title: total RNA-seq from T-helper 1 cell (ENCLB219VEL)

description:
https://www.encodeproject.org/experiments/ENCSR076CCA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR076CCA
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB219VEL

value: ENCBS691LAJ at ENCODE; https://www.encodeproject.org/ENCBS691LAJ/


title: total RNA-seq from T-helper 1 cell (ENCLB864PWF)

status: Public on Feb 28 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/ENCSR073FPO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR073FPO
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB864PWF

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain C57BL/6NJ T-helper 1 primary cell

value: T-helper 1 cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: Sex

value: not collected

tag: dev stage

value: unknown

tag: age

tag: lab

value: Tim Reddy, Duke

tag: source

value: Maria Ciofani

tag: link

value: ENCBS321WXJ at ENCODE; https://www.encodeproject.org/ENCBS321WXJ/


title: total RNA-seq from regulatory T cell (ENCLB308NOT)

description:
https://www.encodeproject.org/experiments/ENCSR687HLO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR687HLO
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB308NOT

source_name: Mus musculus strain C57BL/6NJ regulatory T primary cell

value: regulatory T cell

value: ENCBS079PZY at ENCODE; https://www.encodeproject.org/ENCBS079PZY/


title: total RNA-seq from T-helper 1 cell (ENCLB862XGY)

description:
https://www.encodeproject.org/experiments/ENCSR600QUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR600QUH
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB862XGY

value: ENCBS351KNO at ENCODE; https://www.encodeproject.org/ENCBS351KNO/


title: total RNA-seq from T-helper 1 cell (ENCLB819AOY)

description:
https://www.encodeproject.org/experiments/ENCSR073FPO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR073FPO
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB819AOY

value: ENCBS168KMT at ENCODE; https://www.encodeproject.org/ENCBS168KMT/


title: total RNA-seq from T-helper 1 cell (ENCLB533QHF)

description:
https://www.encodeproject.org/experiments/ENCSR600QUH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR600QUH
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB533QHF

value: ENCBS268OQA at ENCODE; https://www.encodeproject.org/ENCBS268OQA/


title: total RNA-seq from T-cell (ENCLB080LFW)

description:
https://www.encodeproject.org/experiments/ENCSR036EDO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR036EDO
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB080LFW

source_name: Mus musculus strain C57BL/6NJ T-cell primary cell

value: T-cell

value: ENCBS730WCV at ENCODE; https://www.encodeproject.org/ENCBS730WCV/


title: total RNA-seq from T-helper 2 cell (ENCLB245LFE)

description:
https://www.encodeproject.org/experiments/ENCSR100YQC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR100YQC
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB245LFE

source_name: Mus musculus strain C57BL/6NJ T-helper 2 primary cell

value: T-helper 2 cell

value: ENCBS988WZS at ENCODE; https://www.encodeproject.org/ENCBS988WZS/


title: total RNA-seq from T-cell (ENCLB874CNQ)

description:
https://www.encodeproject.org/experiments/ENCSR036EDO/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR036EDO
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB874CNQ

value: ENCBS301LTW at ENCODE; https://www.encodeproject.org/ENCBS301LTW/


title: total RNA-seq from T-helper 1 cell (ENCLB123QAM)

description:
https://www.encodeproject.org/experiments/ENCSR141PRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR141PRV
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB123QAM

value: T-helper 1 cell

value: ENCBS693ZLQ at ENCODE; https://www.encodeproject.org/ENCBS693ZLQ/


title: total RNA-seq from T-helper 17 cell (ENCLB698PDA)

description:
https://www.encodeproject.org/experiments/ENCSR000YRX/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR000YRX
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB698PDA

source_name: Mus musculus strain C57BL/6NJ T-helper 17 primary cell

value: T-helper 17 cell

value: primary cell

value: not collected

value: ENCBS928MPF at ENCODE; https://www.encodeproject.org/ENCBS928MPF/


title: total RNA-seq from T-helper 17 cell (ENCLB470LKO)

description:
https://www.encodeproject.org/experiments/ENCSR000YRX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR000YRX
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB470LKO

value: unknown

value: Tim Reddy, Duke

value: Maria Ciofani

value: ENCBS382UUY at ENCODE; https://www.encodeproject.org/ENCBS382UUY/


title: total RNA-seq from T-helper 2 cell (ENCLB897FPQ)

description:
https://www.encodeproject.org/experiments/ENCSR100YQC/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR100YQC
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB897FPQ

value: ENCBS153PCT at ENCODE; https://www.encodeproject.org/ENCBS153PCT/


title: total RNA-seq from regulatory T cell (ENCLB490IMY)

description:
https://www.encodeproject.org/experiments/ENCSR086CAL/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR086CAL
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB490IMY

value: regulatory T cell

value: ENCBS644OVC at ENCODE; https://www.encodeproject.org/ENCBS644OVC/


title: long read scRNA-seq from layer of hippocampus (ENCLB149QRP)

description:
https://www.encodeproject.org/experiments/ENCSR596GDP/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P25 male normal 2k
experiment encode accession: ENCSR596GDP
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB149QRP
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

tag: description

value: B6/Cast F1 hippocampus P25 male 2

value: male

value: postnatal

value: 25 day

value: Ali Mortazavi, UCI

tag: subcellular fraction term name

value: nucleus

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: long read scRNA-seq from adrenal gland (ENCLB490JHH)

description:
https://www.encodeproject.org/experiments/ENCSR382FLX/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P18-20mo male ont_match 2k
experiment encode accession: ENCSR382FLX
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB490JHH
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: adrenal gland

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

value: adult

value: 18-20 month

value: ENCBS621RNE at ENCODE; https://www.encodeproject.org/ENCBS621RNE/


title: long read scRNA-seq from layer of hippocampus (ENCLB646CGR)

description:
https://www.encodeproject.org/experiments/ENCSR596GDP/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P25 male normal 2k
experiment encode accession: ENCSR596GDP
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB646CGR
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P25 male 1

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


title: long read scRNA-seq from adrenal gland (ENCLB113HHT)

description:
https://www.encodeproject.org/experiments/ENCSR578XKS/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P2mo female ont_match 2k
experiment encode accession: ENCSR578XKS
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB113HHT
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: tissue

value: B6/Cast F1 adrenal P2mo female 2

value: female

value: 2 month

value: ENCBS266BTE at ENCODE; https://www.encodeproject.org/ENCBS266BTE/


title: total RNA-seq from T-helper 1 cell (ENCLB311QUL)

description:
https://www.encodeproject.org/experiments/ENCSR073FPO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR073FPO
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB311QUL

value: T-helper 1 cell

value: primary cell

value: not collected

value: unknown

value: Tim Reddy, Duke

value: Maria Ciofani

value: ENCBS206ZPU at ENCODE; https://www.encodeproject.org/ENCBS206ZPU/


title: total RNA-seq from T-cell (ENCLB348CDB)

description:
https://www.encodeproject.org/experiments/ENCSR036EDO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR036EDO
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB348CDB

value: T-cell

value: ENCBS182KAG at ENCODE; https://www.encodeproject.org/ENCBS182KAG/


title: total RNA-seq from T-cell (ENCLB328QNH)

description:
https://www.encodeproject.org/experiments/ENCSR036EDO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR036EDO
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB328QNH

value: ENCBS592YGS at ENCODE; https://www.encodeproject.org/ENCBS592YGS/


title: long read scRNA-seq from adrenal gland (ENCLB549QVR)

description:
https://www.encodeproject.org/experiments/ENCSR578XKS/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P2mo female ont_match 2k
experiment encode accession: ENCSR578XKS
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB549QVR
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: B6/Cast F1 adrenal P2mo female 1

value: adult

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS194GJK at ENCODE; https://www.encodeproject.org/ENCBS194GJK/

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


title: total RNA-seq from T-helper 17 cell (ENCLB005QSC)

description:
https://www.encodeproject.org/experiments/ENCSR000YRX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR000YRX
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB005QSC

value: T-helper 17 cell

value: primary cell

value: ENCBS123DZT at ENCODE; https://www.encodeproject.org/ENCBS123DZT/


title: long read scRNA-seq from layer of hippocampus (ENCLB180KEO)

description:
https://www.encodeproject.org/experiments/ENCSR299OFL/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P36 female ont_match 2k
experiment encode accession: ENCSR299OFL
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB180KEO
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P36 female 2

value: female

value: postnatal

value: 36 day

value: ENCBS317KAV at ENCODE; https://www.encodeproject.org/ENCBS317KAV/


title: long read scRNA-seq from layer of hippocampus (ENCLB484OFO)

description:
https://www.encodeproject.org/experiments/ENCSR492SHL/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P36 male ont_match 2k
experiment encode accession: ENCSR492SHL
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB484OFO
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: B6/Cast F1 hippocampus P36 male 2

value: male

value: ENCBS373BVD at ENCODE; https://www.encodeproject.org/ENCBS373BVD/


title: long read scRNA-seq from layer of hippocampus (ENCLB901UNF)

description:
https://www.encodeproject.org/experiments/ENCSR297ZAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P18-20mo male normal 2k
experiment encode accession: ENCSR297ZAZ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB901UNF
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 1

value: adult

value: 18-20 month

value: Ali Mortazavi, UCI

value: nucleus

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


title: total RNA-seq from T-helper 17 cell (ENCLB275BAU)

description:
https://www.encodeproject.org/experiments/ENCSR000YRX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR000YRX
assay title: total RNA-seq
assembly: mm10
encode release date: 2025-09-30
lab: Tim Reddy, Duke
library encode accession: ENCLB275BAU

value: T-helper 17 cell

value: primary cell

value: not collected

value: unknown

value: Tim Reddy, Duke

value: Maria Ciofani

value: ENCBS087QUD at ENCODE; https://www.encodeproject.org/ENCBS087QUD/


title: long read scRNA-seq from adrenal gland (ENCLB074XQY)

description:
https://www.encodeproject.org/experiments/ENCSR382FLX/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P18-20mo male ont_match 2k
experiment encode accession: ENCSR382FLX
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB074XQY
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: tissue

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

value: The Jackson Laboratory

value: ENCBS997ZIT at ENCODE; https://www.encodeproject.org/ENCBS997ZIT/

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


title: long read scRNA-seq from layer of hippocampus (ENCLB386AXC)

description:
https://www.encodeproject.org/experiments/ENCSR398ZEK/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P14 female normal 2k
experiment encode accession: ENCSR398ZEK
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB386AXC
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: layer of hippocampus

value: B6/Cast F1 hippocampus P14 female 1

value: female

value: postnatal

value: 14 day

value: ENCBS454DBZ at ENCODE; https://www.encodeproject.org/ENCBS454DBZ/


title: long read scRNA-seq from layer of hippocampus (ENCLB431VVV)

description:
https://www.encodeproject.org/experiments/ENCSR325RRB/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P14 male normal 2k
experiment encode accession: ENCSR325RRB
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB431VVV
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: B6/Cast F1 hippocampus P14 male 1

value: male

value: Ali Mortazavi, UCI

value: nucleus

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


title: long read scRNA-seq from adrenal gland (ENCLB693ASW)

description:
https://www.encodeproject.org/experiments/ENCSR260YIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P25 male ont_match 2k
experiment encode accession: ENCSR260YIQ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB693ASW
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: B6/Cast F1 adrenal P25 male 1

value: 25 day

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


title: long read scRNA-seq from layer of hippocampus (ENCLB777WMI)

description:
https://www.encodeproject.org/experiments/ENCSR253UOM/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P2mo female ont_match 2k
experiment encode accession: ENCSR253UOM
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB777WMI
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: tissue

value: B6/Cast F1 hippocampus P2mo female 1

value: adult

value: 2 month

value: The Jackson Laboratory

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


title: long read scRNA-seq from layer of hippocampus (ENCLB403SMM)

description:
https://www.encodeproject.org/experiments/ENCSR299OFL/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P36 female ont_match 2k
experiment encode accession: ENCSR299OFL
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB403SMM
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: B6/Cast F1 hippocampus P36 female 1

value: female

value: postnatal

value: 36 day

value: ENCBS462MCF at ENCODE; https://www.encodeproject.org/ENCBS462MCF/

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


title: long read scRNA-seq from layer of hippocampus (ENCLB902LTI)

description:
https://www.encodeproject.org/experiments/ENCSR297ZAZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P18-20mo male normal 2k
experiment encode accession: ENCSR297ZAZ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB902LTI
nucleic acid starting quantity: 167
nucleic acid starting quantity units: cells

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

value: male

value: 18-20 month

value: Ali Mortazavi, UCI

value: nucleus

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


title: long read scRNA-seq from layer of hippocampus (ENCLB892PHW)

description:
https://www.encodeproject.org/experiments/ENCSR325RRB/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P14 male normal 2k
experiment encode accession: ENCSR325RRB
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB892PHW
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: tissue

value: B6/Cast F1 hippocampus P14 male 2

value: 14 day

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


title: long read scRNA-seq from layer of hippocampus (ENCLB540QYT)

description:
https://www.encodeproject.org/experiments/ENCSR253UOM/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P2mo female ont_match 2k
experiment encode accession: ENCSR253UOM
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB540QYT
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: B6/Cast F1 hippocampus P2mo female 2

value: adult

value: 2 month

value: The Jackson Laboratory

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


title: long read scRNA-seq from adrenal gland (ENCLB959KDQ)

description:
https://www.encodeproject.org/experiments/ENCSR252DYO/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P36 female ont_match 2k
experiment encode accession: ENCSR252DYO
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB959KDQ
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: adrenal gland

value: B6/Cast F1 adrenal P36 female 2

value: female

value: postnatal

value: 36 day

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

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


title: long read scRNA-seq from layer of hippocampus (ENCLB889RCL)

description:
https://www.encodeproject.org/experiments/ENCSR492SHL/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P36 male ont_match 2k
experiment encode accession: ENCSR492SHL
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB889RCL
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: tissue

value: B6/Cast F1 hippocampus P36 male 1

value: male

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS894OAU at ENCODE; https://www.encodeproject.org/ENCBS894OAU/


title: long read scRNA-seq from layer of hippocampus (ENCLB886EQS)

description:
https://www.encodeproject.org/experiments/ENCSR465BRP/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P10 female ont_match 2k
experiment encode accession: ENCSR465BRP
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB886EQS
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: 10 day

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


title: long read scRNA-seq from layer of hippocampus (ENCLB489WMQ)

description:
https://www.encodeproject.org/experiments/ENCSR245GNB/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P25 female normal 2k
experiment encode accession: ENCSR245GNB
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB489WMQ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: B6/Cast F1 hippocampus P25 female 1

value: 25 day

value: The Jackson Laboratory

value: ENCBS998IGC at ENCODE; https://www.encodeproject.org/ENCBS998IGC/


title: long read scRNA-seq from layer of hippocampus (ENCLB555DJS)

description:
https://www.encodeproject.org/experiments/ENCSR265JEM/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P36 female normal 2k
experiment encode accession: ENCSR265JEM
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB555DJS
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P36 female 2

value: female

value: postnatal

value: 36 day

value: ENCBS317KAV at ENCODE; https://www.encodeproject.org/ENCBS317KAV/


title: long read scRNA-seq from layer of hippocampus (ENCLB786XPW)

description:
https://www.encodeproject.org/experiments/ENCSR265JEM/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P36 female normal 2k
experiment encode accession: ENCSR265JEM
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB786XPW
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: tissue

value: B6/Cast F1 hippocampus P36 female 1

value: ENCBS462MCF at ENCODE; https://www.encodeproject.org/ENCBS462MCF/

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


title: long read scRNA-seq from layer of hippocampus (ENCLB262BED)

description:
https://www.encodeproject.org/experiments/ENCSR398ZEK/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P14 female normal 2k
experiment encode accession: ENCSR398ZEK
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB262BED
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: B6/Cast F1 hippocampus P14 female 2

value: 14 day

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS300KQE at ENCODE; https://www.encodeproject.org/ENCBS300KQE/


title: long read scRNA-seq from adrenal gland (ENCLB165PKL)

description:
https://www.encodeproject.org/experiments/ENCSR260YIQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P25 male ont_match 2k
experiment encode accession: ENCSR260YIQ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB165PKL
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: B6/Cast F1 adrenal P25 male 2

value: male

value: 25 day

value: The Jackson Laboratory

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


title: long read scRNA-seq from layer of hippocampus (ENCLB851ZFM)

description:
https://www.encodeproject.org/experiments/ENCSR449BGI/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P2mo female normal 2k
experiment encode accession: ENCSR449BGI
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB851ZFM
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P2mo female 1

value: female

value: adult

value: 2 month

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


title: long read scRNA-seq from layer of hippocampus (ENCLB678VRJ)

description:
https://www.encodeproject.org/experiments/ENCSR472AKY/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P25 male ont_match 2k
experiment encode accession: ENCSR472AKY
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB678VRJ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P25 male 1

value: postnatal

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

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


title: long read scRNA-seq from adrenal gland (ENCLB020JCQ)

description:
https://www.encodeproject.org/experiments/ENCSR431FYK/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P36 male ont_match 2k
experiment encode accession: ENCSR431FYK
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB020JCQ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: adrenal gland

value: B6/Cast F1 adrenal P36 male 1

value: 36 day

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS254HFK at ENCODE; https://www.encodeproject.org/ENCBS254HFK/


title: long read scRNA-seq from adrenal gland (ENCLB185IQZ)

description:
https://www.encodeproject.org/experiments/ENCSR252DYO/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P36 female ont_match 2k
experiment encode accession: ENCSR252DYO
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB185IQZ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 adrenal P36 female 1

value: The Jackson Laboratory

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


title: long read scRNA-seq from layer of hippocampus (ENCLB368AUX)

description:
https://www.encodeproject.org/experiments/ENCSR465BRP/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P10 female ont_match 2k
experiment encode accession: ENCSR465BRP
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB368AUX
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P10 female 2

value: female

value: 10 day

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


title: long read scRNA-seq from layer of hippocampus (ENCLB345RSB)

description:
https://www.encodeproject.org/experiments/ENCSR449BGI/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P2mo female normal 2k
experiment encode accession: ENCSR449BGI
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB345RSB
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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: long read scRNA-seq from layer of hippocampus (ENCLB622RYM)

description:
https://www.encodeproject.org/experiments/ENCSR472AKY/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P25 male ont_match 2k
experiment encode accession: ENCSR472AKY
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB622RYM
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P25 male 2

value: male

value: postnatal

value: 25 day

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

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


title: FACS CRISPR screen from F123 (ENCLB979XIO)

description:
https://www.encodeproject.org/experiments/ENCSR312ISP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR312ISP
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR180JKQ
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB979XIO

library_source: genomic

molecule: genomic DNA

source_name: Mus musculus F123 cell line genetically modified (insertion) using CRISPR (sgRNA) targeting M. musculus Esrrb, genetically modified (insertion) using transduction, genetically modified using CRISPR cutting (sgRNA)

tag: line

value: cell line

value: not collected

value: unknown

tag: passage number

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS536HEJ at ENCODE; https://www.encodeproject.org/ENCBS536HEJ/


title: long read scRNA-seq from layer of hippocampus (ENCLB853ZGX)

description:
https://www.encodeproject.org/experiments/ENCSR240WAO/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P36 male normal 2k
experiment encode accession: ENCSR240WAO
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB853ZGX
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P36 male 2

value: 36 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS373BVD at ENCODE; https://www.encodeproject.org/ENCBS373BVD/


title: Control CRISPR screen from F123 (ENCLB079DJV)

description:
https://www.encodeproject.org/experiments/ENCSR299NFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR299NFV
assay title: Control CRISPR screen
possible controls: ENCSR864JVZ
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB079DJV
size range: 710-720

source_name: Mus musculus F123 cell line genetically modified (insertion) using transduction, genetically modified using CRISPR cutting (sgRNA)

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS312GRR at ENCODE; https://www.encodeproject.org/ENCBS312GRR/


title: long read scRNA-seq from layer of hippocampus (ENCLB829VBN)

description:
https://www.encodeproject.org/experiments/ENCSR240WAO/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P36 male normal 2k
experiment encode accession: ENCSR240WAO
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB829VBN
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P36 male 1

value: male

value: postnatal

value: ENCBS894OAU at ENCODE; https://www.encodeproject.org/ENCBS894OAU/

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


title: long read scRNA-seq from layer of hippocampus (ENCLB633OLM)

description:
https://www.encodeproject.org/experiments/ENCSR405VKO/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P2mo male normal 2k
experiment encode accession: ENCSR405VKO
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB633OLM
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: B6/Cast F1 hippocampus P2mo male 1

value: adult

value: 2 month

value: ENCBS246YKO at ENCODE; https://www.encodeproject.org/ENCBS246YKO/


title: Control CRISPR screen from F123 (ENCLB960MOH)

description:
https://www.encodeproject.org/experiments/ENCSR572QYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR572QYM
assay title: Control CRISPR screen
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB960MOH
size range: 710-720

value: cell line

value: not collected

value: unknown

value: ENCBS178AKX at ENCODE; https://www.encodeproject.org/ENCBS178AKX/


title: Control CRISPR screen from F123 (ENCLB368MKJ)

description:
https://www.encodeproject.org/experiments/ENCSR299NFV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR299NFV
assay title: Control CRISPR screen
possible controls: ENCSR864JVZ
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB368MKJ
size range: 710-720

value: ENCBS110CII at ENCODE; https://www.encodeproject.org/ENCBS110CII/


title: Control CRISPR screen from F123 (ENCLB912PMD)

description:
https://www.encodeproject.org/experiments/ENCSR572QYM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR572QYM
assay title: Control CRISPR screen
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB912PMD
size range: 710-720

value: Bing Ren, UCSD

value: ENCBS174BRZ at ENCODE; https://www.encodeproject.org/ENCBS174BRZ/


title: long read scRNA-seq from layer of hippocampus (ENCLB914QHQ)

description:
https://www.encodeproject.org/experiments/ENCSR991UOI/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P10 male normal 2k
experiment encode accession: ENCSR991UOI
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB914QHQ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P10 male 2

value: 10 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS578PCE at ENCODE; https://www.encodeproject.org/ENCBS578PCE/


title: FACS CRISPR screen from F123 (ENCLB821KVZ)

description:
https://www.encodeproject.org/experiments/ENCSR552KGE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR552KGE
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR226EZK
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB821KVZ

source_name: Mus musculus F123 cell line genetically modified (insertion) using CRISPR (sgRNA) targeting M. musculus Dppa2, genetically modified (insertion) using transduction, genetically modified using CRISPR cutting (sgRNA)

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS572NGF at ENCODE; https://www.encodeproject.org/ENCBS572NGF/


title: long read scRNA-seq from adrenal gland (ENCLB322HWW)

description:
https://www.encodeproject.org/experiments/ENCSR431FYK/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P36 male ont_match 2k
experiment encode accession: ENCSR431FYK
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB322HWW
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: B6/Cast F1 adrenal P36 male 2

value: male

value: postnatal

value: 36 day

value: ENCBS815NZI at ENCODE; https://www.encodeproject.org/ENCBS815NZI/

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


title: FACS CRISPR screen from F123 (ENCLB133WLH)

description:
https://www.encodeproject.org/experiments/ENCSR552KGE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR552KGE
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR226EZK
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB133WLH

value: cell line

value: not collected

value: unknown

value: ENCBS411FGL at ENCODE; https://www.encodeproject.org/ENCBS411FGL/


title: long read scRNA-seq from layer of hippocampus (ENCLB361YRX)

description:
https://www.encodeproject.org/experiments/ENCSR976OMS/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P10 male ont_match 2k
experiment encode accession: ENCSR976OMS
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB361YRX
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P10 male 2

value: 10 day

value: Ali Mortazavi, UCI

value: nucleus


title: long read scRNA-seq from layer of hippocampus (ENCLB709VFV)

description:
https://www.encodeproject.org/experiments/ENCSR976OMS/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P10 male ont_match 2k
experiment encode accession: ENCSR976OMS
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB709VFV
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P10 male 1

value: The Jackson Laboratory

value: ENCBS749DZM at ENCODE; https://www.encodeproject.org/ENCBS749DZM/


title: FACS CRISPR screen from F123 (ENCLB769FJA)

description:
https://www.encodeproject.org/experiments/ENCSR500VLM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR500VLM
assay title: FACS CRISPR screen
possible controls: ENCSR928AKC
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB769FJA
size range: 710-720

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS406SAR at ENCODE; https://www.encodeproject.org/ENCBS406SAR/


title: long read scRNA-seq from layer of hippocampus (ENCLB198TNV)

description:
https://www.encodeproject.org/experiments/ENCSR405VKO/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P2mo male normal 2k
experiment encode accession: ENCSR405VKO
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB198TNV
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P2mo male 2

value: male

value: adult

value: 2 month

value: ENCBS066BIL at ENCODE; https://www.encodeproject.org/ENCBS066BIL/

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


title: FACS CRISPR screen from F123 (ENCLB914OJK)

description:
https://www.encodeproject.org/experiments/ENCSR312ISP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR312ISP
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR180JKQ
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB914OJK

value: cell line

value: not collected

value: unknown

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS697EJR at ENCODE; https://www.encodeproject.org/ENCBS697EJR/


title: long read scRNA-seq from layer of hippocampus (ENCLB674LMA)

description:
https://www.encodeproject.org/experiments/ENCSR245GNB/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P25 female normal 2k
experiment encode accession: ENCSR245GNB
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB674LMA
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P25 female 2

value: female

value: postnatal

value: 25 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS434NYG at ENCODE; https://www.encodeproject.org/ENCBS434NYG/


title: FACS CRISPR screen from F123 (ENCLB591TLK)

description:
https://www.encodeproject.org/experiments/ENCSR500VLM/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR500VLM
assay title: FACS CRISPR screen
possible controls: ENCSR928AKC
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB591TLK
size range: 710-720

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS314QOV at ENCODE; https://www.encodeproject.org/ENCBS314QOV/


title: long read scRNA-seq from layer of hippocampus (ENCLB022QSX)

description:
https://www.encodeproject.org/experiments/ENCSR991UOI/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P10 male normal 2k
experiment encode accession: ENCSR991UOI
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB022QSX
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P10 male 1

value: male

value: 10 day

value: ENCBS749DZM at ENCODE; https://www.encodeproject.org/ENCBS749DZM/

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


title: Control CRISPR screen from F123 (ENCLB017SZZ)

description:
https://www.encodeproject.org/experiments/ENCSR299NFV/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR299NFV
assay title: Control CRISPR screen
possible controls: ENCSR864JVZ
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB017SZZ
size range: 710-720

value: cell line

value: not collected

value: unknown

value: ENCBS829AIZ at ENCODE; https://www.encodeproject.org/ENCBS829AIZ/


title: long read scRNA-seq from layer of hippocampus (ENCLB821RUM)

description:
https://www.encodeproject.org/experiments/ENCSR975GDE/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P14 female ont_match 2k
experiment encode accession: ENCSR975GDE
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB821RUM
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P14 female 2

value: female

value: postnatal

value: 14 day

value: ENCBS300KQE at ENCODE; https://www.encodeproject.org/ENCBS300KQE/


title: FACS CRISPR screen from F123 (ENCLB390ZQL)

description:
https://www.encodeproject.org/experiments/ENCSR500VLM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR500VLM
assay title: FACS CRISPR screen
possible controls: ENCSR928AKC
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB390ZQL
size range: 710-720

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS143LAK at ENCODE; https://www.encodeproject.org/ENCBS143LAK/


title: FACS CRISPR screen from F123 (ENCLB124QBZ)

description:
https://www.encodeproject.org/experiments/ENCSR473QRW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR473QRW
assay title: FACS CRISPR screen
possible controls: ENCSR928AKC
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB124QBZ
size range: 710-720

value: ENCBS325SDH at ENCODE; https://www.encodeproject.org/ENCBS325SDH/


title: long read scRNA-seq from layer of hippocampus (ENCLB111NFY)

description:
https://www.encodeproject.org/experiments/ENCSR975GDE/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P14 female ont_match 2k
experiment encode accession: ENCSR975GDE
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB111NFY
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P14 female 1

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS454DBZ at ENCODE; https://www.encodeproject.org/ENCBS454DBZ/


title: long read scRNA-seq from layer of hippocampus (ENCLB912EET)

description:
https://www.encodeproject.org/experiments/ENCSR962GMG/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P25 female ont_match 2k
experiment encode accession: ENCSR962GMG
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB912EET
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P25 female 2

value: 25 day

value: ENCBS434NYG at ENCODE; https://www.encodeproject.org/ENCBS434NYG/

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


title: FACS CRISPR screen from F123 (ENCLB038BDU)

description:
https://www.encodeproject.org/experiments/ENCSR473QRW/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR473QRW
assay title: FACS CRISPR screen
possible controls: ENCSR928AKC
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB038BDU
size range: 710-720

value: cell line

value: not collected

value: unknown

value: ENCBS932IUL at ENCODE; https://www.encodeproject.org/ENCBS932IUL/


title: long read scRNA-seq from adrenal gland (ENCLB770PJC)

description:
https://www.encodeproject.org/experiments/ENCSR870HRG/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P10 female ont_match 2k
experiment encode accession: ENCSR870HRG
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB770PJC
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

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

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P10 female 1

value: female

value: postnatal

value: 10 day

value: ENCBS789TOM at ENCODE; https://www.encodeproject.org/ENCBS789TOM/


title: FACS CRISPR screen from F123 (ENCLB684IWJ)

description:
https://www.encodeproject.org/experiments/ENCSR500VLM/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR500VLM
assay title: FACS CRISPR screen
possible controls: ENCSR928AKC
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB684IWJ
size range: 710-720

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS414ZKJ at ENCODE; https://www.encodeproject.org/ENCBS414ZKJ/


title: long read scRNA-seq from layer of hippocampus (ENCLB611WPZ)

description:
https://www.encodeproject.org/experiments/ENCSR955GIF/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P18-20mo male ont_match 2k
experiment encode accession: ENCSR955GIF
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB611WPZ
nucleic acid starting quantity: 167
nucleic acid starting quantity units: cells

value: layer of hippocampus

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

value: male

value: adult

value: 18-20 month

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

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


title: long read scRNA-seq from layer of hippocampus (ENCLB652OOR)

description:
https://www.encodeproject.org/experiments/ENCSR955GIF/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P18-20mo male ont_match 2k
experiment encode accession: ENCSR955GIF
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB652OOR
nucleic acid starting quantity: 167
nucleic acid starting quantity units: cells

value: tissue

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

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

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


title: FACS CRISPR screen from F123 (ENCLB848CNT)

description:
https://www.encodeproject.org/experiments/ENCSR473QRW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR473QRW
assay title: FACS CRISPR screen
possible controls: ENCSR928AKC
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB848CNT
size range: 710-720

value: cell line

value: not collected

value: unknown

value: ENCBS871QCE at ENCODE; https://www.encodeproject.org/ENCBS871QCE/


title: long read scRNA-seq from layer of hippocampus (ENCLB594RXN)

description:
https://www.encodeproject.org/experiments/ENCSR962GMG/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P25 female ont_match 2k
experiment encode accession: ENCSR962GMG
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB594RXN
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: B6/Cast F1 hippocampus P25 female 1

value: female

value: postnatal

value: 25 day

value: ENCBS998IGC at ENCODE; https://www.encodeproject.org/ENCBS998IGC/


title: long read scRNA-seq from layer of hippocampus (ENCLB852KMT)

description:
https://www.encodeproject.org/experiments/ENCSR860HBH/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P2mo male ont_match 2k
experiment encode accession: ENCSR860HBH
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB852KMT
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P2mo male 2

value: male

value: adult

value: 2 month

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS066BIL at ENCODE; https://www.encodeproject.org/ENCBS066BIL/


title: FACS CRISPR screen from F123 (ENCLB245RJA)

description:
https://www.encodeproject.org/experiments/ENCSR473QRW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR473QRW
assay title: FACS CRISPR screen
possible controls: ENCSR928AKC
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB245RJA
size range: 710-720

value: cell line

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS132ULH at ENCODE; https://www.encodeproject.org/ENCBS132ULH/


title: Control CRISPR screen from F123 (ENCLB321JZV)

description:
https://www.encodeproject.org/experiments/ENCSR226EZK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR226EZK
assay title: Control CRISPR screen
assembly: mm10
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB321JZV

value: not collected

value: unknown

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS076DEK at ENCODE; https://www.encodeproject.org/ENCBS076DEK/


title: Control CRISPR screen from F123 (ENCLB934RKZ)

description:
https://www.encodeproject.org/experiments/ENCSR928AKC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR928AKC
assay title: Control CRISPR screen
possible controls: ENCSR559VMG
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB934RKZ
size range: 710-720

value: ENCBS426NPL at ENCODE; https://www.encodeproject.org/ENCBS426NPL/


title: Control CRISPR screen from F123 (ENCLB475BLJ)

description:
https://www.encodeproject.org/experiments/ENCSR928AKC/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR928AKC
assay title: Control CRISPR screen
possible controls: ENCSR559VMG
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB475BLJ
size range: 710-720

value: ENCBS754HTY at ENCODE; https://www.encodeproject.org/ENCBS754HTY/


title: long read scRNA-seq from layer of hippocampus (ENCLB650QHO)

description:
https://www.encodeproject.org/experiments/ENCSR854MEF/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P10 female normal 2k
experiment encode accession: ENCSR854MEF
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB650QHO
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: tissue

value: B6/Cast F1 hippocampus P10 female 1

value: female

value: postnatal

value: 10 day

value: The Jackson Laboratory

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

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


title: long read scRNA-seq from layer of hippocampus (ENCLB006ZHW)

description:
https://www.encodeproject.org/experiments/ENCSR860HBH/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P2mo male ont_match 2k
experiment encode accession: ENCSR860HBH
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB006ZHW
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P2mo male 1

value: male

value: adult

value: 2 month

value: Ali Mortazavi, UCI

value: nucleus

value: ENCBS246YKO at ENCODE; https://www.encodeproject.org/ENCBS246YKO/


title: long read scRNA-seq from adrenal gland (ENCLB992GFQ)

description:
https://www.encodeproject.org/experiments/ENCSR831BQT/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P14 male ont_match 2k
experiment encode accession: ENCSR831BQT
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB992GFQ
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: adrenal gland

value: B6/Cast F1 adrenal P14 male 1

value: 14 day

value: ENCBS459ROD at ENCODE; https://www.encodeproject.org/ENCBS459ROD/


title: Control CRISPR screen from F123 (ENCLB748KKM)

description:
https://www.encodeproject.org/experiments/ENCSR928AKC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR928AKC
assay title: Control CRISPR screen
possible controls: ENCSR559VMG
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB748KKM
size range: 710-720

value: cell line

value: not collected

value: unknown

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS827QWB at ENCODE; https://www.encodeproject.org/ENCBS827QWB/


title: Control CRISPR screen from F123 (ENCLB563CUC)

description:
https://www.encodeproject.org/experiments/ENCSR928AKC/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR928AKC
assay title: Control CRISPR screen
possible controls: ENCSR559VMG
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB563CUC
size range: 710-720

value: ENCBS617RSF at ENCODE; https://www.encodeproject.org/ENCBS617RSF/


title: Control CRISPR screen from F123 (ENCLB941BJZ)

description:
https://www.encodeproject.org/experiments/ENCSR226EZK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR226EZK
assay title: Control CRISPR screen
assembly: mm10
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB941BJZ

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS040PQZ at ENCODE; https://www.encodeproject.org/ENCBS040PQZ/


title: FACS CRISPR screen from F123 (ENCLB438ZDU)

description:
https://www.encodeproject.org/experiments/ENCSR897BBN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR897BBN
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR097OCB
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB438ZDU

source_name: Mus musculus F123 cell line genetically modified (insertion) using CRISPR (sgRNA) targeting M. musculus Sox2, genetically modified (insertion) using transduction, genetically modified using CRISPR cutting (sgRNA)

value: ENCBS026NQQ at ENCODE; https://www.encodeproject.org/ENCBS026NQQ/


title: long read scRNA-seq from adrenal gland (ENCLB935NHQ)

description:
https://www.encodeproject.org/experiments/ENCSR870HRG/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P10 female ont_match 2k
experiment encode accession: ENCSR870HRG
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB935NHQ
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

value: tissue

value: B6/Cast F1 adrenal P10 female 2

value: female

value: postnatal

value: 10 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS204TIR at ENCODE; https://www.encodeproject.org/ENCBS204TIR/

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


title: long read scRNA-seq from adrenal gland (ENCLB372YYZ)

description:
https://www.encodeproject.org/experiments/ENCSR750VIU/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P2mo male ont_match 2k
experiment encode accession: ENCSR750VIU
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB372YYZ
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: male

value: adult

value: 2 month

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


title: long read scRNA-seq from layer of hippocampus (ENCLB451JLG)

description:
https://www.encodeproject.org/experiments/ENCSR854MEF/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P10 female normal 2k
experiment encode accession: ENCSR854MEF
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB451JLG
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: layer of hippocampus

value: B6/Cast F1 hippocampus P10 female 2

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


title: FACS CRISPR screen from F123 (ENCLB277NUJ)

description:
https://www.encodeproject.org/experiments/ENCSR814OXH/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR814OXH
assay title: FACS CRISPR screen
possible controls: ENCSR299NFV
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB277NUJ
size range: 710-720

value: cell line

value: not collected

value: unknown

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS605YKY at ENCODE; https://www.encodeproject.org/ENCBS605YKY/


title: FACS CRISPR screen from F123 (ENCLB857UTQ)

description:
https://www.encodeproject.org/experiments/ENCSR897BBN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR897BBN
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR097OCB
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB857UTQ

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS707MVY at ENCODE; https://www.encodeproject.org/ENCBS707MVY/


title: long read scRNA-seq from adrenal gland (ENCLB590XYR)

description:
https://www.encodeproject.org/experiments/ENCSR744DDC/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P4 female ont_match 2k
experiment encode accession: ENCSR744DDC
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB590XYR
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

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

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P4 female 1

value: female

value: postnatal

value: 4 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS326PIL at ENCODE; https://www.encodeproject.org/ENCBS326PIL/

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


title: Control CRISPR screen from F123 (ENCLB775YVD)

description:
https://www.encodeproject.org/experiments/ENCSR180JKQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR180JKQ
assay title: Control CRISPR screen
assembly: mm10
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB775YVD

value: cell line

value: not collected

value: unknown

value: ENCBS932TXO at ENCODE; https://www.encodeproject.org/ENCBS932TXO/


title: long read scRNA-seq from adrenal gland (ENCLB197MEE)

description:
https://www.encodeproject.org/experiments/ENCSR744DDC/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P4 female ont_match 2k
experiment encode accession: ENCSR744DDC
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB197MEE
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

value: B6/Cast F1 adrenal P4 female 2

value: ENCBS588QYH at ENCODE; https://www.encodeproject.org/ENCBS588QYH/


title: long read scRNA-seq from adrenal gland (ENCLB680TIY)

description:
https://www.encodeproject.org/experiments/ENCSR831BQT/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P14 male ont_match 2k
experiment encode accession: ENCSR831BQT
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB680TIY
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: B6/Cast F1 adrenal P14 male 2

value: male

value: 14 day

value: ENCBS364VBE at ENCODE; https://www.encodeproject.org/ENCBS364VBE/


title: long read scRNA-seq from adrenal gland (ENCLB386GJG)

description:
https://www.encodeproject.org/experiments/ENCSR770VEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P14 female ont_match 2k
experiment encode accession: ENCSR770VEJ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB386GJG
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: tissue

value: B6/Cast F1 adrenal P14 female 1

value: female

value: postnatal

value: ENCBS829KDQ at ENCODE; https://www.encodeproject.org/ENCBS829KDQ/


title: FACS CRISPR screen from F123 (ENCLB085MYA)

description:
https://www.encodeproject.org/experiments/ENCSR705PWZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR705PWZ
assay title: FACS CRISPR screen
possible controls: ENCSR572QYM
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB085MYA
size range: 710-720

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS954QHL at ENCODE; https://www.encodeproject.org/ENCBS954QHL/


title: long read scRNA-seq from adrenal gland (ENCLB863XAF)

description:
https://www.encodeproject.org/experiments/ENCSR728BUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P18-20mo female ont_match 2k
experiment encode accession: ENCSR728BUZ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB863XAF
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: B6/Cast F1 adrenal P18-20mo female 1

value: adult

value: 18-20 month

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

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

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


title: FACS CRISPR screen from F123 (ENCLB408JKI)

description:
https://www.encodeproject.org/experiments/ENCSR705PWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR705PWZ
assay title: FACS CRISPR screen
possible controls: ENCSR572QYM
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB408JKI
size range: 710-720

value: cell line

value: not collected

value: unknown

value: ENCBS168VSH at ENCODE; https://www.encodeproject.org/ENCBS168VSH/


title: long read scRNA-seq from adrenal gland (ENCLB128WPI)

description:
https://www.encodeproject.org/experiments/ENCSR750VIU/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P2mo male ont_match 2k
experiment encode accession: ENCSR750VIU
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB128WPI
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P2mo male 1

value: male

value: 2 month

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


title: long read scRNA-seq from adrenal gland (ENCLB129VEH)

description:
https://www.encodeproject.org/experiments/ENCSR770VEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P14 female ont_match 2k
experiment encode accession: ENCSR770VEJ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB129VEH
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 adrenal P14 female 2

value: female

value: postnatal

value: 14 day

value: ENCBS608STD at ENCODE; https://www.encodeproject.org/ENCBS608STD/


title: FACS CRISPR screen from F123 (ENCLB420ZPP)

description:
https://www.encodeproject.org/experiments/ENCSR814OXH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR814OXH
assay title: FACS CRISPR screen
possible controls: ENCSR299NFV
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB420ZPP
size range: 710-720

value: Bing Ren, UCSD

value: Rudolf Jaenisch

value: ENCBS384QRG at ENCODE; https://www.encodeproject.org/ENCBS384QRG/


title: long read scRNA-seq from adrenal gland (ENCLB606SEM)

description:
https://www.encodeproject.org/experiments/ENCSR030XVR/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P10 male ont_match 2k
experiment encode accession: ENCSR030XVR
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB606SEM
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

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

value: B6/Cast F1 adrenal P10 male 2

value: 10 day

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

value: ENCBS007OHI at ENCODE; https://www.encodeproject.org/ENCBS007OHI/

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


title: FACS CRISPR screen from F123 (ENCLB738CLA)

description:
https://www.encodeproject.org/experiments/ENCSR141PNN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR141PNN
assay title: FACS CRISPR screen
possible controls: ENCSR299NFV
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB738CLA
size range: 710-720

value: cell line

value: not collected

value: unknown

value: ENCBS401MTR at ENCODE; https://www.encodeproject.org/ENCBS401MTR/


title: Control CRISPR screen from F123 (ENCLB009NDH)

description:
https://www.encodeproject.org/experiments/ENCSR180JKQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR180JKQ
assay title: Control CRISPR screen
assembly: mm10
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB009NDH

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS432DVA at ENCODE; https://www.encodeproject.org/ENCBS432DVA/


title: FACS CRISPR screen from F123 (ENCLB143OUP)

description:
https://www.encodeproject.org/experiments/ENCSR141PNN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR141PNN
assay title: FACS CRISPR screen
possible controls: ENCSR299NFV
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB143OUP
size range: 710-720

value: Bing Ren, UCSD

value: ENCBS460IWN at ENCODE; https://www.encodeproject.org/ENCBS460IWN/


title: long read scRNA-seq from layer of hippocampus (ENCLB189QFN)

description:
https://www.encodeproject.org/experiments/ENCSR157ZUT/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P14 male ont_match 2k
experiment encode accession: ENCSR157ZUT
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB189QFN
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: male

value: postnatal

value: 14 day

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


title: long read scRNA-seq from layer of hippocampus (ENCLB325CSO)

description:
https://www.encodeproject.org/experiments/ENCSR157ZUT/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 hippocampus P14 male ont_match 2k
experiment encode accession: ENCSR157ZUT
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB325CSO
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 hippocampus P14 male 1

value: Ali Mortazavi, UCI

value: nucleus

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: FACS CRISPR screen from F123 (ENCLB430XZM)

description:
https://www.encodeproject.org/experiments/ENCSR814OXH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR814OXH
assay title: FACS CRISPR screen
possible controls: ENCSR299NFV
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB430XZM
size range: 710-720

value: cell line

value: not collected

value: unknown

value: Rudolf Jaenisch

value: ENCBS701BCA at ENCODE; https://www.encodeproject.org/ENCBS701BCA/


title: FACS CRISPR screen from F123 (ENCLB984HHG)

description:
https://www.encodeproject.org/experiments/ENCSR141PNN/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR141PNN
assay title: FACS CRISPR screen
possible controls: ENCSR299NFV
encode release date: 2022-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB984HHG
size range: 710-720

value: Bing Ren, UCSD

value: ENCBS968HEB at ENCODE; https://www.encodeproject.org/ENCBS968HEB/


title: Control CRISPR screen from F123 (ENCLB105RST)

description:
https://www.encodeproject.org/experiments/ENCSR097OCB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR097OCB
assay title: Control CRISPR screen
assembly: mm10
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB105RST

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS058FWW at ENCODE; https://www.encodeproject.org/ENCBS058FWW/


title: long read scRNA-seq from adrenal gland (ENCLB923ZGJ)

description:
https://www.encodeproject.org/experiments/ENCSR016VQS/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P4 male ont_match 2k
experiment encode accession: ENCSR016VQS
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB923ZGJ
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

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

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P4 male 1

value: male

value: postnatal

value: 4 day

value: ENCBS865NYD at ENCODE; https://www.encodeproject.org/ENCBS865NYD/


title: long read scRNA-seq from adrenal gland (ENCLB357JSS)

description:
https://www.encodeproject.org/experiments/ENCSR016VQS/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P4 male ont_match 2k
experiment encode accession: ENCSR016VQS
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB357JSS
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

value: B6/Cast F1 adrenal P4 male 2

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

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

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


title: FACS CRISPR screen from F123 (ENCLB885SCY)

description:
https://www.encodeproject.org/experiments/ENCSR004TXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR004TXD
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR097OCB
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB885SCY

value: cell line

value: not collected

value: unknown

value: ENCBS766NUP at ENCODE; https://www.encodeproject.org/ENCBS766NUP/


title: FACS CRISPR screen from F123 (ENCLB362UNP)

description:
https://www.encodeproject.org/experiments/ENCSR063AQH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR063AQH
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR180JKQ
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB362UNP

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS736ICL at ENCODE; https://www.encodeproject.org/ENCBS736ICL/


title: FACS CRISPR screen from F123 (ENCLB750TAZ)

description:
https://www.encodeproject.org/experiments/ENCSR063AQH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR063AQH
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR180JKQ
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB750TAZ

value: ENCBS915RDI at ENCODE; https://www.encodeproject.org/ENCBS915RDI/


title: Tcf21KO 5wk 2 nontdt ATAC

status: Public on Feb 27 2026

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

description: Library name: Tcf21_5wk_ATAC_nontdt2

library_source: genomic single cell

data_processing:
RNA fastq files were processed using Cellranger v7.0.1 (10x Genomics) to obtain transcript count matrices and aligned to mouse transcriptome mm10-2020-A-2.0.0 (10x Genomics) with custom addition of lineage tracing tdTomato transcript. Samples at each timepoint were aggregated and analyzed with R package with Seurat (v4.3)68. Low-quality cells and mitochondrial-rich cells were filtered with parameters mitochondrial percentage < 6%, ribosomal percentage < 25%, and nFeature_RNA > 1250 and < 8000. Gene expression count matrices underwent log-transformation and library-specific scaling. Importantly, no additional batch correction for visualization was required in the pre-processing steps given the uniform processing of mice samples. Principal component analysis was used for dimensionality reduction followed by clustering using the Louvain algorithm. For the full timecourse dataset, aligned scRNA files from Control and Tcf21-KO data were merged and processed with identical QC parameters as above. Clustering was then performed on this merged dataset in order to ensure comparable differential gene analysis and pseudotime comparisons. The processed dataset is then split into Control and Tcf21-KO objects for independent analysis. We further applied logistic regression to determine the optimal tdTomato expression cutoff and subset on SMC-derived lineage cells exclusive to tdTomato fluorescence-activated cell sorting (FACS). For force directed layouts, we followed methods as described in Schiebinger et al. 50 dimensional diffusion components are calculated with SCANPY (1.9.3) with default parameters. For each cell, its 20 nearest neighbors was used to produce a nearest neighbor map. Then we applied leiden clustering at a resolution of 0.36 and generated cluster connectivities via PAGA and visualized the force-directed layout on the k-NN graph using ForceAtlas2. scATAC Raw fastq files were uniformly processed using Cellranger-atac-2.1.0 (10x Genomics) and aligned to cellranger-arc-mm10-2020-A-2.0.0 reference genome (10x Genomics). The data were processed to remove low-quality cells and reads with low mapping quality with parameters peak_region_fragments > 2500, peak_region_fragments < 100000, pct_reads_in_peaks > 30, nucleosome_signal <= 4, TSS.enrichment > 2. The remaining reads were then used to construct a sparse binary matrix, representing chromatin accessibility states across individual cells and genomic regions. A unified set of peaks from all samples (Control and Tcf21-KO) were merged using overlapping and adjacent peaks using CellRanger-ATAC aggr protocol. This unified peak set was re-quantified by term frequency-inverse document frequency (TF-IDF) using Signac69 (1.10) RunTFIDF. To preprocess scRNA and scATAC data for integration, gene activities are first calculated from chromatin accessibility data using GeneActivity() function from Signac with default parameters and log normalization. Datasets were integrated using canonical correlation analysis (CCA) with the Seurat RunCCA() function upon 2000 features using the SelectIntegrationFeatures() in Seurat. We then use the integrated dataset to perform pseudotime ordering using Slingshot70 (2.6) and split the dataset into 30 pseudotime bins for uniform downstream analyses.
Assembly: mm10
Supplementary files format and content: rds file, aggregated scRNA file, aggregated scATAC file

source_name: mouse aortic root and proximal ascending

extract_protocol:
Samples from mouse aorta were dissociated into single cells for RNA and ATAC sequencing using the 10x Genomics Chromium platform. Euthanized mice are perfused with phosphate buffered saline and dissected to obtain the aortic root up to the level of the brachiocephalic artery. The tissue is washed with PBS and incubated in an enzymatic dissociation cocktail containing Liberase (5401127001; Sigma-Aldrich) and Elastase (LS002279; Worthington) in Hank’s Balanced Salt Solution with calcium (HBSS+ Ca2+) for 30 minutes. Mechanical dissociation is performed for 5 minutes followed by visualization under the microscope to ensure single cell suspension. This suspension is strained through a 35µm nylon mesh snap cap into falcon test tubes (352235 BD) followed by FACS sorting (Sony SH800) for tdTomato positive and negative cells in parallel. For single cell ATAC, nuclei was isolated per 10X recommended protocol and captured on the 10X scATAC platform. For both scRNA and scATAC runs, samples at some intermediate time points were processed as pooled samples with tdTomato and non-tdTomato loaded at 1:1 ratio after FACS and listed in Supplementary Data 1.
Each individually sorted cell suspension was loaded onto 10x GEM G or H chips with remainder per 10x protocols (Chromium Single Cell 3’ RNA V3.1, Chromium Single Cell ATAC V2). Single-cell libraries were constructed according to manufacturer’s instructions with index labeling using the Dual Index Kit TT set A for scRNA-seq and Single Index kit NT for scATAC-seq. This allows for library pooling into one lane for sequencing on the Illumina NovaSeq6000 platform with a targeted depth of 40-50,000 reads per cell for RNA and 75,000 reads/cell for ATAC.

tag: tissue

tag: genotype

value: Tcf21f/f, Tdt+/+, ApoE-/-,Myh11Cre


title: Tcf21KO 16wk 2 tdt ATAC

description: Library name: Tcf21_16wk_ATAC_tdt2

value: mouse aortic root and proximal ascending


title: long read scRNA-seq from adrenal gland (ENCLB227ULP)

description:
https://www.encodeproject.org/experiments/ENCSR030XVR/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P10 male ont_match 2k
experiment encode accession: ENCSR030XVR
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB227ULP
nucleic acid starting quantity: 42
nucleic acid starting quantity units: cells

value: adrenal gland

value: tissue

value: B6/Cast F1 adrenal P10 male 1

value: male

value: postnatal

value: 10 day

value: ENCBS498DPL at ENCODE; https://www.encodeproject.org/ENCBS498DPL/


title: long read scRNA-seq from adrenal gland (ENCLB918MBV)

description:
https://www.encodeproject.org/experiments/ENCSR728BUZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P18-20mo female ont_match 2k
experiment encode accession: ENCSR728BUZ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB918MBV
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

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

value: female

value: adult

value: 18-20 month

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

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

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


title: RNA

description: Library name: Tcf21_16wk_ATAC_nontdt

value: mouse aortic root and proximal ascending

value: Tcf21f/f, Tdt+/+, ApoE-/-,Myh11Cre


title: Control CRISPR screen from F123 (ENCLB908DXM)

description:
https://www.encodeproject.org/experiments/ENCSR097OCB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR097OCB
assay title: Control CRISPR screen
assembly: mm10
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB908DXM

value: cell line

value: not collected

value: unknown

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS116WRE at ENCODE; https://www.encodeproject.org/ENCBS116WRE/


title: long read scRNA-seq from adrenal gland (ENCLB004OWF)

description:
https://www.encodeproject.org/experiments/ENCSR027HXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P25 female ont_match 2k
experiment encode accession: ENCSR027HXJ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB004OWF
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: tissue

value: B6/Cast F1 adrenal P25 female 1

value: postnatal

value: 25 day

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


title: Tcf21KO 5wk 1 nontdt ATAC

description: Library name: Tcf21_5wk_ATAC_nontdt


title: long read scRNA-seq from adrenal gland (ENCLB469XPU)

description:
https://www.encodeproject.org/experiments/ENCSR027HXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ONT long-read B6/Cast F1 adrenal P25 female ont_match 2k
experiment encode accession: ENCSR027HXJ
assay title: long read scRNA-seq
assembly: mm10
encode release date: 2023-02-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB469XPU
nucleic acid starting quantity: 83
nucleic acid starting quantity units: cells

value: B6/Cast F1 adrenal P25 female 2

value: female

value: Ali Mortazavi, UCI

value: nucleus

value: The Jackson Laboratory

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


title: Tcf21KO 16wk 1 tdt ATAC

description: Library name: Tcf21_16wk_ATAC_tdt

value: mouse aortic root and proximal ascending

value: Tcf21f/f, Tdt+/+, ApoE-/-,Myh11Cre


title: Control 16wk 1 nontdt ATAC

description: Library name: 16wk_ATAC_nontdt

value: Tdt+/+, ApoE-/-,Myh11Cre


title: Tcf21KO 5wk 2 tdt ATAC

description: Library name: Tcf21_5wk_ATAC_tdt2


title: FACS CRISPR screen from F123 (ENCLB955RIE)

description:
https://www.encodeproject.org/experiments/ENCSR004TXD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR004TXD
assay title: FACS CRISPR screen
assembly: mm10
possible controls: ENCSR097OCB
encode release date: 2020-08-07
lab: Yin Shen, UCSF
library encode accession: ENCLB955RIE

value: cell line

value: not collected

value: unknown

value: Yin Shen, UCSF

value: Bing Ren

value: ENCBS320GQI at ENCODE; https://www.encodeproject.org/ENCBS320GQI/


title: Control 12wk 1 tdt ATAC

description: Library name: 12wk_ATAC_tdt


title: Control 9wk 1 mixed ATAC

description: Library name: 9wk_ATAC


title: Tcf21KO 12wk 1 tdt ATAC

description: Library name: Tcf21_12wk_ATAC_tdt


title: Tcf21KO 5wk 1 tdt ATAC

description: Library name: Tcf21_5wk_ATAC_tdt


title: Control 16wk 2 nontdt ATAC

description: Library name: 16wk_ATAC_nontdt2


title: Control 16wk 2 tdt ATAC

description: Library name: 16wk_ATAC_tdt2


title: Control 0wk tdt ATAC

description: Library name: 0wk_ATAC_tdt


title: Control 0wk nontdt ATAC

description: Library name: 0wk_ATAC_nontdt


title: Control 5wk 1 nontdt ATAC

description: Library name: 5wk_ATAC_nontdt


title: Control 9wk 2 mixed ATAC

description: Library name: 9wk_ATAC_2


title: Control 12wk 1 nontdt ATAC

description: Library name: 12wk_ATAC_nontdt


title: Control 7wk 1 mixed ATAC

description: Library name: 7wk_ATAC


title: Control 16wk 1 tdt ATAC

description: Library name: 16wk_ATAC_tdt


title: Control 5wk 1 tdt ATAC

description: Library name: 5wk_ATAC_tdt


title: Tcf21KO 16wk 2 tdt RNA

description: Library name: Tcf21_16wk_tdt2

library_source: transcriptomic single cell

molecule: polyA RNA


title: Tcf21KO 16wk 1 tdt RNA

description: Library name: Tcf21_16wk_tdt1


title: Control 16wk 5 nontdt RNA

description: Library name: 16wk_nontdt5


title: Control 16wk 4 nontdt RNA

description: Library name: 16wk_nontdt4


title: Tcf21KO 16wk 1 nontdt RNA

description: Library name: Tcf21_16wk_nontdt1


title: DNase-seq from activated T-cell (ENCLB138MDJ)

description:
https://www.encodeproject.org/experiments/ENCSR257DFF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR257DFF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB138MDJ

organism: Homo sapiens

source_name: Homo sapiens female adult (33 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: activated T-cell

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS914MHG at ENCODE; https://www.encodeproject.org/ENCBS914MHG/


title: Tcf21KO 12wk 1 nontdt RNA

description: Library name: Tcf21_12wk_nontdt

value: mouse aortic root and proximal ascending