title: snRNA-seq from layer of hippocampus (ENCLB903KKG)

description:
https://www.encodeproject.org/experiments/ENCSR257VQO/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P10 female normal 2k
experiment encode accession: ENCSR257VQO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB903KKG
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J female postnatal (10 days) layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: B6/Cast F1 hippocampus P10 female 1

value: female

value: 10 day

value: ENCBS830ZRU at ENCODE; https://www.encodeproject.org/ENCBS830ZRU/


title: snRNA-seq from layer of hippocampus (ENCLB219EWD)

status: Public on Mar 06 2026

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/ENCSR257VQO/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P10 female normal 2k
experiment encode accession: ENCSR257VQO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB219EWD
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

value: tissue

tag: description

value: B6/Cast F1 hippocampus P10 female 2

tag: biosample encode accession

tag: Sex

tag: dev stage

value: postnatal

tag: age

tag: lab

value: Ali Mortazavi, UCI

tag: subcellular fraction term name

value: nucleus

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS600VDJ at ENCODE; https://www.encodeproject.org/ENCBS600VDJ/

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


title: snRNA-seq from heart (ENCLB874NGA)

description:
https://www.encodeproject.org/experiments/ENCSR266RTS/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read B6/Cast F1 heart P4 male normal 12k
experiment encode accession: ENCSR266RTS
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB874NGA

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

value: heart

value: B6/Cast F1 heart P4 male 1

value: male

value: 4 day

value: ENCBS212ZGA at ENCODE; https://www.encodeproject.org/ENCBS212ZGA/


title: snRNA-seq from left cerebral cortex (ENCLB475JGQ)

description:
https://www.encodeproject.org/experiments/ENCSR257BOU/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P10 female normal 2k
experiment encode accession: ENCSR257BOU
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB475JGQ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: left cerebral cortex

value: B6/Cast F1 cortex P10 female 2

value: ENCBS955GMS at ENCODE; https://www.encodeproject.org/ENCBS955GMS/


title: snRNA-seq from heart (ENCLB279AAX)

description:
https://www.encodeproject.org/experiments/ENCSR266RTS/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read B6/Cast F1 heart P4 male normal 12k
experiment encode accession: ENCSR266RTS
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB279AAX


title: snRNA-seq from left cerebral cortex (ENCLB603FZI)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB603FZI

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

value: B6/Cast F1 cortex P36 male 1

value: 36 day

value: ENCBS437MUU at ENCODE; https://www.encodeproject.org/ENCBS437MUU/


title: snRNA-seq from adrenal gland (ENCLB944QTS)

description:
https://www.encodeproject.org/experiments/ENCSR263VNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P25 male ont_match 2k
experiment encode accession: ENCSR263VNQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB944QTS
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P25 male 2

value: postnatal

value: 25 day

value: ENCBS683KKF at ENCODE; https://www.encodeproject.org/ENCBS683KKF/


title: snRNA-seq from heart (ENCLB731YVH)

description:
https://www.encodeproject.org/experiments/ENCSR266RTS/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read B6/Cast F1 heart P4 male normal 12k
experiment encode accession: ENCSR266RTS
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB731YVH

value: heart

value: B6/Cast F1 heart P4 male 2

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS356FYU at ENCODE; https://www.encodeproject.org/ENCBS356FYU/

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


title: snRNA-seq from left cerebral cortex (ENCLB901OXL)

description:
https://www.encodeproject.org/experiments/ENCSR308DHB/
***************
biological replicate number: 2
technical replicate number: 6
description: Illumina short-read B6/Cast F1 cortex P18-20mo female normal 12k
experiment encode accession: ENCSR308DHB
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB901OXL

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

value: left cerebral cortex

value: B6/Cast F1 cortex P18-20mo female 2

value: female

value: adult

value: 18-20 month

value: ENCBS527NEL at ENCODE; https://www.encodeproject.org/ENCBS527NEL/


title: snRNA-seq from adrenal gland (ENCLB668FHK)

description:
https://www.encodeproject.org/experiments/ENCSR263VNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P25 male ont_match 2k
experiment encode accession: ENCSR263VNQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB668FHK
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P25 male 1

value: male

value: ENCBS826WGQ at ENCODE; https://www.encodeproject.org/ENCBS826WGQ/


title: snRNA-seq from left cerebral cortex (ENCLB536VVO)

description:
https://www.encodeproject.org/experiments/ENCSR257BOU/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P10 female normal 2k
experiment encode accession: ENCSR257BOU
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB536VVO
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 cortex P10 female 1

value: postnatal

value: 10 day

value: ENCBS613XIS at ENCODE; https://www.encodeproject.org/ENCBS613XIS/


title: snRNA-seq from heart (ENCLB469HGI)

description:
https://www.encodeproject.org/experiments/ENCSR266RTS/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P4 male normal 12k
experiment encode accession: ENCSR266RTS
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB469HGI

value: heart

value: B6/Cast F1 heart P4 male 1

value: 4 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS212ZGA at ENCODE; https://www.encodeproject.org/ENCBS212ZGA/


title: snRNA-seq from left cerebral cortex (ENCLB414KNZ)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB414KNZ

value: left cerebral cortex

value: B6/Cast F1 cortex P36 male 2

value: 36 day

value: ENCBS784PKN at ENCODE; https://www.encodeproject.org/ENCBS784PKN/

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


title: snRNA-seq from left cerebral cortex (ENCLB417EQW)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 1
technical replicate number: 6
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB417EQW

value: tissue

value: B6/Cast F1 cortex P36 male 1

value: male

value: ENCBS437MUU at ENCODE; https://www.encodeproject.org/ENCBS437MUU/


title: snRNA-seq from left cerebral cortex (ENCLB928YMW)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 1
technical replicate number: 5
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB928YMW

value: postnatal


title: snRNA-seq from left cerebral cortex (ENCLB611KSY)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB611KSY


title: snRNA-seq from left cerebral cortex (ENCLB342GBS)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB342GBS


title: snRNA-seq from left cerebral cortex (ENCLB691ZDJ)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB691ZDJ


title: snRNA-seq from left cerebral cortex (ENCLB283GLR)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB283GLR


title: snRNA-seq from left cerebral cortex (ENCLB496OEP)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB496OEP


title: snRNA-seq from left cerebral cortex (ENCLB507JAX)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 2
technical replicate number: 5
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB507JAX


title: snRNA-seq from left cerebral cortex (ENCLB363WTB)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 2
technical replicate number: 6
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB363WTB


title: snRNA-seq from left cerebral cortex (ENCLB223DPT)

description:
https://www.encodeproject.org/experiments/ENCSR250SCW/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P2mo male normal 2k
experiment encode accession: ENCSR250SCW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB223DPT
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: B6/Cast F1 cortex P2mo male 1

value: adult

value: 2 month

value: ENCBS510JLV at ENCODE; https://www.encodeproject.org/ENCBS510JLV/


title: snRNA-seq from gastrocnemius (ENCLB315VLE)

description:
https://www.encodeproject.org/experiments/ENCSR253YLA/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P10 female normal 15k
experiment encode accession: ENCSR253YLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB315VLE

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

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P10 female 2

value: female

value: 10 day

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS933EVB at ENCODE; https://www.encodeproject.org/ENCBS933EVB/


title: snRNA-seq from gastrocnemius (ENCLB145UXM)

description:
https://www.encodeproject.org/experiments/ENCSR253YLA/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read B6/Cast F1 gastrocnemius P10 female normal 15k
experiment encode accession: ENCSR253YLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB145UXM

value: B6/Cast F1 gastrocnemius P10 female 1

value: The Jackson Laboratory

value: ENCBS180IZM at ENCODE; https://www.encodeproject.org/ENCBS180IZM/

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


title: snRNA-seq from gastrocnemius (ENCLB699IMY)

description:
https://www.encodeproject.org/experiments/ENCSR253YLA/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P10 female normal 15k
experiment encode accession: ENCSR253YLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB699IMY

value: tissue


title: snRNA-seq from left cerebral cortex (ENCLB563CRJ)

description:
https://www.encodeproject.org/experiments/ENCSR254SLA/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read B6/Cast F1 cortex P36 male normal 12k
experiment encode accession: ENCSR254SLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB563CRJ

value: left cerebral cortex

value: B6/Cast F1 cortex P36 male 1

value: male

value: postnatal

value: 36 day

value: ENCBS437MUU at ENCODE; https://www.encodeproject.org/ENCBS437MUU/


title: snRNA-seq from left cerebral cortex (ENCLB777CMQ)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB777CMQ

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

value: B6/Cast F1 cortex P25 male 2

value: 25 day

value: ENCBS303GRJ at ENCODE; https://www.encodeproject.org/ENCBS303GRJ/


title: snRNA-seq from left cerebral cortex (ENCLB696ABU)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 2
technical replicate number: 6
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB696ABU

value: Ali Mortazavi, UCI


title: snRNA-seq from left cerebral cortex (ENCLB799LCJ)

description:
https://www.encodeproject.org/experiments/ENCSR250SCW/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P2mo male normal 2k
experiment encode accession: ENCSR250SCW
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB799LCJ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 cortex P2mo male 2

value: adult

value: 2 month

value: nucleus

value: ENCBS522UXP at ENCODE; https://www.encodeproject.org/ENCBS522UXP/


title: snRNA-seq from gastrocnemius (ENCLB189CHU)

description:
https://www.encodeproject.org/experiments/ENCSR253YLA/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 gastrocnemius P10 female normal 15k
experiment encode accession: ENCSR253YLA
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB189CHU

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P10 female 2

value: female

value: 10 day

value: The Jackson Laboratory

value: ENCBS933EVB at ENCODE; https://www.encodeproject.org/ENCBS933EVB/

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


title: snRNA-seq from left cerebral cortex (ENCLB417MYN)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB417MYN

value: left cerebral cortex

value: tissue

value: B6/Cast F1 cortex P25 male 1

value: male

value: postnatal

value: ENCBS752LYQ at ENCODE; https://www.encodeproject.org/ENCBS752LYQ/


title: snRNA-seq from left cerebral cortex (ENCLB412QYC)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 1
technical replicate number: 5
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB412QYC

value: 25 day

value: Ali Mortazavi, UCI


title: snRNA-seq from left cerebral cortex (ENCLB630AUB)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 2
technical replicate number: 5
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB630AUB

value: B6/Cast F1 cortex P25 male 2

value: nucleus

value: ENCBS303GRJ at ENCODE; https://www.encodeproject.org/ENCBS303GRJ/


title: snRNA-seq from left cerebral cortex (ENCLB534DUU)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB534DUU


title: A549-shLDOC1-V (2)

type: RNA

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

hyb_protocol: Samples were hybridized with Clariom™ S Assay, human Arrays (Applied Biosystems) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Applied Biosystems)

data_processing: Data were processed usingTranscriptome Analysis Console (TAC) Software which normalizes array signals using MAS5 algorithm.

label: biotin

organism: Homo sapiens

source_name: Lung adenocarcinoma

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Applied Biosystems) and then fragmented and labeled with the WT Terminal Labeling Kit (Applied Biosystems).

growth_protocol: All A549-derived cell sublines, including A549-shLDOC1 and A549-H2BK120R, and their corresponding control  cell lines were maintained in DMEM (high glucose) medium supplemented with 10% FBS, penicillin (100 U/mL), streptomycin (100 μg/mL) and puromycin (5μg/mL). ed 5% CO2 incubator.

extract_protocol: Total RNA were extracted from cells with more than 90% confluency using RNeasy Mini-kit (Qiagen, MD, USA) followed the manufacturer’s protocol.

tag: genotype

value: WT EGFR

tag: cell line

tag: tumor type

value: lung adenocarcinoma

tag: treatment

value: a vector control cell line of A549-shLDOC1-H2BK120R


title: A549-shLDOC1 (1)

value: an LDOC1-depleted A549 cell line


title: snRNA-seq from left cerebral cortex (ENCLB388FEE)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 1
technical replicate number: 6
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB388FEE

value: The Jackson Laboratory


title: snRNA-seq from left cerebral cortex (ENCLB003XFR)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB003XFR

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


title: snRNA-seq from left cerebral cortex (ENCLB214WZS)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB214WZS

value: left cerebral cortex


title: snRNA-seq from left cerebral cortex (ENCLB372FBK)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB372FBK

value: tissue


title: A549-shCtrl (2)

value: a vector control cell line of A549-shLDOC1


title: A549-shCtrl (1)


title: A549-shLDOC1-V (1)


title: A549-shLDOC1-H2BK120R (2)

value: an LDOC1-depleted A549 cell line expressing muant H2BK120R


title: snATAC-seq, hypothalamus, control, female, pool B

city: Clemson

first: Prakrit

last: Subba

state: SC

address: 132 Long Hall, 230 Parkway Drive

department: Biological Sciences

institute: Clemson University

description:
Library name: S8_ATAC
10x Chromium Next GEM Multiome snATAC-seq; control condition; female; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains ATAC sequence; I1 contains sample index; I2 contains 10x nucleus barcode

library_source: genomic single cell

data_processing:
BCL files were demultiplexed and converted to FASTQ using BCL Convert (v4.1.23).
FASTQ files were aligned to the zebra finch reference genome (bTaeGut1.4.pri; GCF_003957565.2) and processed using 10x Cellranger-arc (v2.0.2) to generate filtered feature-barcode matrices and ATAC peak calls.
Gene expression data imported into Seurat (v5.2.1) were filtered by gene count (200–3,500), UMI count (500–25,000), and mitochondrial content (<5%). Normalized using SCTransform; top 35 PCs used for downstream analysis.
ATAC chromatin accessibility data imported into Signac (v1.14.0): sample-specific peaks were merged and filtered by peak length (20–10,000 bp). Cells retained based on ATAC fragments (100–100,000), fraction of reads in peaks (>15%), nucleosome signal (<4), and TSS enrichment (>2). Normalized using TF-IDF (RunTFIDF); top 20% features retained (FindTopFeatures); dimensionality reduction by SVD (RunSVD, top 50 LSI components, excluding LSI 1).
Joint multimodal clustering performed using Weighted Nearest Neighbor (WNN) analysis integrating RNA PCA (35 PCs) and ATAC LSI (LSI 2–50) in Seurat/Signac, with Smart Local Moving clustering (resolution = 0.6) and UMAP visualization.
Assembly: bTaeGut1.4.pri (GCF_003957565.2)
Supplementary files format and content: Cellranger-arc output: S[1-8]_barcodes.tsv.gz (filtered cell barcodes), S[1-8]_features.tsv.gz (gene features), S[1-8]_matrix.mtx.gz (filtered UMI count matrix in Matrix Market format)
Supplementary files format and content: Cellranger-arc output: S[1-8]_atac_fragments.tsv.gz (ATAC fragment file, position-sorted), S[1-8]_atac_fragments.tsv.gz.tbi (tabix index)
Supplementary files format and content: Cellranger-arc output: S[1-8]_atac_peaks.bed (called ATAC peaks in BED format), S[1-8]_atac_peak_annotation.tsv (peak-to-gene annotations)

molecule: genomic DNA

organism: Taeniopygia guttata

source_name: hypothalamus

growth_protocol: Zebra finch eggs were incubated at 37.5°C in experimental incubators and exposed to either heat call or control call playback (9 hours/day) from embryonic day 9 to embryonic day 13.

extract_protocol:
Medial hypothalamic tissue was collected from frozen heads via a double-punch technique (two 1 mm diameter overlapping circular punches in a figure-8 configuration) during 100 μm coronal cryostat sectioning (Leica CM3050 S). Punching began when the third ventricle became visible (~5,000 μm caudal to the beak). Tissue was collected in cryotubes on dry ice and stored at −80°C. Samples were pooled by sex and condition (n=4 heat call pools, n=4 control pools; 5 punches per pool; 2 pools per sex × condition combination). Nuclei were isolated by lysis for 5 minutes in 500 μL chilled 0.1x lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% Igepal CA-630, 0.001% Digitonin, 1% BSA, 1 mM DTT, 40 U/μL RNase inhibitor) with 15 homogenization strokes. Lysate was washed with 500 μL wash buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 40 U/μL RNase inhibitor) and filtered sequentially through Flowmi 70 μm (330 μL per pass), Flowmi 40 μm, and pluriStrainer Mini 20 μm cell strainers, with centrifugation at 500 rcf, 4°C, 5 min between steps. Final nuclei were resuspended in chilled 1% BSA in 1x PBS (target: 3,200–8,000 nuclei/μL) and quantified on a Countess II FL Cell Counter with DAPI fluorescence quality assessment.
Nuclei were processed using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit (v1, CG000338, Rev G). Nuclei were transposed with ATAC Buffer B and ATAC Enzyme B at 37°C for 60 minutes. Simultaneous barcoding of transposed ATAC fragments and mRNA-derived cDNA was performed on the Chromium iX instrument using Chromium Next GEM Chip J to generate GEMs. Purified nucleic acids were obtained using Dynabeads MyOne SILANE and SPRIselect beads. Purified material underwent pre-amplification PCR before splitting for ATAC and GEX library construction. ATAC libraries were generated by sample index PCR with SI-PCR Primer B and Amp Mix (14–16 cycles) and double-sided SPRIselect size selection. GEX libraries were generated by cDNA PCR (12 cycles), fragmentation, end repair, A-tailing, adaptor ligation, indexing PCR (14–16 cycles), and double-sided SPRIselect size selection. Fragment QC used Agilent TapeStation High Sensitivity D5000 (ATAC) and D1000 (GEX) kits; concentration QC used Qubit 1X dsDNA HS kit. Libraries were pooled and sequenced on the Illumina NovaSeq X+.

treatment_protocol: Viable zebra finch eggs (embryonic stage 15, E2.75) were transferred to a shared artificial incubator (Ovation EX, Brinsea) at 37.5°C and 60% humidity to equalize the pre-playback environment. On the evening of E8, eggs were randomly assigned to one of two experimental incubators (Octagon eco, Brinsea), each delivering a different sound playback treatment. The control group (n=20) received whine calls combined with tet calls; the experimental group (n=20) received whine calls combined with heat calls. Playbacks ran daily from E9 to E13 for 9 hours/day (9am–6pm) at 60–70 dB via speakers (PUI Audio Speaker 3W 8OHM 85DB 300HZ, Part Number: AS05508MO) connected to an amplifier (Facmogu F900s) and Apple iPad (9th gen). A 77-minute looped sequence of alternating whine and heat/control calls played continuously over each 9-hour session. All eggs were within 5 cm of the speaker; trays were rotated daily for uniform acoustic exposure. On the morning of E13, embryos were euthanized by rapid decapitation and heads were flash frozen in OCT-embedded blocks and stored at −80°C.

tag: tissue

value: hypothalamus

value: female

tag: cell type

value: single nucleus, mixed hypothalamic

value: embryonic day 13

value: control

tag: library type

value: ATAC


title: snRNA-seq, hypothalamus, control, male, pool B

description:
Library name: S7_GE
10x Chromium Next GEM Multiome snRNA-seq; control condition; male; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains transcript sequence

library_source: transcriptomic single cell

molecule: nuclear RNA

value: male

value: mRNA


title: snRNA-seq, hypothalamus, control, female, pool B

description:
Library name: S8_GE
10x Chromium Next GEM Multiome snRNA-seq; control condition; female; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains transcript sequence


title: snRNA-seq from left cerebral cortex (ENCLB613KZV)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB613KZV

value: B6/Cast F1 cortex P25 male 1

value: postnatal

value: 25 day

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS752LYQ at ENCODE; https://www.encodeproject.org/ENCBS752LYQ/


title: A549-shLDOC1-H2BK120R (1)

value: WT EGFR

value: lung adenocarcinoma


title: snRNA-seq from layer of hippocampus (ENCLB208PDA)

description:
https://www.encodeproject.org/experiments/ENCSR247QPJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P14 male ont_match 2k
experiment encode accession: ENCSR247QPJ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB208PDA
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P14 male 2

value: 14 day

value: The Jackson Laboratory

value: ENCBS013DIR at ENCODE; https://www.encodeproject.org/ENCBS013DIR/

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


title: snATAC-seq, hypothalamus, control, male, pool B

description:
Library name: S7_ATAC
10x Chromium Next GEM Multiome snATAC-seq; control condition; male; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains ATAC sequence; I1 contains sample index; I2 contains 10x nucleus barcode

value: hypothalamus

value: male

value: single nucleus, mixed hypothalamic

value: embryonic day 13

value: control

value: ATAC


title: A549-shLDOC1 (2)

value: an LDOC1-depleted A549 cell line


title: snATAC-seq, hypothalamus, heat call, female, pool B

description:
Library name: S6_ATAC
10x Chromium Next GEM Multiome snATAC-seq; heat call condition; female; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains ATAC sequence; I1 contains sample index; I2 contains 10x nucleus barcode

value: female

value: heat call


title: snRNA-seq from heart (ENCLB648HBN)

description:
https://www.encodeproject.org/experiments/ENCSR247PQY/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P4 male normal 2k
experiment encode accession: ENCSR247PQY
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB648HBN
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: heart

value: B6/Cast F1 heart P4 male 1

value: postnatal

value: 4 day

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS212ZGA at ENCODE; https://www.encodeproject.org/ENCBS212ZGA/


title: snRNA-seq, hypothalamus, heat call, male, pool B

description:
Library name: S5_GE
10x Chromium Next GEM Multiome snRNA-seq; heat call condition; male; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains transcript sequence

value: mRNA


title: snATAC-seq, hypothalamus, heat call, male, pool B

description:
Library name: S5_ATAC
10x Chromium Next GEM Multiome snATAC-seq; heat call condition; male; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains ATAC sequence; I1 contains sample index; I2 contains 10x nucleus barcode

value: hypothalamus


title: snRNA-seq from layer of hippocampus (ENCLB245USU)

description:
https://www.encodeproject.org/experiments/ENCSR247QPJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P14 male ont_match 2k
experiment encode accession: ENCSR247QPJ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB245USU
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P14 male 1

value: male

value: 14 day

value: The Jackson Laboratory

value: ENCBS857GBI at ENCODE; https://www.encodeproject.org/ENCBS857GBI/

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


title: snATAC-seq, hypothalamus, control, female, pool A

description:
Library name: S4_ATAC
10x Chromium Next GEM Multiome snATAC-seq; control condition; female; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains ATAC sequence; I1 contains sample index; I2 contains 10x nucleus barcode

value: female

value: single nucleus, mixed hypothalamic

value: embryonic day 13

value: control

value: ATAC


title: snRNA-seq, hypothalamus, control, female, pool A

description:
Library name: S4_GE
10x Chromium Next GEM Multiome snRNA-seq; control condition; female; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains transcript sequence


title: snATAC-seq, hypothalamus, control, male, pool A

description:
Library name: S3_ATAC
10x Chromium Next GEM Multiome snATAC-seq; control condition; male; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains ATAC sequence; I1 contains sample index; I2 contains 10x nucleus barcode


title: snRNA-seq from layer of hippocampus (ENCLB217YGZ)

description:
https://www.encodeproject.org/experiments/ENCSR232VMC/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P18-20mo male ont_match 2k
experiment encode accession: ENCSR232VMC
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB217YGZ
nucleic acid starting quantity: 167
nucleic acid starting quantity units: cells

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

value: B6/Cast F1 hippocampus P18-20mo male 2

value: adult

value: 18-20 month

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS414FUV at ENCODE; https://www.encodeproject.org/ENCBS414FUV/


title: snRNA-seq from left cerebral cortex (ENCLB622ADD)

description:
https://www.encodeproject.org/experiments/ENCSR248MFG/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read B6/Cast F1 cortex P25 male normal 12k
experiment encode accession: ENCSR248MFG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB622ADD

value: left cerebral cortex

value: tissue

value: B6/Cast F1 cortex P25 male 1

value: postnatal

value: 25 day

value: ENCBS752LYQ at ENCODE; https://www.encodeproject.org/ENCBS752LYQ/


title: snRNA-seq from heart (ENCLB540ICC)

description:
https://www.encodeproject.org/experiments/ENCSR237OCP/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P25 female normal 2k
experiment encode accession: ENCSR237OCP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB540ICC
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: heart

value: B6/Cast F1 heart P25 female 1

value: female

value: The Jackson Laboratory

value: ENCBS961MPB at ENCODE; https://www.encodeproject.org/ENCBS961MPB/

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


title: snRNA-seq from heart (ENCLB270IKS)

description:
https://www.encodeproject.org/experiments/ENCSR247PQY/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P4 male normal 2k
experiment encode accession: ENCSR247PQY
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB270IKS
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 heart P4 male 2

value: male

value: 4 day

value: ENCBS356FYU at ENCODE; https://www.encodeproject.org/ENCBS356FYU/


title: snRNA-seq from heart (ENCLB574GTO)

description:
https://www.encodeproject.org/experiments/ENCSR237OCP/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P25 female normal 2k
experiment encode accession: ENCSR237OCP
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB574GTO
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 heart P25 female 2

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS851DUN at ENCODE; https://www.encodeproject.org/ENCBS851DUN/


title: snRNA-seq, hypothalamus, heat call, female, pool A

description:
Library name: S2_GE
10x Chromium Next GEM Multiome snRNA-seq; heat call condition; female; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains transcript sequence

value: hypothalamus

value: single nucleus, mixed hypothalamic

value: embryonic day 13

value: heat call

value: mRNA


title: snATAC-seq, hypothalamus, heat call, female, pool A

description:
Library name: S2_ATAC
10x Chromium Next GEM Multiome snATAC-seq; heat call condition; female; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains ATAC sequence; I1 contains sample index; I2 contains 10x nucleus barcode

value: female

value: ATAC


title: snRNA-seq, hypothalamus, heat call, female, pool B

description:
Library name: S6_GE
10x Chromium Next GEM Multiome snRNA-seq; heat call condition; female; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains transcript sequence


title: snRNA-seq from heart (ENCLB928QUX)

description:
https://www.encodeproject.org/experiments/ENCSR266RTS/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 heart P4 male normal 12k
experiment encode accession: ENCSR266RTS
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB928QUX

value: heart

value: tissue

value: postnatal

value: The Jackson Laboratory


title: snRNA-seq, hypothalamus, control, male, pool A

description:
Library name: S3_GE
10x Chromium Next GEM Multiome snRNA-seq; control condition; male; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains transcript sequence

value: male

value: control


title: snRNA-seq from gastrocnemius (ENCLB571LOU)

description:
https://www.encodeproject.org/experiments/ENCSR231VJO/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P36 male normal 2k
experiment encode accession: ENCSR231VJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB571LOU
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

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

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P36 male 1

value: 36 day

value: ENCBS325GUZ at ENCODE; https://www.encodeproject.org/ENCBS325GUZ/

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


title: snATAC-seq, hypothalamus, heat call, male, pool A

description:
Library name: S1_ATAC
10x Chromium Next GEM Multiome snATAC-seq; heat call condition; male; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains ATAC sequence; I1 contains sample index; I2 contains 10x nucleus barcode

value: hypothalamus

value: single nucleus, mixed hypothalamic


title: snRNA-seq from adrenal gland (ENCLB126DIM)

description:
https://www.encodeproject.org/experiments/ENCSR216UTT/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P2mo male ont_match 2k
experiment encode accession: ENCSR216UTT
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB126DIM
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: adrenal gland

value: B6/Cast F1 adrenal P2mo male 2

value: adult

value: 2 month

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS606AOJ at ENCODE; https://www.encodeproject.org/ENCBS606AOJ/


title: snRNA-seq, hypothalamus, heat call, male, pool A

description:
Library name: S1_GE
10x Chromium Next GEM Multiome snRNA-seq; heat call condition; male; pool of 5 hypothalamic tissue punches; read1 contains cell barcode and UMI; read2 contains transcript sequence

value: embryonic day 13

value: heat call

value: mRNA


title: snRNA-seq from layer of hippocampus (ENCLB690SEK)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB690SEK

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

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P2mo female 1

value: female

value: The Jackson Laboratory

value: ENCBS554AFJ at ENCODE; https://www.encodeproject.org/ENCBS554AFJ/


title: snRNA-seq from left cerebral cortex (ENCLB927HPV)

description:
https://www.encodeproject.org/experiments/ENCSR220GBV/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P4 male normal 2k
experiment encode accession: ENCSR220GBV
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB927HPV
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: left cerebral cortex

value: B6/Cast F1 cortex P4 male 2

value: male

value: postnatal

value: 4 day

value: ENCBS546HYE at ENCODE; https://www.encodeproject.org/ENCBS546HYE/

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


title: snRNA-seq from gastrocnemius (ENCLB567VTD)

description:
https://www.encodeproject.org/experiments/ENCSR231VJO/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P36 male normal 2k
experiment encode accession: ENCSR231VJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB567VTD
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P36 male 2

value: 36 day

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS875BWJ at ENCODE; https://www.encodeproject.org/ENCBS875BWJ/


title: snRNA-seq from layer of hippocampus (ENCLB960KQB)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 2
technical replicate number: 5
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB960KQB

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P2mo female 2

value: adult

value: 2 month

value: ENCBS772CYI at ENCODE; https://www.encodeproject.org/ENCBS772CYI/


title: snRNA-seq from layer of hippocampus (ENCLB590LPL)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB590LPL

value: female

value: The Jackson Laboratory


title: DNase-seq from NCI-H1694 (ENCLB242KBE)

description:
https://www.encodeproject.org/experiments/ENCSR965SOG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR965SOG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB242KBE
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

library_source: genomic

source_name: Homo sapiens NCI-H1694 cell line treated with 0.1% DMSO for 48 hours

tag: line

value: cell line

tag: encode accession

value: male

value: 61 year

value: John Stamatoyannopoulos, UW

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:DMSO; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS719LYF at ENCODE; https://www.encodeproject.org/ENCBS719LYF/


title: snRNA-seq from layer of hippocampus (ENCLB925PUE)

description:
https://www.encodeproject.org/experiments/ENCSR232VMC/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P18-20mo male ont_match 2k
experiment encode accession: ENCSR232VMC
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB925PUE
nucleic acid starting quantity: 167
nucleic acid starting quantity units: cells

tag: description

value: B6/Cast F1 hippocampus P18-20mo male 1

tag: biosample encode accession

tag: Sex

value: 18-20 month

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS448REP at ENCODE; https://www.encodeproject.org/ENCBS448REP/

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


title: DNase-seq from NCI-H748 (ENCLB043RML)

description:
https://www.encodeproject.org/experiments/ENCSR409ZBU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR409ZBU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB043RML
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens NCI-H748 cell line treated with 0.1% DMSO for 48 hours

tag: dev stage

value: adult

tag: age

value: 62 year

tag: lab

value: ENCBS940RVG at ENCODE; https://www.encodeproject.org/ENCBS940RVG/


title: PC9-LDOC1 depletion-Rep1

description: A stable clone was selected from PC9 cells infected with lentivirus carrying an shRNA specifically targeting LDOC1.

hyb_protocol: Samples were hybridized with Human Genome U133 Plus 2.0 Array (Affymetrix) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were analyzed using Affymetrix Transcriptome Analysis Console (TAC) Software (version 4.0.2) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

label: Biotin

source_name: NSCLC cell line_LDOC1 depletion

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells are cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and optionally 1% penicillin-streptomycin. The cells are maintained at 37°C in a humidified incubator with 5% CO₂. They should be passaged at a ratio of 1:3 to 1:5 when reaching approximately 70-80% confluency, using 0.25% trypsin-EDTA for detachment. Cells are typically cultured on tissue culture-treated flasks or dishes.

extract_protocol: Total RNA was isolated cultured cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Without any pretreatment before total RNA extraction

tag: gender

value: female

value: lung adenocarcinoma

tag: tumor stage

tag: tumor subtype

value: EGFR exon 19 del


title: snRNA-seq from left cerebral cortex (ENCLB807BQV)

description:
https://www.encodeproject.org/experiments/ENCSR220GBV/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P4 male normal 2k
experiment encode accession: ENCSR220GBV
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB807BQV
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: left cerebral cortex

value: tissue

value: B6/Cast F1 cortex P4 male 1

value: male

value: postnatal

value: 4 day

tag: subcellular fraction term name

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS091LPB at ENCODE; https://www.encodeproject.org/ENCBS091LPB/


title: snRNA-seq from adrenal gland (ENCLB419YTE)

description:
https://www.encodeproject.org/experiments/ENCSR216UTT/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P2mo male ont_match 2k
experiment encode accession: ENCSR216UTT
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB419YTE
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: B6/Cast F1 adrenal P2mo male 1

value: 2 month

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS709OTD at ENCODE; https://www.encodeproject.org/ENCBS709OTD/


title: snRNA-seq from layer of hippocampus (ENCLB351VZT)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB351VZT

value: layer of hippocampus

value: B6/Cast F1 hippocampus P2mo female 1

value: female

value: adult

value: ENCBS554AFJ at ENCODE; https://www.encodeproject.org/ENCBS554AFJ/

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


title: snRNA-seq from layer of hippocampus (ENCLB856XKJ)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB856XKJ

value: tissue


title: DNase-seq from NCI-H2081 (ENCLB823DCZ)

description:
https://www.encodeproject.org/experiments/ENCSR376MYJ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR376MYJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB823DCZ

source_name: Homo sapiens NCI-H2081 cell line

value: cell line

value: 59 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS152ETE at ENCODE; https://www.encodeproject.org/ENCBS152ETE/


title: PC9-LDOC1 depletion-Rep2

tag: tissue

value: lung adenocarcinoma

value: EGFR exon 19 del


title: snRNA-seq from layer of hippocampus (ENCLB175XVH)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB175XVH

value: 2 month

value: Ali Mortazavi, UCI

value: The Jackson Laboratory


title: DNase-seq from GF-D8 (ENCLB691MCC)

description:
https://www.encodeproject.org/experiments/ENCSR342FHH/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR342FHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB691MCC
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens GF-D8 cell line

value: male

value: 82 year

value: DSMZ

value: ENCBS799MRB at ENCODE; https://www.encodeproject.org/ENCBS799MRB/


title: snRNA-seq from layer of hippocampus (ENCLB979DTC)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB979DTC

value: layer of hippocampus

value: B6/Cast F1 hippocampus P2mo female 2

value: female

value: adult

value: nucleus

value: ENCBS772CYI at ENCODE; https://www.encodeproject.org/ENCBS772CYI/


title: snRNA-seq from layer of hippocampus (ENCLB393NYF)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 1
technical replicate number: 5
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB393NYF

value: tissue

value: B6/Cast F1 hippocampus P2mo female 1

value: ENCBS554AFJ at ENCODE; https://www.encodeproject.org/ENCBS554AFJ/

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


title: PC9-LDOC1 expressing-Rep1

description: A stable clone was selected from PC9 cells infected with lentivirus carrying a scramble control shRNA.

source_name: NSCLC cell line_LDOC1 expressing

value: lung adenocarcinoma

value: EGFR exon 19 del


title: DNase-seq from K562 (ENCLB408ZUQ)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB408ZUQ
instrument models: Illumina HiSeq 2500,Illumina HiSeq 4000

source_name: Homo sapiens K562 cell line

value: cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS294ZYF at ENCODE; https://www.encodeproject.org/ENCBS294ZYF/


title: DNase-seq from GF-D8 (ENCLB762FNL)

description:
https://www.encodeproject.org/experiments/ENCSR342FHH/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR342FHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB762FNL

tag: line

value: male

value: 82 year

value: DSMZ

value: ENCBS298HSZ at ENCODE; https://www.encodeproject.org/ENCBS298HSZ/


title: snRNA-seq from layer of hippocampus (ENCLB027GNG)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB027GNG

value: layer of hippocampus

value: B6/Cast F1 hippocampus P2mo female 2

value: female

value: adult

value: 2 month

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS772CYI at ENCODE; https://www.encodeproject.org/ENCBS772CYI/


title: DNase-seq from GF-D8 (ENCLB362AAJ)

description:
https://www.encodeproject.org/experiments/ENCSR342FHH/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR342FHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB362AAJ
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: cell line

tag: encode accession

value: ENCBS987QKT at ENCODE; https://www.encodeproject.org/ENCBS987QKT/


title: snRNA-seq from adrenal gland (ENCLB048VRI)

description:
https://www.encodeproject.org/experiments/ENCSR201SNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P18-20mo female ont_match 2k
experiment encode accession: ENCSR201SNQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB048VRI
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P18-20mo female 1

value: 18-20 month

value: ENCBS537RFX at ENCODE; https://www.encodeproject.org/ENCBS537RFX/

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


title: DNase-seq from K562 (ENCLB902VHC)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB902VHC

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS833MNG at ENCODE; https://www.encodeproject.org/ENCBS833MNG/


title: DNase-seq from K562 (ENCLB063XDO)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB063XDO

value: female

value: adult

value: ENCBS531JHG at ENCODE; https://www.encodeproject.org/ENCBS531JHG/


title: DNase-seq from K562 (ENCLB734HZU)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 13
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB734HZU

value: ENCBS866UEE at ENCODE; https://www.encodeproject.org/ENCBS866UEE/


title: snRNA-seq from gastrocnemius (ENCLB445HCF)

description:
https://www.encodeproject.org/experiments/ENCSR187HKH/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P18-20mo male normal 1k
experiment encode accession: ENCSR187HKH
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB445HCF
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

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

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P18-20mo male 1

value: male

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS077XIS at ENCODE; https://www.encodeproject.org/ENCBS077XIS/


title: snRNA-seq from adrenal gland (ENCLB866KKG)

description:
https://www.encodeproject.org/experiments/ENCSR201SNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P18-20mo female ont_match 2k
experiment encode accession: ENCSR201SNQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB866KKG
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P18-20mo female 2

value: 18-20 month

value: ENCBS336XYG at ENCODE; https://www.encodeproject.org/ENCBS336XYG/

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


title: DNase-seq from K562 (ENCLB751VMS)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 14
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB751VMS

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS729GJX at ENCODE; https://www.encodeproject.org/ENCBS729GJX/


title: snRNA-seq from adrenal gland (ENCLB785BIJ)

description:
https://www.encodeproject.org/experiments/ENCSR196TWX/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P36 female normal 2k
experiment encode accession: ENCSR196TWX
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB785BIJ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: B6/Cast F1 adrenal P36 female 1

value: postnatal

value: 36 day

value: Ali Mortazavi, UCI

value: ENCBS291QIZ at ENCODE; https://www.encodeproject.org/ENCBS291QIZ/


title: snRNA-seq from adrenal gland (ENCLB683BBT)

description:
https://www.encodeproject.org/experiments/ENCSR196TWX/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P36 female normal 2k
experiment encode accession: ENCSR196TWX
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB683BBT
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P36 female 2

value: nucleus

value: The Jackson Laboratory

value: ENCBS231UDN at ENCODE; https://www.encodeproject.org/ENCBS231UDN/


title: DNase-seq from K562 (ENCLB421YWV)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 11
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB421YWV

value: cell line

value: female

value: adult

value: ENCBS206OIR at ENCODE; https://www.encodeproject.org/ENCBS206OIR/


title: snRNA-seq from gastrocnemius (ENCLB112QYE)

description:
https://www.encodeproject.org/experiments/ENCSR182SMX/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P10 male normal 2k
experiment encode accession: ENCSR182SMX
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB112QYE
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J male postnatal (10 days) gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P10 male 2

value: male

value: 10 day

value: ENCBS973VUK at ENCODE; https://www.encodeproject.org/ENCBS973VUK/

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


title: PC9-LDOC1 expressing-Rep2

value: lung adenocarcinoma

value: EGFR exon 19 del


title: DNase-seq from K562 (ENCLB929AYM)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 20
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB929AYM

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS759VMM at ENCODE; https://www.encodeproject.org/ENCBS759VMM/


title: DNase-seq from K562 (ENCLB714ARI)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 16
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB714ARI
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: cell line

value: ENCBS854BOQ at ENCODE; https://www.encodeproject.org/ENCBS854BOQ/


title: snRNA-seq from gastrocnemius (ENCLB697UFJ)

description:
https://www.encodeproject.org/experiments/ENCSR187HKH/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P18-20mo male normal 1k
experiment encode accession: ENCSR187HKH
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB697UFJ
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

value: tissue

value: B6/Cast F1 gastrocnemius P18-20mo male 2

value: adult

value: 18-20 month

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS331TRK at ENCODE; https://www.encodeproject.org/ENCBS331TRK/


title: snRNA-seq from gastrocnemius (ENCLB057CVT)

description:
https://www.encodeproject.org/experiments/ENCSR182SMX/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 gastrocnemius P10 male normal 2k
experiment encode accession: ENCSR182SMX
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB057CVT
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

value: gastrocnemius

value: B6/Cast F1 gastrocnemius P10 male 1

value: male

value: postnatal

value: 10 day

value: ENCBS164HJY at ENCODE; https://www.encodeproject.org/ENCBS164HJY/

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


title: DNase-seq from K562 (ENCLB056KKK)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 25
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB056KKK

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS371GOW at ENCODE; https://www.encodeproject.org/ENCBS371GOW/


title: DNase-seq from K562 (ENCLB051EMW)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 19
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB051EMW
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: adult

value: ENCBS707LNG at ENCODE; https://www.encodeproject.org/ENCBS707LNG/


title: DNase-seq from K562 (ENCLB295BYB)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 18
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB295BYB

value: ENCBS204RTN at ENCODE; https://www.encodeproject.org/ENCBS204RTN/


title: snRNA-seq from layer of hippocampus (ENCLB617GJX)

description:
https://www.encodeproject.org/experiments/ENCSR203XJO/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read B6/Cast F1 hippocampus P2mo female normal 12k
experiment encode accession: ENCSR203XJO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB617GJX

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P2mo female 2

value: 2 month

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS772CYI at ENCODE; https://www.encodeproject.org/ENCBS772CYI/


title: snRNA-seq from left cerebral cortex (ENCLB972QSW)

description:
https://www.encodeproject.org/experiments/ENCSR178PKG/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P2mo female normal 2k
experiment encode accession: ENCSR178PKG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB972QSW
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) left cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: B6/Cast F1 cortex P2mo female 2

value: female

value: ENCBS174PCZ at ENCODE; https://www.encodeproject.org/ENCBS174PCZ/

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


title: DNase-seq from K562 (ENCLB998ITK)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 22
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB998ITK
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS519UPS at ENCODE; https://www.encodeproject.org/ENCBS519UPS/


title: snRNA-seq from left cerebral cortex (ENCLB891WAL)

description:
https://www.encodeproject.org/experiments/ENCSR178PKG/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 cortex P2mo female normal 2k
experiment encode accession: ENCSR178PKG
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB891WAL
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: tissue

value: B6/Cast F1 cortex P2mo female 1

value: adult

value: ENCBS043EST at ENCODE; https://www.encodeproject.org/ENCBS043EST/


title: snRNA-seq from heart (ENCLB007MSY)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB007MSY

source_name: Mus musculus strain B6CASTF1/J male adult (8 months) heart tissue nuclear fraction

value: heart

value: B6/Cast F1 heart P8mo male 2

value: male

value: 8 month

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS444FZI at ENCODE; https://www.encodeproject.org/ENCBS444FZI/


title: snRNA-seq from heart (ENCLB435OZT)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 1
technical replicate number: 3
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB435OZT

value: B6/Cast F1 heart P8mo male 1

value: ENCBS545BQV at ENCODE; https://www.encodeproject.org/ENCBS545BQV/

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


title: DNase-seq from K562 (ENCLB999FYU)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 17
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB999FYU

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS687PNE at ENCODE; https://www.encodeproject.org/ENCBS687PNE/


title: DNase-seq from K562 (ENCLB193XCE)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 12
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB193XCE

value: adult

value: ENCBS036RKB at ENCODE; https://www.encodeproject.org/ENCBS036RKB/


title: snRNA-seq from heart (ENCLB541XRJ)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 1
technical replicate number: 2
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB541XRJ

value: heart

value: tissue

value: male

value: 8 month


title: DNase-seq from K562 (ENCLB670TIP)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 15
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB670TIP
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: ENCBS725VUZ at ENCODE; https://www.encodeproject.org/ENCBS725VUZ/


title: snRNA-seq from heart (ENCLB187ZXT)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 2
technical replicate number: 6
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB187ZXT

value: B6/Cast F1 heart P8mo male 2

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS444FZI at ENCODE; https://www.encodeproject.org/ENCBS444FZI/


title: DNase-seq from K562 (ENCLB963CGW)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 21
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB963CGW
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS089MFO at ENCODE; https://www.encodeproject.org/ENCBS089MFO/


title: snRNA-seq from heart (ENCLB749UBX)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB749UBX

value: B6/Cast F1 heart P8mo male 1

value: ENCBS545BQV at ENCODE; https://www.encodeproject.org/ENCBS545BQV/

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


title: DNase-seq from K562 (ENCLB561MWW)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB561MWW
instrument models: Illumina HiSeq 2500,Illumina HiSeq 4000

value: adult

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS575TQW at ENCODE; https://www.encodeproject.org/ENCBS575TQW/


title: snRNA-seq from heart (ENCLB229NTE)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 1
technical replicate number: 4
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB229NTE

value: heart

value: tissue

value: male

value: 8 month


title: DNase-seq from NCI-H1092 (ENCLB038IIY)

description:
https://www.encodeproject.org/experiments/ENCSR297WFP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR297WFP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB038IIY
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens NCI-H1092 cell line treated with 0.1% DMSO for 48 hours

value: 67 year

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:DMSO; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS009MDC at ENCODE; https://www.encodeproject.org/ENCBS009MDC/


title: snRNA-seq from heart (ENCLB687YTT)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 1
technical replicate number: 6
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB687YTT

tag: description

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory


title: snRNA-seq from heart (ENCLB157GBC)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 2
technical replicate number: 5
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB157GBC

value: B6/Cast F1 heart P8mo male 2

tag: biosample encode accession

value: ENCBS444FZI at ENCODE; https://www.encodeproject.org/ENCBS444FZI/


title: snRNA-seq from heart (ENCLB163TZE)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 1
technical replicate number: 5
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB163TZE

value: B6/Cast F1 heart P8mo male 1

tag: Sex

value: adult

value: ENCBS545BQV at ENCODE; https://www.encodeproject.org/ENCBS545BQV/

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


title: DNase-seq from K562 (ENCLB504RZW)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB504RZW

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS355DPM at ENCODE; https://www.encodeproject.org/ENCBS355DPM/


title: snRNA-seq from heart (ENCLB779LFP)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 2
technical replicate number: 2
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB779LFP

value: heart

value: tissue

value: male

tag: age

value: 8 month


title: DNase-seq from NCI-H446 (ENCLB115UYJ)

description:
https://www.encodeproject.org/experiments/ENCSR292BRC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR292BRC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB115UYJ
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens NCI-H446 cell line treated with 0.1% DMSO for 48 hours

value: 61 year

tag: lab

value: treatment_term_id:CHEBI:28262; treatment_term_name:DMSO; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS891AKH at ENCODE; https://www.encodeproject.org/ENCBS891AKH/


title: total RNA-seq from dorsolateral prefrontal cortex (ENCLB348FDI)

description:
https://www.encodeproject.org/experiments/ENCSR944UJZ/
***************
biological replicate number: 1
technical replicate number: 1
description: human_brain_Rush ID_E6090948_BS101_ENC4_cDNA678
experiment encode accession: ENCSR944UJZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB348FDI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December

source_name: Homo sapiens female adult (87 years) middle frontal area 46 tissue

value: dorsolateral prefrontal cortex

value: adult

value: 87 year

value: Barbara Wold, Caltech

value: Rush University

value: ENCBS439FJF at ENCODE; https://www.encodeproject.org/ENCBS439FJF/

value: Derived from ENCODE donor ENCDO423GGP; https://www.encodeproject.org/ENCDO423GGP/


title: total RNA-seq from dorsolateral prefrontal cortex (ENCLB842ZJN)

description:
https://www.encodeproject.org/experiments/ENCSR944UJZ/
***************
biological replicate number: 2
technical replicate number: 1
description: human_brain_Rush ID_E6090948_BS101_ENC4_cDNA678
experiment encode accession: ENCSR944UJZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2022-04-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB842ZJN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: female

value: ENCBS243KIR at ENCODE; https://www.encodeproject.org/ENCBS243KIR/


title: DNase-seq from NCI-H2171 (ENCLB468PCM)

description:
https://www.encodeproject.org/experiments/ENCSR176FAH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR176FAH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB468PCM
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens NCI-H2171 cell line treated with 0.1% DMSO for 48 hours

value: cell line

value: 50 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS403QGW at ENCODE; https://www.encodeproject.org/ENCBS403QGW/


title: snRNA-seq from heart (ENCLB299PDF)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB299PDF

value: heart

value: tissue

value: B6/Cast F1 heart P8mo male 2

value: male

value: 8 month

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS444FZI at ENCODE; https://www.encodeproject.org/ENCBS444FZI/

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


title: 9-Tdp-KO-RNAPII-input: ChIP input from HEK293 cells after CRISPR targeting of TARDBP

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

data_processing:
Reads were extracted and demultiplexed from BCL files with blc2fastq version 1.8.3.
Reads were aligned to the human genome, build hg19, using Bowtie2 with settings -5 1 -3 2 –local. Duplicate reads were removed to generate BAM files.
To generate 'meta-gene' alignment plots, reads were extended to 300 bp. Pileups – the number of fragments overlapping each genomic bp – were calculated, and were normalized by million mappable reads in the ChIP-seq library. Normalized pileups from different replicates (done with different antibodies) were then averaged to create FPM (fragments per million reads).
Genome_build: hg19
Supplementary_files_format_and_content: Figures showing the average (across represented genes) density of aligned ChIP fragments per million in the library, for each aligned base. Plots were generated directly from BAM files.

source_name: Human embryonic kidney cells

growth_protocol: HEK293 cells were grown in DMEM plus FBS , and stably transduced cell lines were maintained with 2μg/ml puromycin or with 2ul/ml hygromycin selection. Cells were passaged and grown for 3 days before harvesting at ~90% confluency.

extract_protocol:
10e7-10e8 cells were cross-linked for 10 min in 1% formaldehyde. Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). RNAPII was immunoprecipitated with 2ug of antibodies and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic).
Sequencing libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina) according the manufacturer's instructions.

treatment_protocol: For CRISPR/Cas9-mediated gene knock-outs, CRISPR/Cas9 plasmids (pCMV-Cas9-GFP) were purchased from Sigma-Aldrich to express a control scrambled guide RNA, or guide RNAs for the knockout of TDP-43 or FUS. 2 µg of the plasmids were transfected into HEK293 cells, and 1 day after lipofectamine 3000 transfection, cells were sorted using a BD FACSAria flow cytometer, and single GFP-positive cells were plated into 48-well plate. Positive clones were expanded, and the expression level of TDP-43 or FUS in each clone was detected by western blotting.

value: Human embryonic kidney cells

tag: cell line

tag: antibody


title: 8-Fus-KO-RNAPII-input: ChIP input from HEK293 cells after CRISPR targeting of FUS


title: snRNA-seq from heart (ENCLB494DNT)

description:
https://www.encodeproject.org/experiments/ENCSR174ZVM/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read B6/Cast F1 heart P8mo male 8mo 12k
experiment encode accession: ENCSR174ZVM
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB494DNT

value: adult


title: snRNA-seq from adrenal gland (ENCLB903CLN)

description:
https://www.encodeproject.org/experiments/ENCSR165VMQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P25 female ont_match 2k
experiment encode accession: ENCSR165VMQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB903CLN
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6CASTF1/J female postnatal (25 days) adrenal gland tissue nuclear fraction

value: adrenal gland

value: B6/Cast F1 adrenal P25 female 2

value: female

value: postnatal

value: 25 day

value: ENCBS711QUR at ENCODE; https://www.encodeproject.org/ENCBS711QUR/


title: snRNA-seq from layer of hippocampus (ENCLB078HYI)

description:
https://www.encodeproject.org/experiments/ENCSR167HUO/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P25 male ont_match 2k
experiment encode accession: ENCSR167HUO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB078HYI
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P25 male 1

value: ENCBS747PJX at ENCODE; https://www.encodeproject.org/ENCBS747PJX/


title: 6-Tdp-KO-RNAPII-2: ChIP of RNA polymerase II in HEK293 cells after CRISPR targeting of TARDBP

value: POLR2A (N20) Santa Cruz pAb Cat # sc-899


title: 5-Fus-KO-RNAPII-2: ChIP of RNA polymerase II in HEK293 cells after CRISPR targeting of FUS


title: 7-Scr-RNAPII-input: ChIP input from HEK293 cells after control CRISPR treatment


title: snRNA-seq from adrenal gland (ENCLB679MGP)

description:
https://www.encodeproject.org/experiments/ENCSR165VMQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Illumina short-read B6/Cast F1 adrenal P25 female ont_match 2k
experiment encode accession: ENCSR165VMQ
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB679MGP
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 adrenal P25 female 1

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS321JYG at ENCODE; https://www.encodeproject.org/ENCBS321JYG/


title: snRNA-seq from layer of hippocampus (ENCLB958FDX)

description:
https://www.encodeproject.org/experiments/ENCSR167HUO/
***************
biological replicate number: 2
technical replicate number: 1
description: Illumina short-read B6/Cast F1 hippocampus P25 male ont_match 2k
experiment encode accession: ENCSR167HUO
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB958FDX
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P25 male 2

value: male

value: The Jackson Laboratory

value: ENCBS929ZLW at ENCODE; https://www.encodeproject.org/ENCBS929ZLW/

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


title: 4-Scr-RNAPII-2: ChIP of RNA polymerase II in HEK293 cells after control CRISPR treatment

value: Human embryonic kidney cells


title: snRNA-seq from adrenal gland (ENCLB489DGU)

description:
https://www.encodeproject.org/experiments/ENCSR165FLF/
***************
biological replicate number: 2
technical replicate number: 4
description: Illumina short-read B6/Cast F1 adrenal P4 male normal 12k
experiment encode accession: ENCSR165FLF
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB489DGU

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

value: adrenal gland

value: B6/Cast F1 adrenal P4 male 2

value: postnatal

value: 4 day

value: ENCBS112ZTO at ENCODE; https://www.encodeproject.org/ENCBS112ZTO/


title: snRNA-seq from adrenal gland (ENCLB465IEH)

description:
https://www.encodeproject.org/experiments/ENCSR165FLF/
***************
biological replicate number: 2
technical replicate number: 3
description: Illumina short-read B6/Cast F1 adrenal P4 male normal 12k
experiment encode accession: ENCSR165FLF
assay title: snRNA-seq
assembly: mm10
encode release date: 2022-03-25
lab: Ali Mortazavi, UCI
library encode accession: ENCLB465IEH

value: tissue