

value: 30 year

value: Kevin White

value: ENCBS724XUU at ENCODE; https://www.encodeproject.org/ENCBS724XUU/

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


title: R6924


title: total RNA-seq from gastrocnemius (ENCLB666MVG)

description:
https://www.encodeproject.org/experiments/ENCSR510HZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND25 Female
experiment encode accession: ENCSR510HZQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB666MVG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: gastrocnemius

value: B6Cast F1 PND25 Female 03 gastrocnemius for Wold core

tag: biosample encode accession

value: female

value: 25 day

value: ENCBS508VOV at ENCODE; https://www.encodeproject.org/ENCBS508VOV/

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


title: R6651

source_name: Whole Blood


title: CC017_rep4

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

data_processing:
The PEPATAC pipeline with default parameters was used to perform adapter trimming, alignment, and peaking calling.
Sequenced reads were aligned to CC strain-specific pseudogenomes (Build 37, http://csbio.unc.edu/CCstatus/index.py?run=Pseudo).
Uniquely mapped reads were converted to mm9 genome coordinates, to allow for cross-strain comparisons, and alignments overlapping regions in the mm9 blocklist were removed.
Final alignments were converted to BED format and shifted by -5 and +5 base pairs for the negative and positive strain alignments, respectively.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BED files containing ATAC-seq sequence read alignments to the mm9 genome.

source_name: Airway macrophages

growth_protocol: Female and male CC mice were obtained from the UNC Systems Genetics Core Facility as weanlings and aged on investigator's racks. All experiments were performed when animals were between 10-12 weeks of age.

extract_protocol:
Airway macrophage pellets were gently lysed to release nuclei, which were pelleted by centrifugation and used directly for transposition reaction.
PCR amplification of the transposed DNA fragments was performed to add custom indexing primers. Final libraries were purified by double-sided size selection using Agencourt AMPure XP magnetic beads.

treatment_protocol: Mice were exposed to filtered air or 2 ppm ozone for 3 hours in individual wire-mesh cages without access to food or water, then returned to their home cages for 21 hours before necropsy.

tag: strain

tag: cell type

value: Airway macrophages

tag: treatment

value: 2 ppm ozone for 3 hours


title: CC017_rep3


title: CC017_rep2

value: filtered air for 3 hours


title: CC017_rep5


title: ATAC-seq from natural killer cell (ENCLB613WVF)

description:
https://www.encodeproject.org/experiments/ENCSR044ATC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR044ATC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB613WVF
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (41 years) natural killer primary cell

value: natural killer cell

value: primary cell

tag: Sex

tag: dev stage

value: adult

tag: age

value: 41 year

tag: lab

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS414QCP at ENCODE; https://www.encodeproject.org/ENCBS414QCP/

value: Derived from ENCODE donor ENCDO911LCI; https://www.encodeproject.org/ENCDO911LCI/