title: long read RNA-seq from layer of hippocampus (ENCLB552WDU)

description:
https://www.encodeproject.org/experiments/ENCSR972DID/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_439, ENC4_440 hippocampus_B6Cast F1_2 months_male_5_ENC4_cDNA511
experiment encode accession: ENCSR972DID
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB552WDU
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS762CAG at ENCODE; https://www.encodeproject.org/ENCBS762CAG/

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


title: long read RNA-seq from heart (ENCLB267YMP)

status: Public on Dec 04 2022

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR938RPH/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_495, ENC4_496 heart_B6Cast F1 PND 2 months Female 03 heart_ENC4_cDNA607, cDNA608
experiment encode accession: ENCSR938RPH
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB267YMP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

value: heart

value: tissue

tag: description

value: B6Cast F1 PND 2 months Female 04 heart for Wold biobank

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: unknown

tag: age

value: 2 month

tag: lab

tag: source

tag: link

value: ENCBS353NKX at ENCODE; https://www.encodeproject.org/ENCBS353NKX/


title: long read RNA-seq from gastrocnemius (ENCLB110YGF)

description:
https://www.encodeproject.org/experiments/ENCSR920WYI/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_391a, ENC4_392a B6Cast F1 PND14 Females Gastrocnemius
experiment encode accession: ENCSR920WYI
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB110YGF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: gastrocnemius

value: B6Cast F1 PND14 Female 04 gastrocnemius for Wold core

value: 14 day

value: ENCBS838OKI at ENCODE; https://www.encodeproject.org/ENCBS838OKI/


title: long read RNA-seq from heart (ENCLB218ATL)

description:
https://www.encodeproject.org/experiments/ENCSR938RPH/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_495, ENC4_496 heart_B6Cast F1 PND 2 months Female 03 heart_ENC4_cDNA607, cDNA608
experiment encode accession: ENCSR938RPH
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB218ATL
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: B6Cast F1 PND 2 months Female 03 heart for Wold biobank

value: ENCBS759GYL at ENCODE; https://www.encodeproject.org/ENCBS759GYL/


title: long read RNA-seq from gastrocnemius (ENCLB676FHV)

description:
https://www.encodeproject.org/experiments/ENCSR964OKW/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_381a, ENC4_382a B6Cast F1 PND4_Male Gastrocnemius
experiment encode accession: ENCSR964OKW
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB676FHV
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: B6Cast F1 PND4 Male 03 gastrocnemius for Wold core

value: male

value: 4 day

value: Barbara Wold, Caltech

value: ENCBS895ZIH at ENCODE; https://www.encodeproject.org/ENCBS895ZIH/


title: long read RNA-seq from gastrocnemius (ENCLB601QDP)

description:
https://www.encodeproject.org/experiments/ENCSR920WYI/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_391a, ENC4_392a B6Cast F1 PND14 Females Gastrocnemius
experiment encode accession: ENCSR920WYI
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB601QDP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

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

value: The Jackson Laboratory

value: ENCBS205QFK at ENCODE; https://www.encodeproject.org/ENCBS205QFK/

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


title: long read RNA-seq from gastrocnemius (ENCLB896LMO)

description:
https://www.encodeproject.org/experiments/ENCSR964OKW/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_381a, ENC4_382a B6Cast F1 PND4_Male Gastrocnemius
experiment encode accession: ENCSR964OKW
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB896LMO
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: B6Cast F1 PND4 Male 04 gastrocnemius for Wold core

value: unknown

value: ENCBS659ATN at ENCODE; https://www.encodeproject.org/ENCBS659ATN/


title: long read RNA-seq from layer of hippocampus (ENCLB703ILF)

description:
https://www.encodeproject.org/experiments/ENCSR909NPF/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_437, ENC4_438 hippocampus_B6Cast F1_2 months_female_6_ENC4_cDNA510
experiment encode accession: ENCSR909NPF
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB703ILF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: layer of hippocampus

value: female

value: 2 month

value: ENCBS422YFH at ENCODE; https://www.encodeproject.org/ENCBS422YFH/


title: long read RNA-seq from layer of hippocampus (ENCLB505CBY)

description:
https://www.encodeproject.org/experiments/ENCSR909NPF/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_437, ENC4_438 hippocampus_B6Cast F1_2 months_female_6_ENC4_cDNA510
experiment encode accession: ENCSR909NPF
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB505CBY
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: ENCBS912RBR at ENCODE; https://www.encodeproject.org/ENCBS912RBR/


title: long read RNA-seq from adrenal gland (ENCLB678NFI)

description:
https://www.encodeproject.org/experiments/ENCSR295PVQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_227 - B6Cast F1 PND25_Male 03_Adrenals
experiment encode accession: ENCSR295PVQ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB678NFI
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

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

value: adrenal gland

value: B6Cast F1 PND25 Male 04 adrenal gland for Wold core

value: male

value: 25 day

value: ENCBS536PZT at ENCODE; https://www.encodeproject.org/ENCBS536PZT/


title: long read RNA-seq from adrenal gland (ENCLB764WTP)

description:
https://www.encodeproject.org/experiments/ENCSR893GCO/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_229 B6Cast F1 PND25_ Female 03_Adrenals
experiment encode accession: ENCSR893GCO
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB764WTP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: tissue

value: B6Cast F1 PND25 Female 04 adrenal gland for Wold core

value: Barbara Wold, Caltech

value: ENCBS214IJR at ENCODE; https://www.encodeproject.org/ENCBS214IJR/


title: long read RNA-seq from left cerebral cortex (ENCLB919LYF)

description:
https://www.encodeproject.org/experiments/ENCSR862DMK/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_465, ENC4_466 B6Cast F1 PND 2 months Male 03 L. cortex
experiment encode accession: ENCSR862DMK
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB919LYF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: left cerebral cortex

value: B6Cast F1 PND 2 months Male 04 left cerebral cortex for Wold biobank

value: The Jackson Laboratory

value: ENCBS790MBN at ENCODE; https://www.encodeproject.org/ENCBS790MBN/

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


title: long read RNA-seq from layer of hippocampus (ENCLB722NJT)

description:
https://www.encodeproject.org/experiments/ENCSR926OGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Hippocampus from 6 mo C57BL/6 male
experiment encode accession: ENCSR926OGQ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-03-21
lab: Ali Mortazavi, UCI
library encode accession: ENCLB722NJT
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 3
nucleic acid starting quantity units: µg

source_name: Mus musculus strain B6NCrl adult (6 months) layer of hippocampus tissue

value: layer of hippocampus

value: Hippocampus from 6 mo C57BL/6 male

value: not collected

value: adult

value: 6 month

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS604NYS at ENCODE; https://www.encodeproject.org/ENCBS604NYS/

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


title: long read RNA-seq from adrenal gland (ENCLB492ZUG)

description:
https://www.encodeproject.org/experiments/ENCSR454ECK/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_223 - B6Cast F1 PND14_3x Males 03_Adrenals
experiment encode accession: ENCSR454ECK
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB492ZUG
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: adrenal gland

value: tissue

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

value: male

value: unknown

value: 14 day

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


title: long read RNA-seq from adrenal gland (ENCLB424BRE)

description:
https://www.encodeproject.org/experiments/ENCSR454ECK/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_223 - B6Cast F1 PND14_3x Males 03_Adrenals
experiment encode accession: ENCSR454ECK
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB424BRE
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: Barbara Wold, Caltech

value: The Jackson Laboratory

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

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


title: long read RNA-seq from layer of hippocampus (ENCLB186LWF)

description:
https://www.encodeproject.org/experiments/ENCSR926OGQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Hippocampus from 6 mo C57BL/6 male
experiment encode accession: ENCSR926OGQ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-03-21
lab: Ali Mortazavi, UCI
library encode accession: ENCLB186LWF
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: layer of hippocampus

value: Hippocampus from 6 mo C57BL/6 male

value: not collected

value: adult

value: 6 month

value: ENCBS398AWS at ENCODE; https://www.encodeproject.org/ENCBS398AWS/


title: long read RNA-seq from adrenal gland (ENCLB090NTH)

description:
https://www.encodeproject.org/experiments/ENCSR885NRP/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_239 B6Cast F1 PND 18-20 months_Male 03_Adrenals
experiment encode accession: ENCSR885NRP
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB090NTH
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: adrenal gland

value: tissue

value: adrenal gland_B6Cast F1 PND 18-20 months_Male 03_ENC4_cDNA462

value: 18-20 month

value: ENCBS999WBI at ENCODE; https://www.encodeproject.org/ENCBS999WBI/


title: long read RNA-seq from adrenal gland (ENCLB197NET)

description:
https://www.encodeproject.org/experiments/ENCSR893GCO/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_229 B6Cast F1 PND25_ Female 03_Adrenals
experiment encode accession: ENCSR893GCO
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB197NET
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: B6Cast F1 PND25 Female 03 adrenal gland for Wold core

value: female

value: unknown

value: 25 day

value: ENCBS430IOM at ENCODE; https://www.encodeproject.org/ENCBS430IOM/


title: long read RNA-seq from left cerebral cortex (ENCLB142MWW)

description:
https://www.encodeproject.org/experiments/ENCSR862DMK/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_465, ENC4_466 B6Cast F1 PND 2 months Male 03 L. cortex
experiment encode accession: ENCSR862DMK
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB142MWW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: left cerebral cortex

value: B6Cast F1 PND 2 months Male 03 left cerebral cortex for Wold biobank

value: male

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS350BQS at ENCODE; https://www.encodeproject.org/ENCBS350BQS/

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


title: long read RNA-seq from gastrocnemius (ENCLB997FCG)

description:
https://www.encodeproject.org/experiments/ENCSR437WYC/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_397a, ENC4_398a B6Cast F1 PND36_ Male Gastrocnemius
experiment encode accession: ENCSR437WYC
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB997FCG
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: gastrocnemius

value: tissue

value: B6Cast F1 PND36 Male 03 gastrocnemius for Wold core

value: 36 day

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


title: long read RNA-seq from adrenal gland (ENCLB763PIX)

description:
https://www.encodeproject.org/experiments/ENCSR852HRM/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_237 - B6Cast F1 PND 2 months_Female 03 _Adrenals
experiment encode accession: ENCSR852HRM
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB763PIX
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

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

value: adrenal gland

value: B6Cast F1 PND 2 months Female 03 adrenal gland for Wold core

value: female

value: ENCBS393LTW at ENCODE; https://www.encodeproject.org/ENCBS393LTW/


title: long read RNA-seq from left cerebral cortex (ENCLB717VRE)

description:
https://www.encodeproject.org/experiments/ENCSR861RCH/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_467, ENC4_468 B6Cast F1 PND 2 months Female 03 L. cortex
experiment encode accession: ENCSR861RCH
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB717VRE
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: left cerebral cortex

value: B6Cast F1 PND 2 months Female 04 left cerebral cortex for Wold biobank

value: unknown

value: ENCBS235YYJ at ENCODE; https://www.encodeproject.org/ENCBS235YYJ/


title: long read RNA-seq from adrenal gland (ENCLB962ZUQ)

description:
https://www.encodeproject.org/experiments/ENCSR852HRM/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_237 - B6Cast F1 PND 2 months_Female 03 _Adrenals
experiment encode accession: ENCSR852HRM
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB962ZUQ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: B6Cast F1 PND 2 months Female 04 adrenal gland for Wold core

value: 2 month

value: Barbara Wold, Caltech

value: ENCBS838VBH at ENCODE; https://www.encodeproject.org/ENCBS838VBH/


title: long read RNA-seq from heart (ENCLB102UYL)

description:
https://www.encodeproject.org/experiments/ENCSR842KTN/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_481, ENC4_482 heart_B6Cast F1 PND14 3x Males 03 heart_ENC4_cDNA593, cDNA_594
experiment encode accession: ENCSR842KTN
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB102UYL
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: heart

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

value: male

value: 14 day

value: The Jackson Laboratory

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

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


title: long read RNA-seq from left cerebral cortex (ENCLB450ZAE)

description:
https://www.encodeproject.org/experiments/ENCSR861RCH/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_467, ENC4_468 B6Cast F1 PND 2 months Female 03 L. cortex
experiment encode accession: ENCSR861RCH
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB450ZAE
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

value: B6Cast F1 PND 2 months Female 03 left cerebral cortex for Wold biobank

value: female

value: ENCBS121OPX at ENCODE; https://www.encodeproject.org/ENCBS121OPX/


title: long read RNA-seq from heart (ENCLB602RMO)

description:
https://www.encodeproject.org/experiments/ENCSR842KTN/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_481, ENC4_482 heart_B6Cast F1 PND14 3x Males 03 heart_ENC4_cDNA593, cDNA_594
experiment encode accession: ENCSR842KTN
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB602RMO
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: unknown

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


title: long read RNA-seq from gastrocnemius (ENCLB327LUX)

description:
https://www.encodeproject.org/experiments/ENCSR845IUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_401a, ENC4_402a B6Cast F1 PND 2 months_Male Gastrocnemius
experiment encode accession: ENCSR845IUJ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB327LUX
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: gastrocnemius

value: B6Cast F1 PND 2 months Male 03 gastrocnemius for Wold core

value: 2 month

value: ENCBS258UBR at ENCODE; https://www.encodeproject.org/ENCBS258UBR/


title: long read RNA-seq from gastrocnemius (ENCLB198ETW)

description:
https://www.encodeproject.org/experiments/ENCSR845IUJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_401a, ENC4_402a B6Cast F1 PND 2 months_Male Gastrocnemius
experiment encode accession: ENCSR845IUJ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB198ETW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: B6Cast F1 PND 2 months Male 04 gastrocnemius for Wold core

value: Barbara Wold, Caltech

value: ENCBS689CSE at ENCODE; https://www.encodeproject.org/ENCBS689CSE/


title: long read RNA-seq from heart (ENCLB607FYB)

description:
https://www.encodeproject.org/experiments/ENCSR410XGE/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_497, ENC4_498 heart_B6Cast F1 PND 18-20 months Male 03 heart_ENC4_cDNA609, cDNA610
experiment encode accession: ENCSR410XGE
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB607FYB
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: heart

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS540JOT at ENCODE; https://www.encodeproject.org/ENCBS540JOT/


title: long read RNA-seq from heart (ENCLB579AAE)

description:
https://www.encodeproject.org/experiments/ENCSR410XGE/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_497, ENC4_498 heart_B6Cast F1 PND 18-20 months Male 03 heart_ENC4_cDNA609, cDNA610
experiment encode accession: ENCSR410XGE
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB579AAE
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

value: ENCBS897MIA at ENCODE; https://www.encodeproject.org/ENCBS897MIA/

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


title: long read RNA-seq from layer of hippocampus (ENCLB771GFC)

description:
https://www.encodeproject.org/experiments/ENCSR404AEI/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD hippo 8 mo Male
experiment encode accession: ENCSR404AEI
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB771GFC
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax adult (8 months) layer of hippocampus tissue

value: layer of hippocampus

value: 5xFAD hippo 8 mo Male

value: not collected

value: 8 month

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS772JNS at ENCODE; https://www.encodeproject.org/ENCBS772JNS/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: long read RNA-seq from layer of hippocampus (ENCLB202DYG)

description:
https://www.encodeproject.org/experiments/ENCSR404AEI/
***************
biological replicate number: 2
technical replicate number: 1
description: 5xFAD hippo 8 mo Male
experiment encode accession: ENCSR404AEI
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB202DYG
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: ENCBS329OHE at ENCODE; https://www.encodeproject.org/ENCBS329OHE/


title: long read RNA-seq from gastrocnemius (ENCLB926POT)

description:
https://www.encodeproject.org/experiments/ENCSR402DOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_389a, ENC4_390a B6Cast F1 PND14 Males Gastrocnemius
experiment encode accession: ENCSR402DOZ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB926POT
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: gastrocnemius

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

value: male

value: unknown

value: 14 day

value: Barbara Wold, Caltech

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


title: long read RNA-seq from gastrocnemius (ENCLB443EAP)

description:
https://www.encodeproject.org/experiments/ENCSR402DOZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_389a, ENC4_390a B6Cast F1 PND14 Males Gastrocnemius
experiment encode accession: ENCSR402DOZ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB443EAP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

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

value: The Jackson Laboratory

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

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


title: long read RNA-seq from gastrocnemius (ENCLB956PNY)

description:
https://www.encodeproject.org/experiments/ENCSR818JQK/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_395a, ENC4_396a B6Cast F1 PND25_ Female Gastrocnemius
experiment encode accession: ENCSR818JQK
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB956PNY
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: B6Cast F1 PND25 Female 03 gastrocnemius for Wold core

value: female

value: 25 day

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


title: long read RNA-seq from gastrocnemius (ENCLB529JJB)

description:
https://www.encodeproject.org/experiments/ENCSR818JQK/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_395a, ENC4_396a B6Cast F1 PND25_ Female Gastrocnemius
experiment encode accession: ENCSR818JQK
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB529JJB
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: B6Cast F1 PND25 Female 04 gastrocnemius for Wold core

value: ENCBS549WDN at ENCODE; https://www.encodeproject.org/ENCBS549WDN/


title: HUVEC, CNTF_R_VEGF, STAT3 siRNA, rep4

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

country: Germany

institute: University Medical Center Freiburg

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.6.14. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
STAR aligner (Galaxy Version 2.7.5b) for mapping using standard settings
Merging BAM Files of Flow Cell 1 and 2
featureCounts (Galaxy Version 1.6.4) for generating count matrix using standard settings
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with counts generated by featureCounts and corresponding Ensembl Stable IDs

molecule: polyA RNA

organism: Homo sapiens

source_name: Human umbilical vein endothelial cells

growth_protocol: HUVECs (Cat#: C2519A, Lonza Group) were transfected with 15 nM STAT3 siRNA (Cat#: 1299001, siRNA ID: VHS40491 Thermo Fisher Scientific) or 15 nM Control siRNA (Cat#: 12935300, Thermo Fisher Scientific) for 6h and incubated in medium for additional 42h.

extract_protocol:
Qiazol (Cat#: 79306, Qiagen) and RNeasy Micro Kit (Cat#: 74004, Qiagen) was used for RNA extraction
Librarys were generated by Illumina TruSeq Stranded mRNA Sample Preparation Guide (Cat#: 20020594, Illumina)

treatment_protocol: Cells were stimulated for 24h by cytokines. The following concentrations were used: VEGF (25 ng/mL), OSM+VEGF (100 ng/mL + 25 ng/mL),  CNTF+CNTFR+VEGF (100 ng/mL + 200 ng/mL + 25 ng/mL)

tag: cell type

value: Human umbilical vein endothelial cells (HUVECs)

tag: treatment

value: 100 ng/mL CNTF, 200ng/mL CNTFR alpha and 25 ng/mL VEGF for 24h

tag: transfection

value: STAT3 siRNA

tag: genotype

value: STAT3 knockdown


title: HUVEC, CNTF_R_VEGF, STAT3 siRNA, rep2


title: HUVEC, CNTF_R_VEGF, STAT3 siRNA, rep3


title: long read RNA-seq from gastrocnemius (ENCLB670XXR)

description:
https://www.encodeproject.org/experiments/ENCSR437WYC/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_397a, ENC4_398a B6Cast F1 PND36_ Male Gastrocnemius
experiment encode accession: ENCSR437WYC
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB670XXR
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: gastrocnemius

value: B6Cast F1 PND36 Male 04 gastrocnemius for Wold core

value: male

value: unknown

value: 36 day

value: Barbara Wold, Caltech

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


title: long read RNA-seq from heart (ENCLB052PXO)

description:
https://www.encodeproject.org/experiments/ENCSR375EOW/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_493, ENC4_494 heart_B6Cast F1 PND 2 months Male 03 heart_ENC4_cDNA605, cDNA606
experiment encode accession: ENCSR375EOW
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB052PXO
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: heart

value: tissue

value: B6Cast F1 PND 2 months Male 04 heart for Wold biobank

value: 2 month

value: The Jackson Laboratory

value: ENCBS297GPP at ENCODE; https://www.encodeproject.org/ENCBS297GPP/

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


title: long read RNA-seq from heart (ENCLB940GOW)

description:
https://www.encodeproject.org/experiments/ENCSR375EOW/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_493, ENC4_494 heart_B6Cast F1 PND 2 months Male 03 heart_ENC4_cDNA605, cDNA606
experiment encode accession: ENCSR375EOW
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB940GOW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: B6Cast F1 PND 2 months Male 03 heart for Wold biobank

value: ENCBS154PWG at ENCODE; https://www.encodeproject.org/ENCBS154PWG/


title: long read RNA-seq from gastrocnemius (ENCLB128RUW)

description:
https://www.encodeproject.org/experiments/ENCSR370BHF/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_403a, ENC4_404a B6Cast F1 PND 2 months_Female Gastrocnemius
experiment encode accession: ENCSR370BHF
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB128RUW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: B6Cast F1 PND 2 months Female 03 gastrocnemius for Wold core

value: female

value: ENCBS821KNX at ENCODE; https://www.encodeproject.org/ENCBS821KNX/


title: HUVEC, CNTF_R_VEGF, STAT3 siRNA, rep1

value: Human umbilical vein endothelial cells (HUVECs)

value: 100 ng/mL CNTF, 200ng/mL CNTFR alpha and 25 ng/mL VEGF for 24h

value: STAT3 siRNA

value: STAT3 knockdown


title: HUVEC, OSM_VEGF, STAT3 siRNA, rep4

value: 100 ng/mL OSM and 25 ng/mL VEGF for 24h


title: HUVEC, OSM_VEGF, STAT3 siRNA, rep2


title: long read RNA-seq from gastrocnemius (ENCLB794DNZ)

description:
https://www.encodeproject.org/experiments/ENCSR370BHF/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_403a, ENC4_404a B6Cast F1 PND 2 months_Female Gastrocnemius
experiment encode accession: ENCSR370BHF
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB794DNZ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: gastrocnemius

value: B6Cast F1 PND 2 months Female 04 gastrocnemius for Wold core

value: unknown

value: Barbara Wold, Caltech

value: ENCBS523ZPG at ENCODE; https://www.encodeproject.org/ENCBS523ZPG/


title: HUVEC, OSM_VEGF, STAT3 siRNA, rep1


title: long read RNA-seq from gastrocnemius (ENCLB620VBF)

description:
https://www.encodeproject.org/experiments/ENCSR791CDT/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_393a, ENC4_394a B6Cast F1 PND25_Male Gastrocnemius
experiment encode accession: ENCSR791CDT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB620VBF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: tissue

value: B6Cast F1 PND25 Male 04 gastrocnemius for Wold core

value: male

value: 25 day

value: The Jackson Laboratory

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


title: long read RNA-seq from gastrocnemius (ENCLB545HZH)

description:
https://www.encodeproject.org/experiments/ENCSR791CDT/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_393a, ENC4_394a B6Cast F1 PND25_Male Gastrocnemius
experiment encode accession: ENCSR791CDT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB545HZH
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: B6Cast F1 PND25 Male 03 gastrocnemius for Wold core

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

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


title: long read RNA-seq from left cerebral cortex (ENCLB043ZJF)

description:
https://www.encodeproject.org/experiments/ENCSR791JQO/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_453, ENC4_454 B6Cast F1 PND14 3x Males 03 L. cortex
experiment encode accession: ENCSR791JQO
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB043ZJF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: left cerebral cortex

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

value: 14 day

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


title: long read RNA-seq from layer of hippocampus (ENCLB498TZI)

description:
https://www.encodeproject.org/experiments/ENCSR411ZHA/
***************
biological replicate number: 2
technical replicate number: 1
description: Control hippo Female
experiment encode accession: ENCSR411ZHA
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB498TZI
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Mus musculus strain B6NCrl layer of hippocampus tissue

value: layer of hippocampus

value: Control hippo Female

value: not collected

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS177UPU at ENCODE; https://www.encodeproject.org/ENCBS177UPU/

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


title: long read RNA-seq from gastrocnemius (ENCLB807CLC)

description:
https://www.encodeproject.org/experiments/ENCSR754VEZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_387a, ENC4_388a B6Cast F1 PND10_Female Gastrocnemius
experiment encode accession: ENCSR754VEZ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB807CLC
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: gastrocnemius

value: tissue

value: B6Cast F1 PND10 Female 03 gastrocnemius for Wold core

value: female

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: ENCBS927BKO at ENCODE; https://www.encodeproject.org/ENCBS927BKO/


title: HUVEC, VEGF, STAT3 siRNA, rep4

value: Human umbilical vein endothelial cells (HUVECs)

value: 25 ng/mL VEGF for 24h

value: STAT3 siRNA

value: STAT3 knockdown


title: long read RNA-seq from gastrocnemius (ENCLB099EXH)

description:
https://www.encodeproject.org/experiments/ENCSR754VEZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_387a, ENC4_388a B6Cast F1 PND10_Female Gastrocnemius
experiment encode accession: ENCSR754VEZ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB099EXH
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: B6Cast F1 PND10 Female 04 gastrocnemius for Wold core

value: The Jackson Laboratory

value: ENCBS900JGS at ENCODE; https://www.encodeproject.org/ENCBS900JGS/

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


title: HUVEC, VEGF, STAT3 siRNA, rep2


title: HUVEC, VEGF, STAT3 siRNA, rep3


title: HUVEC, VEGF, STAT3 siRNA, rep1


title: long read RNA-seq from gastrocnemius (ENCLB153QQT)

description:
https://www.encodeproject.org/experiments/ENCSR734WEK/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_385a, ENC4_386a B6Cast F1 PND10_Male Gastrocnemius
experiment encode accession: ENCSR734WEK
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB153QQT
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: B6Cast F1 PND10 Male 03 gastrocnemius for Wold core

value: male

value: ENCBS766LFK at ENCODE; https://www.encodeproject.org/ENCBS766LFK/


title: long read RNA-seq from gastrocnemius (ENCLB532CCA)

description:
https://www.encodeproject.org/experiments/ENCSR734WEK/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_385a, ENC4_386a B6Cast F1 PND10_Male Gastrocnemius
experiment encode accession: ENCSR734WEK
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB532CCA
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: gastrocnemius

value: tissue

value: B6Cast F1 PND10 Male 04 gastrocnemius for Wold core

value: ENCBS078GAU at ENCODE; https://www.encodeproject.org/ENCBS078GAU/


title: long read RNA-seq from left cerebral cortex (ENCLB113NLF)

description:
https://www.encodeproject.org/experiments/ENCSR791JQO/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_453, ENC4_454 B6Cast F1 PND14 3x Males 03 L. cortex
experiment encode accession: ENCSR791JQO
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB113NLF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: left cerebral cortex

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

value: unknown

value: 14 day

value: Barbara Wold, Caltech

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


title: HUVEC, CNTF_R_VEGF, Control  siRNA, rep3

value: Human umbilical vein endothelial cells (HUVECs)

value: 100 ng/mL CNTF, 200ng/mL CNTFR alpha and 25 ng/mL VEGF for 24h

value: Control siRNA

value: control


title: HUVEC, OSM_VEGF, STAT3 siRNA, rep3

value: 100 ng/mL OSM and 25 ng/mL VEGF for 24h

value: STAT3 siRNA

value: STAT3 knockdown


title: HUVEC, CNTF_R_VEGF, Control  siRNA, rep4


title: long read RNA-seq from heart (ENCLB369BLY)

description:
https://www.encodeproject.org/experiments/ENCSR267XBT/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_499, ENC4_500 heart_B6Cast F1 PND 18-20 months Female 03 heart_ENC4_cDNA611, cDNA612
experiment encode accession: ENCSR267XBT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB369BLY
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: heart

value: B6Cast F1 DPN18-20months

value: female

value: adult

value: 18-20 month

value: The Jackson Laboratory

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

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


title: long read RNA-seq from heart (ENCLB795KSJ)

description:
https://www.encodeproject.org/experiments/ENCSR267XBT/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_499, ENC4_500 heart_B6Cast F1 PND 18-20 months Female 03 heart_ENC4_cDNA611, cDNA612
experiment encode accession: ENCSR267XBT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB795KSJ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

value: Barbara Wold, Caltech

value: ENCBS007ZPS at ENCODE; https://www.encodeproject.org/ENCBS007ZPS/


title: HUVEC, CNTF_R_VEGF, Control  siRNA, rep2

value: Human umbilical vein endothelial cells (HUVECs)

value: 100 ng/mL CNTF, 200ng/mL CNTFR alpha and 25 ng/mL VEGF for 24h


title: HUVEC, OSM_VEGF, Control  siRNA, rep3

value: Control siRNA

value: control


title: HUVEC, CNTF_R_VEGF, Control  siRNA, rep1


title: HUVEC, OSM_VEGF, Control  siRNA, rep2

value: 100 ng/mL OSM and 25 ng/mL VEGF for 24h


title: HUVEC, OSM_VEGF, Control  siRNA, rep4


title: HUVEC, OSM_VEGF, Control  siRNA, rep1


title: long read RNA-seq from layer of hippocampus (ENCLB780UPA)

description:
https://www.encodeproject.org/experiments/ENCSR411ZHA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control hippo Female
experiment encode accession: ENCSR411ZHA
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB780UPA
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: layer of hippocampus

value: Control hippo Female

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS271YAL at ENCODE; https://www.encodeproject.org/ENCBS271YAL/

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


title: HUVEC, VEGF, Control  siRNA, rep4

value: 25 ng/mL VEGF for 24h


title: long read RNA-seq from adrenal gland (ENCLB237EMB)

description:
https://www.encodeproject.org/experiments/ENCSR242UEB/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_231 B6Cast F1 PND36_ Male 03_Adrenals
experiment encode accession: ENCSR242UEB
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB237EMB
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: adrenal gland

value: tissue

value: B6Cast F1 PND36 Male 03 adrenal gland for Wold core

value: male

value: 36 day

value: The Jackson Laboratory

value: ENCBS758KRR at ENCODE; https://www.encodeproject.org/ENCBS758KRR/

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


title: long read RNA-seq from adrenal gland (ENCLB982SXH)

description:
https://www.encodeproject.org/experiments/ENCSR242UEB/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_231 B6Cast F1 PND36_ Male 03_Adrenals
experiment encode accession: ENCSR242UEB
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB982SXH
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: B6Cast F1 PND36 Male 04 adrenal gland for Wold core

value: Barbara Wold, Caltech

value: ENCBS414TUZ at ENCODE; https://www.encodeproject.org/ENCBS414TUZ/


title: long read RNA-seq from adrenal gland (ENCLB089YXR)

description:
https://www.encodeproject.org/experiments/ENCSR665XLM/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_221 - B6Cast F1 PND10_Female 03_Adrenals
experiment encode accession: ENCSR665XLM
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB089YXR
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

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

value: female

value: unknown

value: 10 day

value: ENCBS824HLN at ENCODE; https://www.encodeproject.org/ENCBS824HLN/


title: HUVEC, VEGF, Control  siRNA, rep2

value: Human umbilical vein endothelial cells (HUVECs)

value: 25 ng/mL VEGF for 24h

value: Control siRNA

value: control


title: HUVEC, VEGF, Control  siRNA, rep3


title: long read RNA-seq from adrenal gland (ENCLB728YOB)

description:
https://www.encodeproject.org/experiments/ENCSR309XOR/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_240 - B6Cast F1 PND 18-20 months_Female 03 _Adrenals
experiment encode accession: ENCSR309XOR
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB728YOB
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

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

value: adrenal gland

value: tissue

value: adrenal gland_B6Cast F1 PND 18-20 months_Female 03 _ENC4_cDNA463

value: 18-20 month

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


title: long read RNA-seq from adrenal gland (ENCLB483YFT)

description:
https://www.encodeproject.org/experiments/ENCSR309XOR/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_240 - B6Cast F1 PND 18-20 months_Female 03 _Adrenals
experiment encode accession: ENCSR309XOR
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB483YFT
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

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

value: The Jackson Laboratory

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

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


title: long read RNA-seq from gastrocnemius (ENCLB689RIL)

description:
https://www.encodeproject.org/experiments/ENCSR223AZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_407, ENC4_408 B6Cast F1 PND 18-20 months_Female Gastrocnemius
experiment encode accession: ENCSR223AZQ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB689RIL
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: gastrocnemius

value: B6Cast F1 DPN18-20months

value: female

value: adult

value: Barbara Wold, Caltech

value: ENCBS619XVK at ENCODE; https://www.encodeproject.org/ENCBS619XVK/


title: HUVEC, VEGF, Control  siRNA, rep1

value: Human umbilical vein endothelial cells (HUVECs)

value: 25 ng/mL VEGF for 24h

value: Control siRNA


title: long read RNA-seq from gastrocnemius (ENCLB605NIU)

description:
https://www.encodeproject.org/experiments/ENCSR223AZQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_407, ENC4_408 B6Cast F1 PND 18-20 months_Female Gastrocnemius
experiment encode accession: ENCSR223AZQ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB605NIU
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

value: ENCBS138KFH at ENCODE; https://www.encodeproject.org/ENCBS138KFH/


title: long read RNA-seq from adrenal gland (ENCLB024YEP)

description:
https://www.encodeproject.org/experiments/ENCSR649MEZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_235 B6Cast F1 PND 2 months_Male 03_Adrenals
experiment encode accession: ENCSR649MEZ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB024YEP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: adrenal gland

value: B6Cast F1 PND 2 months Male 04 adrenal gland for Wold core

value: male

value: unknown

value: 2 month

value: ENCBS886TIW at ENCODE; https://www.encodeproject.org/ENCBS886TIW/


title: long read RNA-seq from adrenal gland (ENCLB029CAG)

description:
https://www.encodeproject.org/experiments/ENCSR649MEZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_235 B6Cast F1 PND 2 months_Male 03_Adrenals
experiment encode accession: ENCSR649MEZ
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB029CAG
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: B6Cast F1 PND 2 months Male 03 adrenal gland for Wold core

value: The Jackson Laboratory

value: ENCBS110BLI at ENCODE; https://www.encodeproject.org/ENCBS110BLI/

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


title: PAS-seq from GM12878 (ENCLB901ALQ)

description:
https://www.encodeproject.org/experiments/ENCSR275KDL/
***************
biological replicate number: 1
technical replicate number: 2
description: GM12878 QuantSeq
experiment encode accession: ENCSR275KDL
assay title: PAS-seq
assembly: GRCh38
encode release date: 2021-12-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB901ALQ
nucleic acid starting quantity: 36
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 cell line

tag: line

value: cell line

tag: organism

value: Homo sapiens

value: female

tag: health state

value: adult

value: Ali Mortazavi, UCI

value: Coriell

value: ENCBS016YPR at ENCODE; https://www.encodeproject.org/ENCBS016YPR/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: long read RNA-seq from heart (ENCLB284UCQ)

description:
https://www.encodeproject.org/experiments/ENCSR187TGD/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_483, ENC4_484 heart_B6Cast F1 PND14 3x Females 03 heart_ENC4_cDNA595, cDNA_596
experiment encode accession: ENCSR187TGD
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB284UCQ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: heart

value: tissue

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

value: 14 day

value: Barbara Wold, Caltech

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


title: long read RNA-seq from heart (ENCLB815IHK)

description:
https://www.encodeproject.org/experiments/ENCSR187TGD/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_483, ENC4_484 heart_B6Cast F1 PND14 3x Females 03 heart_ENC4_cDNA595, cDNA_596
experiment encode accession: ENCSR187TGD
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB815IHK
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: B6Cast F1 PND14 Female 04 heart for Wold biobank

value: unknown

value: The Jackson Laboratory

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


title: long read RNA-seq from F121-9 (ENCLB398QBT)

description:
https://www.encodeproject.org/experiments/ENCSR172GXL/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP Mouse ES
experiment encode accession: ENCSR172GXL
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB398QBT
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).

source_name: Mus musculus F121-9 cell line

value: cell line

value: Cast X 129 F121-9 hybrid mouse ES cells R2 p14

value: not collected

value: David Gilbert

value: ENCBS951CRC at ENCODE; https://www.encodeproject.org/ENCBS951CRC/

value: Derived from ENCODE donor ENCDO817NHY; https://www.encodeproject.org/ENCDO817NHY/


title: long read RNA-seq from left cerebral cortex (ENCLB359UEW)

description:
https://www.encodeproject.org/experiments/ENCSR631KNS/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_455, ENC4_456 B6Cast F1 PND14 3x Females 03 L. cortex
experiment encode accession: ENCSR631KNS
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB359UEW
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: left cerebral cortex

value: B6Cast F1 PND14 Female 04 left cerebral cortex for Wold biobank

value: female

value: ENCBS120AVS at ENCODE; https://www.encodeproject.org/ENCBS120AVS/

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


title: long read RNA-seq from left cerebral cortex (ENCLB139KRK)

description:
https://www.encodeproject.org/experiments/ENCSR631KNS/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_455, ENC4_456 B6Cast F1 PND14 3x Females 03 L. cortex
experiment encode accession: ENCSR631KNS
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB139KRK
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

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

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS374ENP at ENCODE; https://www.encodeproject.org/ENCBS374ENP/


title: long read RNA-seq from F121-9 (ENCLB552HPG)

description:
https://www.encodeproject.org/experiments/ENCSR172GXL/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP Mouse ES
experiment encode accession: ENCSR172GXL
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB552HPG
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).

value: Cast X 129 F121-9 hybrid mouse ES cells R1 p14

value: unknown

value: ENCBS648HXY at ENCODE; https://www.encodeproject.org/ENCBS648HXY/


title: long read RNA-seq from adrenal gland (ENCLB905VPT)

description:
https://www.encodeproject.org/experiments/ENCSR665XLM/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_221 - B6Cast F1 PND10_Female 03_Adrenals
experiment encode accession: ENCSR665XLM
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB905VPT
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: adrenal gland

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

value: 10 day

value: The Jackson Laboratory

value: ENCBS622FYD at ENCODE; https://www.encodeproject.org/ENCBS622FYD/


title: long read RNA-seq from left cerebral cortex (ENCLB712BTA)

description:
https://www.encodeproject.org/experiments/ENCSR628IMW/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_469, ENC4_470 B6Cast F1 PND 18-20 months Female 03 L. cortex
experiment encode accession: ENCSR628IMW
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB712BTA
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: left cerebral cortex

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: ENCBS321KXV at ENCODE; https://www.encodeproject.org/ENCBS321KXV/


title: PAS-seq from H1 (ENCLB399ELO)

description:
https://www.encodeproject.org/experiments/ENCSR813AOB/
***************
biological replicate number: 1
technical replicate number: 1
description: H1 QuantSeq
experiment encode accession: ENCSR813AOB
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB399ELO
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

source_name: Homo sapiens H1 cell line

value: cell line

value: embryonic

value: not collected

value: René Maehr

value: healthy

value: ENCBS664DSZ at ENCODE; https://www.encodeproject.org/ENCBS664DSZ/

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


title: PAS-seq from H1 (ENCLB589YRA)

description:
https://www.encodeproject.org/experiments/ENCSR813AOB/
***************
biological replicate number: 3
technical replicate number: 1
description: H1 QuantSeq
experiment encode accession: ENCSR813AOB
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB589YRA
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: Barbara Wold, Caltech

value: ENCBS667PZC at ENCODE; https://www.encodeproject.org/ENCBS667PZC/


title: long read RNA-seq from layer of hippocampus (ENCLB185DCT)

description:
https://www.encodeproject.org/experiments/ENCSR152PAT/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_443, ENC4_444 hippocampus_B6Cast F1_18 - 20 months_male_6_ENC4_cDNA515
experiment encode accession: ENCSR152PAT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB185DCT
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: layer of hippocampus

value: tissue

value: unknown

value: The Jackson Laboratory

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

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


title: PAS-seq from H1 (ENCLB804LPD)

description:
https://www.encodeproject.org/experiments/ENCSR813AOB/
***************
biological replicate number: 2
technical replicate number: 1
description: H1 QuantSeq
experiment encode accession: ENCSR813AOB
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB804LPD
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: male

value: ENCBS872CFG at ENCODE; https://www.encodeproject.org/ENCBS872CFG/


title: long read RNA-seq from left cerebral cortex (ENCLB728AIA)

description:
https://www.encodeproject.org/experiments/ENCSR131CES/
***************
biological replicate number: 1
technical replicate number: 1
description: Control cortex Female
experiment encode accession: ENCSR131CES
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB728AIA
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Mus musculus strain B6NCrl cerebral cortex tissue

value: left cerebral cortex

value: Control cortex Female

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS093QAO at ENCODE; https://www.encodeproject.org/ENCBS093QAO/

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


title: long read RNA-seq from layer of hippocampus (ENCLB770HGD)

description:
https://www.encodeproject.org/experiments/ENCSR146ZFC/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_413, ENC4_414 hippocampus_B6CastF1_PND14_3x female_4,5,6_ENC4_cDNA497
experiment encode accession: ENCSR146ZFC
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB770HGD
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: female

value: 14 day

value: ENCBS229LCL at ENCODE; https://www.encodeproject.org/ENCBS229LCL/


title: long read RNA-seq from left cerebral cortex (ENCLB629QSH)

description:
https://www.encodeproject.org/experiments/ENCSR131CES/
***************
biological replicate number: 2
technical replicate number: 1
description: Control cortex Female
experiment encode accession: ENCSR131CES
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB629QSH
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

value: not collected

value: ENCBS417IYY at ENCODE; https://www.encodeproject.org/ENCBS417IYY/


title: long read RNA-seq from left cerebral cortex (ENCLB135JON)

description:
https://www.encodeproject.org/experiments/ENCSR628IMW/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_469, ENC4_470 B6Cast F1 PND 18-20 months Female 03 L. cortex
experiment encode accession: ENCSR628IMW
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB135JON
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: Barbara Wold, Caltech

value: ENCBS972OCB at ENCODE; https://www.encodeproject.org/ENCBS972OCB/


title: long read RNA-seq from gastrocnemius (ENCLB169UGQ)

description:
https://www.encodeproject.org/experiments/ENCSR116DUT/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_405, ENC4_406 B6Cast F1 PND 18-20 months_Male Gastrocnemius
experiment encode accession: ENCSR116DUT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB169UGQ
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: gastrocnemius

value: male

value: The Jackson Laboratory

value: ENCBS983BLX at ENCODE; https://www.encodeproject.org/ENCBS983BLX/

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


title: long read RNA-seq from gastrocnemius (ENCLB987ZEY)

description:
https://www.encodeproject.org/experiments/ENCSR588IRT/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_399a, ENC4_400a B6Cast F1 PND36_Female Gastrocnemius
experiment encode accession: ENCSR588IRT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB987ZEY
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: B6Cast F1 PND36 Female 04 gastrocnemius for Wold core

value: unknown

value: 36 day

value: ENCBS062SUO at ENCODE; https://www.encodeproject.org/ENCBS062SUO/


title: PAS-seq from GM12878 (ENCLB055RET)

description:
https://www.encodeproject.org/experiments/ENCSR275KDL/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 QuantSeq
experiment encode accession: ENCSR275KDL
assay title: PAS-seq
assembly: GRCh38
encode release date: 2021-12-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB055RET
nucleic acid starting quantity: 36
nucleic acid starting quantity units: ng

value: cell line

value: Homo sapiens

value: female

value: Ali Mortazavi, UCI

value: Coriell

value: ENCBS016YPR at ENCODE; https://www.encodeproject.org/ENCBS016YPR/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: long read RNA-seq from gastrocnemius (ENCLB498ZID)

description:
https://www.encodeproject.org/experiments/ENCSR588IRT/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_399a, ENC4_400a B6Cast F1 PND36_Female Gastrocnemius
experiment encode accession: ENCSR588IRT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-12-09
lab: Ali Mortazavi, UCI
library encode accession: ENCLB498ZID
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: tissue

value: B6Cast F1 PND36 Female 03 gastrocnemius for Wold core

value: Barbara Wold, Caltech

value: ENCBS342UJO at ENCODE; https://www.encodeproject.org/ENCBS342UJO/


title: long read RNA-seq from gastrocnemius (ENCLB770ZZH)

description:
https://www.encodeproject.org/experiments/ENCSR116DUT/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_405, ENC4_406 B6Cast F1 PND 18-20 months_Male Gastrocnemius
experiment encode accession: ENCSR116DUT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB770ZZH
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: gastrocnemius

value: B6Cast F1 DPN18-20months

value: male

value: adult

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS074HMM at ENCODE; https://www.encodeproject.org/ENCBS074HMM/


title: long read RNA-seq from adrenal gland (ENCLB378LQA)

description:
https://www.encodeproject.org/experiments/ENCSR084MKR/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_233 - B6Cast F1 PND36_Female 03_Adrenals
experiment encode accession: ENCSR084MKR
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB378LQA
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: adrenal gland

value: B6Cast F1 PND36 Female 04 adrenal gland for Wold core

value: unknown

value: 36 day

value: ENCBS668OIM at ENCODE; https://www.encodeproject.org/ENCBS668OIM/

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


title: long read RNA-seq from adrenal gland (ENCLB732JJI)

description:
https://www.encodeproject.org/experiments/ENCSR084MKR/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_233 - B6Cast F1 PND36_Female 03_Adrenals
experiment encode accession: ENCSR084MKR
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB732JJI
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

value: tissue

value: B6Cast F1 PND36 Female 03 adrenal gland for Wold core

value: female

value: ENCBS681BGW at ENCODE; https://www.encodeproject.org/ENCBS681BGW/


title: PAS-seq from WTC11 (ENCLB224PGI)

description:
https://www.encodeproject.org/experiments/ENCSR322MWL/
***************
biological replicate number: 3
technical replicate number: 1
description: WTC11 QuantSeq
experiment encode accession: ENCSR322MWL
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB224PGI
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

source_name: Homo sapiens WTC11 cell line

value: cell line

value: Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal

value: 30 year

value: Barbara Wold, Caltech

value: Yiing Lin, MD, PhD

tag: passage number

value: ENCBS474NOC at ENCODE; https://www.encodeproject.org/ENCBS474NOC/

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


title: PAS-seq from WTC11 (ENCLB460DHC)

description:
https://www.encodeproject.org/experiments/ENCSR322MWL/
***************
biological replicate number: 2
technical replicate number: 1
description: WTC11 QuantSeq
experiment encode accession: ENCSR322MWL
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB460DHC
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: male

value: adult

value: ENCBS593PKA at ENCODE; https://www.encodeproject.org/ENCBS593PKA/


title: long read RNA-seq from adrenal gland (ENCLB250WTF)

description:
https://www.encodeproject.org/experiments/ENCSR530ZLE/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_225 - B6Cast F1 PND14_3x Females 03_Adrenals
experiment encode accession: ENCSR530ZLE
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB250WTF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: adrenal gland

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

value: unknown

value: 14 day

value: The Jackson Laboratory

value: ENCBS403EIL at ENCODE; https://www.encodeproject.org/ENCBS403EIL/


title: long read RNA-seq from layer of hippocampus (ENCLB531ESP)

description:
https://www.encodeproject.org/experiments/ENCSR152PAT/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_443, ENC4_444 hippocampus_B6Cast F1_18 - 20 months_male_6_ENC4_cDNA515
experiment encode accession: ENCSR152PAT
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB531ESP
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: layer of hippocampus

value: tissue

value: hippocampus_B6Cast F1_18 - 20 months_male_7_ENC4_cDNA516

value: 18-20 month

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

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


title: long read RNA-seq from F121-9 (ENCLB379AJL)

description:
https://www.encodeproject.org/experiments/ENCSR172GXL/
***************
biological replicate number: 3
technical replicate number: 1
description: LRGASP Mouse ES
experiment encode accession: ENCSR172GXL
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB379AJL
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).

value: cell line

value: Cast X 129 F121-9 hybrid mouse ES cells R3 p14

value: not collected

value: Barbara Wold, Caltech

value: David Gilbert

value: ENCBS418RDP at ENCODE; https://www.encodeproject.org/ENCBS418RDP/

value: Derived from ENCODE donor ENCDO817NHY; https://www.encodeproject.org/ENCDO817NHY/


title: long read RNA-seq from layer of hippocampus (ENCLB528IFE)

description:
https://www.encodeproject.org/experiments/ENCSR060OTU/
***************
biological replicate number: 1
technical replicate number: 1
description: 5xFAD hippo het Female
experiment encode accession: ENCSR060OTU
assay title: long read RNA-seq
assembly: mm10
encode release date: 2020-07-30
lab: Ali Mortazavi, UCI
library encode accession: ENCLB528IFE
spikeins used: SIRV reference spike-ins used for ENCODE long read RNA-seq pipeline, Ambion mix 1 spike-ins

source_name: Mus musculus strain B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax layer of hippocampus tissue

value: 5xFAD hippo het Female

value: unknown

value: Ali Mortazavi, UCI

value: MODEL-AD

value: ENCBS418KFY at ENCODE; https://www.encodeproject.org/ENCBS418KFY/

value: Derived from ENCODE donor ENCDO835CXP; https://www.encodeproject.org/ENCDO835CXP/


title: long read RNA-seq from left cerebral cortex (ENCLB193VLN)

description:
https://www.encodeproject.org/experiments/ENCSR550KPM/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_471, ENC4_472 B6Cast F1 PND 18-20 months Male 03 L. cortex
experiment encode accession: ENCSR550KPM
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB193VLN
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: left cerebral cortex

value: tissue

value: B6Cast F1 DPN18-20months

value: female

value: adult

value: The Jackson Laboratory

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


title: long read RNA-seq from adrenal gland (ENCLB060NMM)

description:
https://www.encodeproject.org/experiments/ENCSR530ZLE/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_225 - B6Cast F1 PND14_3x Females 03_Adrenals
experiment encode accession: ENCSR530ZLE
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB060NMM
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

value: adrenal gland

value: B6Cast F1 PND14 Female 04 adrenal gland for Wold core

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS232UIC at ENCODE; https://www.encodeproject.org/ENCBS232UIC/

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


title: long read RNA-seq from adrenal gland (ENCLB272EYF)

description:
https://www.encodeproject.org/experiments/ENCSR512EWP/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_215 B6Cast F1 PND4_Male 03_Adrenals
experiment encode accession: ENCSR512EWP
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-08-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB272EYF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins

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

value: adrenal gland_B6Cast F1 PND4_Male 03_ENC4_cDNA438

value: male

value: unknown

value: 4 day

value: ENCBS886OBH at ENCODE; https://www.encodeproject.org/ENCBS886OBH/


title: long read RNA-seq from layer of hippocampus (ENCLB072FPC)

description:
https://www.encodeproject.org/experiments/ENCSR026WRM/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_415, ENC4_416 hippocampus_B6CastF1_PND14_3x male_7,8,9_ENC4_cDNA499
experiment encode accession: ENCSR026WRM
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB072FPC
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: layer of hippocampus

value: tissue

value: ENCBS642ONZ at ENCODE; https://www.encodeproject.org/ENCBS642ONZ/


title: long read RNA-seq from layer of hippocampus (ENCLB740GXC)

description:
https://www.encodeproject.org/experiments/ENCSR146ZFC/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_413, ENC4_414 hippocampus_B6CastF1_PND14_3x female_4,5,6_ENC4_cDNA497
experiment encode accession: ENCSR146ZFC
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB740GXC
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: female

value: ENCBS708FHL at ENCODE; https://www.encodeproject.org/ENCBS708FHL/


title: long read RNA-seq from gastrocnemius (ENCLB560WSN)

description:
https://www.encodeproject.org/experiments/ENCSR524XLA/
***************
biological replicate number: 1
technical replicate number: 1
description: ENC4_383a, ENC4_384a B6Cast F1 PND4_Female Gastrocnemius
experiment encode accession: ENCSR524XLA
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB560WSN
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: gastrocnemius

value: B6Cast F1 PND4 Female 03 gastrocnemius for Wold core

value: The Jackson Laboratory

value: ENCBS559PTX at ENCODE; https://www.encodeproject.org/ENCBS559PTX/


title: PAS-seq from WTC11 (ENCLB597PEY)

description:
https://www.encodeproject.org/experiments/ENCSR322MWL/
***************
biological replicate number: 1
technical replicate number: 1
description: WTC11 QuantSeq
experiment encode accession: ENCSR322MWL
assay title: PAS-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB597PEY
nucleic acid starting quantity: 500
nucleic acid starting quantity units: ng

value: cell line

value: Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal

value: adult

value: 30 year

value: Barbara Wold, Caltech

value: Yiing Lin, MD, PhD

value: ENCBS944CBA at ENCODE; https://www.encodeproject.org/ENCBS944CBA/

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


title: long read RNA-seq from layer of hippocampus (ENCLB372NUT)

description:
https://www.encodeproject.org/experiments/ENCSR472CHU/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_441, ENC4_442 hippocampus_B6Cast F1_18 - 20 months_female_6_ENC4_cDNA513
experiment encode accession: ENCSR472CHU
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-09-01
lab: Ali Mortazavi, UCI
library encode accession: ENCLB372NUT
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

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

value: layer of hippocampus

value: hippocampus_B6Cast F1_18 - 20 months_female_7_ENC4_cDNA514

value: unknown

value: 18-20 month

value: ENCBS953PDK at ENCODE; https://www.encodeproject.org/ENCBS953PDK/

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


title: long read RNA-seq from gastrocnemius (ENCLB260MVR)

description:
https://www.encodeproject.org/experiments/ENCSR524XLA/
***************
biological replicate number: 2
technical replicate number: 1
description: ENC4_383a, ENC4_384a B6Cast F1 PND4_Female Gastrocnemius
experiment encode accession: ENCSR524XLA
assay title: long read RNA-seq
assembly: mm10
encode release date: 2021-11-10
lab: Ali Mortazavi, UCI
library encode accession: ENCLB260MVR
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., Ambion mix 1 spike-ins
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

value: gastrocnemius

value: tissue

value: B6Cast F1 PND4 Female 04 gastrocnemius for Wold core

value: female

value: 4 day

value: ENCBS519KGT at ENCODE; https://www.encodeproject.org/ENCBS519KGT/