title: total RNA-seq from heart (ENCLB835IBO)

description:
https://www.encodeproject.org/experiments/ENCSR597UZW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse heart
experiment encode accession: ENCSR597UZW
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB835IBO
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (15.5 days)

value: heart

value: Heart from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS909LOF at ENCODE; https://www.encodeproject.org/ENCBS909LOF/


title: total RNA-seq from hindbrain (ENCLB989QNS)

status: Public on Mar 18 2016

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/ENCSR559TRB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse hindbrain
experiment encode accession: ENCSR559TRB
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB989QNS
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (14.5 days)

extract_protocol:
extraction method: Ambion mirVana
extraction protocol: https://www.encodeproject.org/documents/428a184d-7fa1-4599-9d8d-749c2eba7edd/@@download/attachment/cms_055740.pdf, extraction protocol: https://www.encodeproject.org/documents/f0cc5a7f-96a5-4970-9f46-317cc8e2d6a4/@@download/attachment/cms_055423.pdf, general protocol: https://www.encodeproject.org/documents/5f5193b0-0c61-40c6-a286-b1f6d6f0c0da/@@download/attachment/SmartSeqProtocol.pdf

value: hindbrain

value: tissue

tag: description

value: single hindbrain from pup 1 pregnant 2 collected 7/24/2014

tag: biosample encode accession

tag: age

tag: dev stage

tag: Sex

tag: lab

value: Barbara Wold, Caltech

tag: link

value: ENCBS909QXI at ENCODE; https://www.encodeproject.org/ENCBS909QXI/

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


title: total RNA-seq from liver (ENCLB215FCS)

description:
https://www.encodeproject.org/experiments/ENCSR611PTP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse liver
experiment encode accession: ENCSR611PTP
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB215FCS
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (15.5 days)

value: liver

value: Liver from 78 embryonic 15.5 day mice

tag: health state

value: ENCBS734ENZ at ENCODE; https://www.encodeproject.org/ENCBS734ENZ/


title: total RNA-seq from hindbrain (ENCLB567WFL)

description:
https://www.encodeproject.org/experiments/ENCSR559TRB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse hindbrain
experiment encode accession: ENCSR559TRB
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB567WFL
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: single hindbrain from pup 1 pregnant 2 collected 7/30/2014

value: ENCBS233QWW at ENCODE; https://www.encodeproject.org/ENCBS233QWW/


title: single cell RNA-seq from Purkinje cell (ENCLB708TZF)

description:
https://www.encodeproject.org/experiments/ENCSR559QTE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR559QTE
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB708TZF
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl Purkinje primary cell male adult (8 months)

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: ENCBS295ZNO at ENCODE; https://www.encodeproject.org/ENCBS295ZNO/


title: total RNA-seq from midbrain (ENCLB073YDX)

description:
https://www.encodeproject.org/experiments/ENCSR557RMA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR557RMA
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB073YDX
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (15.5 days)

value: midbrain

value: Midbrain from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS190ETJ at ENCODE; https://www.encodeproject.org/ENCBS190ETJ/


title: total RNA-seq from limb (ENCLB495FUZ)

description:
https://www.encodeproject.org/experiments/ENCSR541XZK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse limb
experiment encode accession: ENCSR541XZK
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB495FUZ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (11.5 days)

value: limb

value: tissue

value: Limb from 109 embyronic 11.5 day mice

value: ENCBS066IEL at ENCODE; https://www.encodeproject.org/ENCBS066IEL/

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


title: total RNA-seq from midbrain (ENCLB028XWK)

description:
https://www.encodeproject.org/experiments/ENCSR557RMA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR557RMA
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB028XWK
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: Midbrain from 62 embryonic 15.5 day mice

value: ENCBS381PEJ at ENCODE; https://www.encodeproject.org/ENCBS381PEJ/


title: total RNA-seq from limb (ENCLB979DZW)

description:
https://www.encodeproject.org/experiments/ENCSR541XZK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse limb
experiment encode accession: ENCSR541XZK
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB979DZW
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: Limb from 88 embyronic 11.5 day mice

value: ENCBS681XPR at ENCODE; https://www.encodeproject.org/ENCBS681XPR/


title: total RNA-seq from kidney (ENCLB540BPI)

description:
https://www.encodeproject.org/experiments/ENCSR537GNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse kidney
experiment encode accession: ENCSR537GNQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB540BPI
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (16.5 days)

value: kidney

value: Kidney from 41 embyonic 16.5 day mice

value: ENCBS529OHA at ENCODE; https://www.encodeproject.org/ENCBS529OHA/


title: total RNA-seq from heart (ENCLB526KEI)

description:
https://www.encodeproject.org/experiments/ENCSR597UZW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse heart
experiment encode accession: ENCSR597UZW
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB526KEI
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: heart

value: Heart from 78 embryonic 15.5 day mice

value: embryonic

value: ENCBS595EMK at ENCODE; https://www.encodeproject.org/ENCBS595EMK/


title: total RNA-seq from kidney (ENCLB496KJW)

description:
https://www.encodeproject.org/experiments/ENCSR537GNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse kidney
experiment encode accession: ENCSR537GNQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB496KJW
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: Kidney pooled from embyonic 16.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS519MUD at ENCODE; https://www.encodeproject.org/ENCBS519MUD/


title: single cell RNA-seq from Purkinje cell (ENCLB640QPM)

description:
https://www.encodeproject.org/experiments/ENCSR527DQV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR527DQV
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB640QPM
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: Barbara Wold, Caltech

value: ENCBS585NUK at ENCODE; https://www.encodeproject.org/ENCBS585NUK/

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


title: single cell RNA-seq from forebrain (ENCLB181TCJ)

description:
https://www.encodeproject.org/experiments/ENCSR527RFK/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse forebrain (13pgs)
experiment encode accession: ENCSR527RFK
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB181TCJ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

source_name: Mus musculus strain B6NCrl forebrain tissue postnatal (0 days)

tag: antibody

value: Control

value: forebrain

value: tissue

value: single forebrain from pup 3

value: 0 day

value: postnatal

value: not collected

value: ENCBS804WMS at ENCODE; https://www.encodeproject.org/ENCBS804WMS/


title: total RNA-seq from embryonic facial prominence (ENCLB304NDN)

description:
https://www.encodeproject.org/experiments/ENCSR538WYL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse cranio-facial prominence
experiment encode accession: ENCSR538WYL
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB304NDN
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (13.5 days)

value: embryonic facial prominence

value: Embryonic facial prominence from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS847MIW at ENCODE; https://www.encodeproject.org/ENCBS847MIW/


title: total RNA-seq from embryonic facial prominence (ENCLB032PUJ)

description:
https://www.encodeproject.org/experiments/ENCSR538WYL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse cranio-facial prominence
experiment encode accession: ENCSR538WYL
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB032PUJ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: ENCBS764ZZN at ENCODE; https://www.encodeproject.org/ENCBS764ZZN/


title: single cell RNA-seq from heart (ENCLB348BMH)

description:
https://www.encodeproject.org/experiments/ENCSR510ADJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse heart (13pg)
experiment encode accession: ENCSR510ADJ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB348BMH
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

source_name: Mus musculus strain B6NCrl heart tissue postnatal (0 days)

value: heart

value: single heart from pup 3

value: Barbara Wold, Caltech

value: ENCBS569APS at ENCODE; https://www.encodeproject.org/ENCBS569APS/

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


title: total RNA-seq from heart (ENCLB658ICO)

description:
https://www.encodeproject.org/experiments/ENCSR526SEX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on postnatal 0 day mouse heart
experiment encode accession: ENCSR526SEX
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB658ICO
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: tissue

value: single heart from pup2 pregnant 1

value: 0 day

value: ENCBS337KCK at ENCODE; https://www.encodeproject.org/ENCBS337KCK/


title: single cell RNA-seq from Purkinje cell (ENCLB678FAD)

description:
https://www.encodeproject.org/experiments/ENCSR521YLY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR521YLY
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB678FAD
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: ENCBS283ZOF at ENCODE; https://www.encodeproject.org/ENCBS283ZOF/


title: total RNA-seq from heart (ENCLB741KQB)

description:
https://www.encodeproject.org/experiments/ENCSR526SEX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on postnatal 0 day mouse heart
experiment encode accession: ENCSR526SEX
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB741KQB
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: single heart from pup3 pregnant 1

value: postnatal

value: not collected

value: ENCBS694SYF at ENCODE; https://www.encodeproject.org/ENCBS694SYF/


title: single cell RNA-seq from forebrain (ENCLB766UOB)

description:
https://www.encodeproject.org/experiments/ENCSR527RFK/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse forebrain (13pgs)
experiment encode accession: ENCSR527RFK
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB766UOB
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: forebrain

value: single forebrain from pup 1

value: Barbara Wold, Caltech

value: ENCBS033OJJ at ENCODE; https://www.encodeproject.org/ENCBS033OJJ/


title: total RNA-seq from kidney (ENCLB949WIO)

description:
https://www.encodeproject.org/experiments/ENCSR504GEG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse kidney
experiment encode accession: ENCSR504GEG
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB949WIO
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (14.5 days)

value: kidney

value: tissue

value: 2 kidneys from pup 1 pregnant 2 collected 7/17/2014

value: embryonic

value: pooled male and female

value: ENCBS454WSU at ENCODE; https://www.encodeproject.org/ENCBS454WSU/

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


title: single cell RNA-seq from heart (ENCLB652HKH)

description:
https://www.encodeproject.org/experiments/ENCSR510ADJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse heart (13pg)
experiment encode accession: ENCSR510ADJ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB652HKH
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: heart

value: single heart from pup 1

value: 0 day

value: ENCBS066TRB at ENCODE; https://www.encodeproject.org/ENCBS066TRB/


title: total RNA-seq from kidney (ENCLB813BQB)

description:
https://www.encodeproject.org/experiments/ENCSR504GEG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse kidney
experiment encode accession: ENCSR504GEG
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB813BQB
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: 2 kidneys from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS731ALA at ENCODE; https://www.encodeproject.org/ENCBS731ALA/


title: single cell RNA-seq from Purkinje cell (ENCLB417MEI)

description:
https://www.encodeproject.org/experiments/ENCSR474NEW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR474NEW
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB417MEI
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: ENCBS284SWA at ENCODE; https://www.encodeproject.org/ENCBS284SWA/


title: total RNA-seq from stomach (ENCLB852NKM)

description:
https://www.encodeproject.org/experiments/ENCSR466KZY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR466KZY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB852NKM
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (16.5 days)

value: stomach

value: tissue

value: Stomach pooled from embyonic 16.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS243DCE at ENCODE; https://www.encodeproject.org/ENCBS243DCE/


title: total RNA-seq from lung (ENCLB873UUE)

description:
https://www.encodeproject.org/experiments/ENCSR457RRW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR457RRW
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB873UUE
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (15.5 days)

value: lung

value: Lung from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS467HSM at ENCODE; https://www.encodeproject.org/ENCBS467HSM/

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


title: single cell RNA-seq from pyramidal neuron (ENCLB481FJQ)

description:
https://www.encodeproject.org/experiments/ENCSR427FOY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC768)
experiment encode accession: ENCSR427FOY
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB481FJQ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl pyramidal neuron primary cell adult (8 months)

value: pyramidal neuron

value: primary cell

value: not collected

value: Barbara Wold, Caltech

value: ENCBS071RLE at ENCODE; https://www.encodeproject.org/ENCBS071RLE/


title: total RNA-seq from intestine (ENCLB079XWZ)

description:
https://www.encodeproject.org/experiments/ENCSR370SFB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse intestine
experiment encode accession: ENCSR370SFB
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB079XWZ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl intestine tissue mixed sex embryo (15.5 days)

value: intestine

value: Intestine from 78 embryonic 15.5 day mice

value: ENCBS401LLS at ENCODE; https://www.encodeproject.org/ENCBS401LLS/


title: total RNA-seq from intestine (ENCLB042OTC)

description:
https://www.encodeproject.org/experiments/ENCSR370SFB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse intestine
experiment encode accession: ENCSR370SFB
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB042OTC
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: tissue

value: Intestine from 62 embryonic 15.5 day mice

value: healthy

value: ENCBS836WEU at ENCODE; https://www.encodeproject.org/ENCBS836WEU/


title: total RNA-seq from liver (ENCLB863LLT)

description:
https://www.encodeproject.org/experiments/ENCSR448MXQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR448MXQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB863LLT
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (13.5 days)

value: liver

value: Liver from embryonic 13.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS373XWZ at ENCODE; https://www.encodeproject.org/ENCBS373XWZ/


title: total RNA-seq from hindbrain (ENCLB614EHD)

description:
https://www.encodeproject.org/experiments/ENCSR401BSG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse hindbrain
experiment encode accession: ENCSR401BSG
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB614EHD
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (15.5 days)

value: hindbrain

value: Hindbrain from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS948UKU at ENCODE; https://www.encodeproject.org/ENCBS948UKU/

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


title: single cell RNA-seq from pyramidal neuron (ENCLB071PKW)

description:
https://www.encodeproject.org/experiments/ENCSR390KQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC769)
experiment encode accession: ENCSR390KQJ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB071PKW
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: not collected

value: Barbara Wold, Caltech

value: ENCBS032FVQ at ENCODE; https://www.encodeproject.org/ENCBS032FVQ/


title: single cell RNA-seq from Purkinje cell (ENCLB809LQF)

description:
https://www.encodeproject.org/experiments/ENCSR367DUL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR367DUL
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB809LQF
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: male

value: ENCBS114FIK at ENCODE; https://www.encodeproject.org/ENCBS114FIK/


title: total RNA-seq from midbrain (ENCLB733PDT)

description:
https://www.encodeproject.org/experiments/ENCSR367ZPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse midbrain
experiment encode accession: ENCSR367ZPZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB733PDT
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (16.5 days)

value: midbrain

value: tissue

value: Midbrain pooled from embyonic 16.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS684MLE at ENCODE; https://www.encodeproject.org/ENCBS684MLE/


title: total RNA-seq from forebrain (ENCLB055JUC)

description:
https://www.encodeproject.org/experiments/ENCSR362AIZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR362AIZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB055JUC
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: forebrain

value: single forebrain from pup 3

value: 0 day

value: postnatal

value: ENCBS804WMS at ENCODE; https://www.encodeproject.org/ENCBS804WMS/

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


title: total RNA-seq from hindbrain (ENCLB507CWD)

description:
https://www.encodeproject.org/experiments/ENCSR401BSG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse hindbrain
experiment encode accession: ENCSR401BSG
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB507CWD
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: hindbrain

value: Hindbrain from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS958AHU at ENCODE; https://www.encodeproject.org/ENCBS958AHU/


title: total RNA-seq from forebrain (ENCLB266LCY)

description:
https://www.encodeproject.org/experiments/ENCSR362AIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR362AIZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB266LCY
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: single forebrain from pup 1

value: not collected

value: Barbara Wold, Caltech

value: ENCBS033OJJ at ENCODE; https://www.encodeproject.org/ENCBS033OJJ/


title: total RNA-seq from limb (ENCLB238AFW)

description:
https://www.encodeproject.org/experiments/ENCSR347SQR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR347SQR
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB238AFW
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (13.5 days)

value: limb

value: tissue

value: Limb from embryonic 13.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS176PGP at ENCODE; https://www.encodeproject.org/ENCBS176PGP/


title: total RNA-seq from lung (ENCLB975KAO)

description:
https://www.encodeproject.org/experiments/ENCSR457RRW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR457RRW
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB975KAO
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: lung

value: Lung from 62 embryonic 15.5 day mice

value: ENCBS217WPC at ENCODE; https://www.encodeproject.org/ENCBS217WPC/


title: total RNA-seq from stomach (ENCLB732ZDB)

description:
https://www.encodeproject.org/experiments/ENCSR466KZY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR466KZY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB732ZDB
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: stomach

value: Stomach from 41 embyonic 16.5 day mice

value: ENCBS793TEW at ENCODE; https://www.encodeproject.org/ENCBS793TEW/

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


title: total RNA-seq from limb (ENCLB724HXC)

description:
https://www.encodeproject.org/experiments/ENCSR347SQR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR347SQR
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB724HXC
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: embryonic

value: pooled male and female

value: ENCBS896ZED at ENCODE; https://www.encodeproject.org/ENCBS896ZED/


title: total RNA-seq from midbrain (ENCLB841PIC)

description:
https://www.encodeproject.org/experiments/ENCSR367ZPZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse midbrain
experiment encode accession: ENCSR367ZPZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB841PIC
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: midbrain

value: Midbrain from 37 embryonic 16.5 day mice

value: ENCBS463JSE at ENCODE; https://www.encodeproject.org/ENCBS463JSE/


title: total RNA-seq from midbrain (ENCLB597GRF)

description:
https://www.encodeproject.org/experiments/ENCSR343YLB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse midbrain
experiment encode accession: ENCSR343YLB
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB597GRF
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (14.5 days)

value: tissue

value: single midbrain from pup 1 pregnant 2 collected 7/30/2014

value: Barbara Wold, Caltech

value: ENCBS849BXE at ENCODE; https://www.encodeproject.org/ENCBS849BXE/


title: total RNA-seq from neural tube (ENCLB627LDZ)

description:
https://www.encodeproject.org/experiments/ENCSR337FYI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse neural tube
experiment encode accession: ENCSR337FYI
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB627LDZ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (11.5 days)

value: neural tube

value: Neural tube from 88 embyronic 11.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS183YVD at ENCODE; https://www.encodeproject.org/ENCBS183YVD/


title: single cell RNA-seq from Purkinje cell (ENCLB857GUO)

description:
https://www.encodeproject.org/experiments/ENCSR351YGY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR351YGY
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB857GUO
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl Purkinje primary cell male adult (8 months)

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: ENCBS600UKT at ENCODE; https://www.encodeproject.org/ENCBS600UKT/


title: single cell RNA-seq from pyramidal neuron (ENCLB818SQI)

description:
https://www.encodeproject.org/experiments/ENCSR323FHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC773)
experiment encode accession: ENCSR323FHJ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB818SQI
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: not collected

value: ENCBS652SMK at ENCODE; https://www.encodeproject.org/ENCBS652SMK/

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


title: single cell RNA-seq from Purkinje cell (ENCLB518MNF)

description:
https://www.encodeproject.org/experiments/ENCSR320PXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR320PXZ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB518MNF
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Barbara Wold, Caltech

value: ENCBS123MQR at ENCODE; https://www.encodeproject.org/ENCBS123MQR/


title: total RNA-seq from intestine (ENCLB159SLV)

description:
https://www.encodeproject.org/experiments/ENCSR331XCE/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR331XCE
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB159SLV
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl intestine tissue postnatal (0 days)

value: intestine

value: tissue

value: 1 intestine from pup2 pregnant 1

value: 0 day

value: postnatal

value: ENCBS623WQD at ENCODE; https://www.encodeproject.org/ENCBS623WQD/


title: total RNA-seq from midbrain (ENCLB000EUQ)

description:
https://www.encodeproject.org/experiments/ENCSR343YLB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse midbrain
experiment encode accession: ENCSR343YLB
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB000EUQ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: midbrain

value: single midbrain from pup 1 pregnant 2 collected 7/24/2014

value: embryonic

value: pooled male and female

value: ENCBS825LGT at ENCODE; https://www.encodeproject.org/ENCBS825LGT/


title: total RNA-seq from intestine (ENCLB217DSV)

description:
https://www.encodeproject.org/experiments/ENCSR331XCE/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR331XCE
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB217DSV
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: 1 intestine from pup1 pregnant 1

value: ENCBS182YRY at ENCODE; https://www.encodeproject.org/ENCBS182YRY/


title: total RNA-seq from liver (ENCLB504REE)

description:
https://www.encodeproject.org/experiments/ENCSR448MXQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR448MXQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB504REE
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: liver

value: Liver from embryonic 13.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS146FGW at ENCODE; https://www.encodeproject.org/ENCBS146FGW/


title: single cell RNA-seq from Purkinje cell (ENCLB587ZYP)

description:
https://www.encodeproject.org/experiments/ENCSR316RMA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR316RMA
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB587ZYP
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: Barbara Wold, Caltech

value: ENCBS066FBE at ENCODE; https://www.encodeproject.org/ENCBS066FBE/

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


title: total RNA-seq from midbrain (ENCLB659UFY)

description:
https://www.encodeproject.org/experiments/ENCSR307BCA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR307BCA
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB659UFY
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (11.5 days)

value: midbrain

value: tissue

value: Midbrain of 109 embyronic 11.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS228OBS at ENCODE; https://www.encodeproject.org/ENCBS228OBS/


title: total RNA-seq from thymus (ENCLB415KPR)

description:
https://www.encodeproject.org/experiments/ENCSR438XCG/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse thymus
experiment encode accession: ENCSR438XCG
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB415KPR
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl thymus tissue postnatal (0 days)

value: thymus

value: two thymus lobes from pup3 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: ENCBS898VIJ at ENCODE; https://www.encodeproject.org/ENCBS898VIJ/


title: total RNA-seq from thymus (ENCLB074REG)

description:
https://www.encodeproject.org/experiments/ENCSR438XCG/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse thymus
experiment encode accession: ENCSR438XCG
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB074REG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: two thymus lobes from pup2 pregnant 1

value: ENCBS079WTJ at ENCODE; https://www.encodeproject.org/ENCBS079WTJ/


title: single cell RNA-seq from pyramidal neuron (ENCLB411BLU)

description:
https://www.encodeproject.org/experiments/ENCSR298YHA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC777)
experiment encode accession: ENCSR298YHA
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB411BLU
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: Barbara Wold, Caltech

value: ENCBS803TKE at ENCODE; https://www.encodeproject.org/ENCBS803TKE/


title: total RNA-seq from midbrain (ENCLB426JKF)

description:
https://www.encodeproject.org/experiments/ENCSR307BCA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR307BCA
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB426JKF
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: midbrain

value: tissue

value: Midbrain from 88 embyronic 11.5 day mice

value: embryonic

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS802FTI at ENCODE; https://www.encodeproject.org/ENCBS802FTI/

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


title: single cell RNA-seq from pyramidal neuron (ENCLB676ISC)

description:
https://www.encodeproject.org/experiments/ENCSR295UJP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC774)
experiment encode accession: ENCSR295UJP
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB676ISC
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: not collected

value: ENCBS006ZAQ at ENCODE; https://www.encodeproject.org/ENCBS006ZAQ/


title: total RNA-seq from stomach (ENCLB409LKR)

description:
https://www.encodeproject.org/experiments/ENCSR290RRR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR290RRR
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB409LKR
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (14.5 days)

value: stomach

value: single stomach from pup 1 pregnant 2 collected 7/15/2014

value: pooled male and female

value: ENCBS715ONU at ENCODE; https://www.encodeproject.org/ENCBS715ONU/


title: total RNA-seq from neural tube (ENCLB162EJJ)

description:
https://www.encodeproject.org/experiments/ENCSR337FYI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 11.5 day mouse neural tube
experiment encode accession: ENCSR337FYI
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB162EJJ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: neural tube

value: Neural tube from 109 embyronic 11.5 day mice

value: ENCBS402TUS at ENCODE; https://www.encodeproject.org/ENCBS402TUS/


title: total RNA-seq from hindbrain (ENCLB987VRV)

description:
https://www.encodeproject.org/experiments/ENCSR285WZV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR285WZV
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB987VRV
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (16.5 days)

value: hindbrain

value: Hindbrain from 37 embryonic 16.5 day mice

value: ENCBS281ZLI at ENCODE; https://www.encodeproject.org/ENCBS281ZLI/


title: total RNA-seq from heart (ENCLB351WRP)

description:
https://www.encodeproject.org/experiments/ENCSR284YKY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse heart
experiment encode accession: ENCSR284YKY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB351WRP
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (13.5 days)

value: heart

value: tissue

value: Heart from embryonic 13.5 day mice

value: embryonic

value: ENCBS814PLT at ENCODE; https://www.encodeproject.org/ENCBS814PLT/


title: total RNA-seq from heart (ENCLB690TFQ)

description:
https://www.encodeproject.org/experiments/ENCSR284YKY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse heart
experiment encode accession: ENCSR284YKY
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB690TFQ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS490ZWZ at ENCODE; https://www.encodeproject.org/ENCBS490ZWZ/

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


title: single cell RNA-seq from pyramidal neuron (ENCLB893OOW)

description:
https://www.encodeproject.org/experiments/ENCSR268AXN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on a 50 cell pool of layer V pyramidal neurons from an 8 month old male wild type C57Bl5 mouse
experiment encode accession: ENCSR268AXN
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-07-15
lab: Barbara Wold, Caltech
library encode accession: ENCLB893OOW
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 50.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl pyramidal neuron primary cell male adult (8 months)

value: Control

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: male

value: Barbara Wold, Caltech

value: ENCBS599JIO at ENCODE; https://www.encodeproject.org/ENCBS599JIO/


title: single cell RNA-seq from skeletal muscle tissue (ENCLB096HAH)

description:
https://www.encodeproject.org/experiments/ENCSR265YFZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse skeletal muscle (13pgs)
experiment encode accession: ENCSR265YFZ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB096HAH
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

source_name: Mus musculus strain B6NCrl skeletal muscle tissue postnatal (0 days)

value: skeletal muscle tissue

value: single organ portion from 1 pup

value: 0 day

value: postnatal

value: not collected

value: ENCBS482FSQ at ENCODE; https://www.encodeproject.org/ENCBS482FSQ/


title: total RNA-seq from liver (ENCLB055KYV)

description:
https://www.encodeproject.org/experiments/ENCSR284AMY/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 11.5 day mouse liver
experiment encode accession: ENCSR284AMY
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB055KYV
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (11.5 days)

value: liver

value: tissue

value: Liver from 109 embyronic 11.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS746POP at ENCODE; https://www.encodeproject.org/ENCBS746POP/


title: total RNA-seq from liver (ENCLB357KYA)

description:
https://www.encodeproject.org/experiments/ENCSR284AMY/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 11.5 day mouse liver
experiment encode accession: ENCSR284AMY
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB357KYA
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: Liver from pooled embryonic 11.5 day mice

value: ENCBS522YOW at ENCODE; https://www.encodeproject.org/ENCBS522YOW/

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


title: single cell RNA-seq from skeletal muscle tissue (ENCLB304LFK)

description:
https://www.encodeproject.org/experiments/ENCSR265YFZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse skeletal muscle (13pgs)
experiment encode accession: ENCSR265YFZ
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB304LFK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: skeletal muscle tissue

value: Barbara Wold, Caltech

value: ENCBS015TUQ at ENCODE; https://www.encodeproject.org/ENCBS015TUQ/


title: total RNA-seq from hindbrain (ENCLB662TIG)

description:
https://www.encodeproject.org/experiments/ENCSR285WZV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR285WZV
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB662TIG
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: hindbrain

value: Hindbrain pooled from embyonic 16.5 day mice

value: ENCBS436LSH at ENCODE; https://www.encodeproject.org/ENCBS436LSH/


title: single cell RNA-seq from pyramidal neuron (ENCLB074NCD)

description:
https://www.encodeproject.org/experiments/ENCSR220HFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC776)
experiment encode accession: ENCSR220HFQ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB074NCD
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl pyramidal neuron primary cell adult (8 months)

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: not collected

value: ENCBS250TNJ at ENCODE; https://www.encodeproject.org/ENCBS250TNJ/


title: single cell RNA-seq from pyramidal neuron (ENCLB730HDZ)

description:
https://www.encodeproject.org/experiments/ENCSR268AXN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on a 50 cell pool of layer V pyramidal neurons from an 8 month old male wild type C57Bl5 mouse
experiment encode accession: ENCSR268AXN
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2015-07-15
lab: Barbara Wold, Caltech
library encode accession: ENCLB730HDZ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 50.0
nucleic acid starting quantity units: cells

value: male

value: ENCBS880BCZ at ENCODE; https://www.encodeproject.org/ENCBS880BCZ/


title: total RNA-seq from forebrain (ENCLB964APA)

description:
https://www.encodeproject.org/experiments/ENCSR185LWM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse forebrain
experiment encode accession: ENCSR185LWM
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB964APA
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (14.5 days)

value: forebrain

value: tissue

value: single forebrain from pup1 pregnant 2 collected 7/30/2014

value: embryonic

value: pooled male and female

value: ENCBS295MUN at ENCODE; https://www.encodeproject.org/ENCBS295MUN/


title: total RNA-seq from limb (ENCLB949YQN)

description:
https://www.encodeproject.org/experiments/ENCSR216NEG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse limb
experiment encode accession: ENCSR216NEG
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB949YQN
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (14.5 days)

value: limb

value: 4 limbs from pup 1 pregnant 2 collected 7/17/2014

value: Barbara Wold, Caltech

value: ENCBS471PIU at ENCODE; https://www.encodeproject.org/ENCBS471PIU/

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


title: total RNA-seq from limb (ENCLB906TKN)

description:
https://www.encodeproject.org/experiments/ENCSR216NEG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse limb
experiment encode accession: ENCSR216NEG
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB906TKN
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: 4 limbs from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS300NIO at ENCODE; https://www.encodeproject.org/ENCBS300NIO/


title: total RNA-seq from forebrain (ENCLB336GOL)

description:
https://www.encodeproject.org/experiments/ENCSR185LWM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse forebrain
experiment encode accession: ENCSR185LWM
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB336GOL
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: single forebrain from pup1 pregnant 2 collected 7/24/2014

value: ENCBS567ABO at ENCODE; https://www.encodeproject.org/ENCBS567ABO/


title: single cell RNA-seq from pyramidal neuron (ENCLB735YLI)

description:
https://www.encodeproject.org/experiments/ENCSR198EIH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC759)
experiment encode accession: ENCSR198EIH
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB735YLI
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: primary cell

value: 8 month

value: adult

value: not collected

value: ENCBS237ZAG at ENCODE; https://www.encodeproject.org/ENCBS237ZAG/


title: single cell RNA-seq from cerebral cortex, layer 5 (ENCLB700NFV)

description:
https://www.encodeproject.org/experiments/ENCSR236EGS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on a dissected area of layer V from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR236EGS
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB700NFV
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 50.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl cerebral cortex, layer 5 tissue male adult (8 months)

value: Control

value: cerebral cortex, layer 5

value: tissue

value: Mm_C57Bl6_8mo_M_WT_layerV_area 8000 square microns

value: male

value: ENCBS852EUH at ENCODE; https://www.encodeproject.org/ENCBS852EUH/


title: total RNA-seq from kidney (ENCLB416HZP)

description:
https://www.encodeproject.org/experiments/ENCSR173PJN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on postnatal 0 day mouse kidney
experiment encode accession: ENCSR173PJN
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB416HZP
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl kidney tissue postnatal (0 days)

value: kidney

value: 2 kidneys from pup2 pregnant 1

value: 0 day

value: postnatal

value: Barbara Wold, Caltech

value: ENCBS540QNA at ENCODE; https://www.encodeproject.org/ENCBS540QNA/

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


title: total RNA-seq from kidney (ENCLB022VFG)

description:
https://www.encodeproject.org/experiments/ENCSR173PJN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on postnatal 0 day mouse kidney
experiment encode accession: ENCSR173PJN
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB022VFG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: 2 kidneys from pup1 pregnant 1

value: ENCBS103FKB at ENCODE; https://www.encodeproject.org/ENCBS103FKB/


title: total RNA-seq from stomach (ENCLB595PNG)

description:
https://www.encodeproject.org/experiments/ENCSR290RRR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR290RRR
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB595PNG
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: stomach

value: single stomach from pup 1 pregnant 2 collected 7/17/2014

value: embryonic

value: pooled male and female

value: ENCBS987ARB at ENCODE; https://www.encodeproject.org/ENCBS987ARB/


title: total RNA-seq from stomach (ENCLB169SNA)

description:
https://www.encodeproject.org/experiments/ENCSR178GUS/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR178GUS
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB169SNA
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl stomach tissue postnatal (0 days)

value: tissue

value: 1 stomach from pup1 pregnant 1

value: not collected

value: ENCBS762UVC at ENCODE; https://www.encodeproject.org/ENCBS762UVC/


title: single cell RNA-seq from cerebral cortex, layer 5 (ENCLB229LFR)

description:
https://www.encodeproject.org/experiments/ENCSR236EGS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on a dissected area of layer V from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR236EGS
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB229LFR
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 50.0
nucleic acid starting quantity units: cells

value: Control

value: cerebral cortex, layer 5

value: Mm_C57Bl6_8mo_M_WT_layerV_area 8000 square microns

value: 8 month

value: adult

value: male

value: ENCBS891GJO at ENCODE; https://www.encodeproject.org/ENCBS891GJO/


title: single cell RNA-seq from Purkinje cell (ENCLB112DAD)

description:
https://www.encodeproject.org/experiments/ENCSR282DYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR282DYQ
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB112DAD
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: Barbara Wold, Caltech

value: ENCBS815YNS at ENCODE; https://www.encodeproject.org/ENCBS815YNS/

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


title: total RNA-seq from forebrain (ENCLB835LVO)

description:
https://www.encodeproject.org/experiments/ENCSR160IIN/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR160IIN
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB835LVO
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (11.5 days)

value: forebrain

value: Forebrain from 109 embyronic 11.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS745VOM at ENCODE; https://www.encodeproject.org/ENCBS745VOM/


title: single cell RNA-seq from Purkinje cell (ENCLB663WPK)

description:
https://www.encodeproject.org/experiments/ENCSR167AWS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR167AWS
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB663WPK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

source_name: Mus musculus strain B6NCrl Purkinje primary cell male adult (8 months)

value: ENCBS552GIO at ENCODE; https://www.encodeproject.org/ENCBS552GIO/


title: total RNA-seq from forebrain (ENCLB471QMM)

description:
https://www.encodeproject.org/experiments/ENCSR160IIN/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR160IIN
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Barbara Wold, Caltech
library encode accession: ENCLB471QMM
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: tissue

value: Forebrain from 88 embyronic 11.5 day mice

value: ENCBS720JOH at ENCODE; https://www.encodeproject.org/ENCBS720JOH/


title: single cell RNA-seq from pyramidal neuron (ENCLB081GEB)

description:
https://www.encodeproject.org/experiments/ENCSR138VRG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC770)
experiment encode accession: ENCSR138VRG
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB081GEB
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: 8 month

value: adult

value: not collected

value: ENCBS577QIY at ENCODE; https://www.encodeproject.org/ENCBS577QIY/


title: single cell RNA-seq from pyramidal neuron (ENCLB542OIM)

description:
https://www.encodeproject.org/experiments/ENCSR195BCE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC772)
experiment encode accession: ENCSR195BCE
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB542OIM
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: primary cell

value: Barbara Wold, Caltech

value: ENCBS918UDX at ENCODE; https://www.encodeproject.org/ENCBS918UDX/

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


title: total RNA-seq from neural tube (ENCLB327XFF)

description:
https://www.encodeproject.org/experiments/ENCSR115TWD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR115TWD
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB327XFF
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (13.5 days)

value: neural tube

value: Neural tube from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS549OYR at ENCODE; https://www.encodeproject.org/ENCBS549OYR/


title: single cell RNA-seq from Purkinje cell (ENCLB001WPP)

description:
https://www.encodeproject.org/experiments/ENCSR145EKP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR145EKP
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB001WPP
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: male

value: ENCBS941HLR at ENCODE; https://www.encodeproject.org/ENCBS941HLR/


title: single cell RNA-seq from pyramidal neuron (ENCLB133WXD)

description:
https://www.encodeproject.org/experiments/ENCSR100KRK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single pyramidal neuron cell from cerebral cortex layer V in a C57Bl6 mouse (LC761)
experiment encode accession: ENCSR100KRK
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR734SOQ
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB133WXD
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: pyramidal neuron

value: ENCBS078AYN at ENCODE; https://www.encodeproject.org/ENCBS078AYN/


title: total RNA-seq from liver (ENCLB370ZFK)

description:
https://www.encodeproject.org/experiments/ENCSR096STK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse liver
experiment encode accession: ENCSR096STK
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB370ZFK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl liver tissue postnatal (0 days)

value: liver

value: tissue

value: 1 liver from pup1 pregnant 1

value: 0 day

value: postnatal

value: ENCBS196YDO at ENCODE; https://www.encodeproject.org/ENCBS196YDO/


title: total RNA-seq from stomach (ENCLB459OYG)

description:
https://www.encodeproject.org/experiments/ENCSR178GUS/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR178GUS
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB459OYG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: stomach

value: 1 stomach from pup2 pregnant 1

value: not collected

value: Barbara Wold, Caltech

value: ENCBS796AGC at ENCODE; https://www.encodeproject.org/ENCBS796AGC/

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


title: total RNA-seq from liver (ENCLB273BPC)

description:
https://www.encodeproject.org/experiments/ENCSR096STK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse liver
experiment encode accession: ENCSR096STK
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB273BPC
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: 1 liver from pup2 pregnant 1

value: ENCBS270QZU at ENCODE; https://www.encodeproject.org/ENCBS270QZU/


title: total RNA-seq from forebrain (ENCLB430WXG)

description:
https://www.encodeproject.org/experiments/ENCSR080EVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR080EVZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB430WXG
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (16.5 days)

value: forebrain

value: Forebrain pooled from embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS156DHU at ENCODE; https://www.encodeproject.org/ENCBS156DHU/


title: total RNA-seq from kidney (ENCLB783FQC)

description:
https://www.encodeproject.org/experiments/ENCSR062VTB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR062VTB
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB783FQC
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (15.5 days)

value: kidney

value: tissue

value: Kidney from 78 embryonic 15.5 day mice

value: ENCBS899UOK at ENCODE; https://www.encodeproject.org/ENCBS899UOK/


title: single cell RNA-seq from midbrain (ENCLB719BQO)

description:
https://www.encodeproject.org/experiments/ENCSR026ZRP/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse midbrain (13pgs)
experiment encode accession: ENCSR026ZRP
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB719BQO
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

source_name: Mus musculus strain B6NCrl midbrain tissue postnatal (0 days)

value: Control

value: midbrain

value: single midbrain from pup 1

value: 0 day

value: postnatal

value: not collected

value: ENCBS169PZD at ENCODE; https://www.encodeproject.org/ENCBS169PZD/


title: single cell RNA-seq from midbrain (ENCLB669AEL)

description:
https://www.encodeproject.org/experiments/ENCSR026ZRP/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on postnatal 0 day mouse midbrain (13pgs)
experiment encode accession: ENCSR026ZRP
assay title: single cell RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB669AEL
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: single midbrain from pup 3

value: Barbara Wold, Caltech

value: ENCBS960FNV at ENCODE; https://www.encodeproject.org/ENCBS960FNV/

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


title: single cell RNA-seq from Purkinje cell (ENCLB108LLJ)

description:
https://www.encodeproject.org/experiments/ENCSR027CXR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from an 8 month old male wild type C57Bl6 mouse
experiment encode accession: ENCSR027CXR
assay title: single cell RNA-seq
assembly: mm10
possible controls: ENCSR637NLF
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB108LLJ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1.0
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: 8 month

value: adult

value: male

value: ENCBS027VXR at ENCODE; https://www.encodeproject.org/ENCBS027VXR/


title: total RNA-seq from lung (ENCLB220DVX)

description:
https://www.encodeproject.org/experiments/ENCSR039ADS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse lung
experiment encode accession: ENCSR039ADS
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB220DVX
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (14.5 days)

value: lung

value: tissue

value: single lung from pup 1 pregnant 2 collected 7/17/2014

value: embryonic

value: pooled male and female

value: ENCBS133FDE at ENCODE; https://www.encodeproject.org/ENCBS133FDE/


title: total RNA-seq from lung (ENCLB819PZM)

description:
https://www.encodeproject.org/experiments/ENCSR039ADS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on embryonic 14.5 day mouse lung
experiment encode accession: ENCSR039ADS
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-12-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB819PZM
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: single lung from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS581DHV at ENCODE; https://www.encodeproject.org/ENCBS581DHV/


title: total RNA-seq from heart (ENCLB535BBV)

description:
https://www.encodeproject.org/experiments/ENCSR020DGG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR020DGG
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB535BBV
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (16.5 days)

value: heart

value: Heart from 41 embyonic 16.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS217XWR at ENCODE; https://www.encodeproject.org/ENCBS217XWR/


title: RN319

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

library_source: genomic

data_processing:
Data were mapped using BOWTIE
For each nucleotide, the amount of mapped fragments was considered (= coverage)
Data files were compressed by merging neighbouring nucleotides with equal coverages into single rows, with indication of start and end position of nucleotides with that specific coverage
Genome_build: HG19
Supplementary_files_format_and_content: txt files with columns containing resp. line number, chromosome, start and end position (nucleotide) and amount of mapped fragments

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney sample_Biopsie

extract_protocol:
DNA extracted using Qiagen Blood and Tissue Kit according to manufacturers Instuctions
Libraries were prepared using standard multiplexed paired-end Chip-seq protocol (Illumina). In summary, 500 ng of DNA per sample was fragmented by ultrasound mediated DNA shearing (Covaris S2, Covaris, Woburn, Massachusetts, USA) set to obtain fragments with an average length of 200bp. We employed the MethylCap kit (Diagenode AF-100-0048, Liège, Belgium) to obtain methylated DNA fragments using the highest salt concentration single elution step option. This was followed by the library preparation for the enriched DNA, which was performed with a modified 'multiplexed paired-end ChIP protocol' (Illumina, San Diego, California, USA). Therefore, the NEBNext® DNA Sample Prep Master Mix Set 1 (New England BioLabs (NEB) E6040, Ipswich, Massachusetts, USA) was combined with the Multiplexing Sample Preparation Oligo Kit (Illumina PE-400-1001). Per sample, 22µl of the prepared sample was subjected to PCR (21 cycles) following the Illumina Library Amplification Index Protocol. After purification (Qiaquick PCR Purification columns, Qiagen), elution and concentration (evaporation), the libraries were pooled and denaturated (NaOH), followed by Illumina HiSeq 2000 sequencing ('multiplexed paired-end run, 2 times 45 cycles) of 10pM/pool.

tag: gender

tag: age (yrs)

tag: fuhrman grade

tag: t stage

tag: m stage

tag: warm ischemia time* (mins)

tag: previous treatment

tag: tissue

value: kidney

tag: tissue type

value: Biopsie


title: RN319 I

value: male


title: ChIP-seq N20 acrylamide

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

data_processing:
Filtering reads and alignments:
Paired-end fastq files were filtered for low quality reads with Sickle using a minimal quality threshold of 20 and discarding resulting sequences shorter than 20 basepairs long. Eventual remaining adapter sequences (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were filtered from the respective 5’ and 3’ ends of forward and reverse reads using a two-pass cutadapt strategy with paired-output option (maximum allowed error rate of 0.15, Minimum overlap length of 6bp, and filtering out resulting reads shorter than 15 basepairs).
Sequences were then aligned on human reference genome (GRCh37/HG19) using Bowtie paired-end option allowing for up to two mismatches and discarding all reads aligning to multiple locations and inserts size longer than 10kb (-v 2 -X 10000 -k 1 -m 1).
Piling for average profiles:
BAM files containing paired alignments were used as input for Pasha pipeline with default parameters except that an automatic separation in 10 ranges of inserts size has been processed using the ‘rangeSelection’ option.
Genome_build: Human reference genome (GRCh37/HG19)
Supplementary_files_format_and_content: WIG files in variable step format

source_name: Lymphoblastoid cells derived from a Burkitt lymphoma

growth_protocol: Human Raji cells were cultured in RPMI medium supplemented with 10% fetal calf serum and penicillin (100 I.U./mL) and streptomycin (100µg/mL).

extract_protocol:
Chromatin Immunoprecipitation was perform as described previously (PMID: 24842994) from 50 million Raji cells by using 10µg anti-PolII antibody (sc-899, Santa Cruz Biotech). After immuoprecipitation, chromatin was reverse-crosslinked and DNA was purified by ethanol precipitation using linear acrylamide as carrier.
Sequencing libraries were prepared by using TruSeq ChIP Sample Preparation Kit (Illumina) according to manufacturer’s instructions with slight modification of the protocol, whereby the size-selection step to select a tight band of library fragments on agarose gel was omitted to keep all sizes of library fragments. These libraries were the sequenced using Illumina HiSeq sequencing machine to generate paired-end sequencing reads.

tag: cell line

value: Raji line of lymphoblast-like cells

tag: chip antibody


title: total RNA-seq from kidney (ENCLB209CGK)

description:
https://www.encodeproject.org/experiments/ENCSR062VTB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR062VTB
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB209CGK
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

tag: description

value: Kidney from 62 embryonic 15.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: ENCBS924ZKF at ENCODE; https://www.encodeproject.org/ENCBS924ZKF/

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


title: total RNA-seq from hindbrain (ENCLB441AFS)

description:
https://www.encodeproject.org/experiments/ENCSR017JEG/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse hindbrain
experiment encode accession: ENCSR017JEG
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB441AFS
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl hindbrain tissue postnatal (0 days)

value: hindbrain

value: tissue

value: single hindbrain from pup 3

value: 0 day

value: postnatal

tag: Sex

value: not collected

tag: lab

value: Barbara Wold, Caltech

tag: link

value: ENCBS901BYV at ENCODE; https://www.encodeproject.org/ENCBS901BYV/


title: total RNA-seq from neural tube (ENCLB082UHO)

description:
https://www.encodeproject.org/experiments/ENCSR004XCU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR004XCU
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB082UHO
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (15.5 days)

value: neural tube

value: Neural tube from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

tag: health state

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS944KEZ at ENCODE; https://www.encodeproject.org/ENCBS944KEZ/


title: total RNA-seq from hindbrain (ENCLB274VUA)

description:
https://www.encodeproject.org/experiments/ENCSR017JEG/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-Seq on postnatal 0 day mouse hindbrain
experiment encode accession: ENCSR017JEG
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-06-23
lab: Barbara Wold, Caltech
library encode accession: ENCLB274VUA
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: single hindbrain from pup 1

value: ENCBS489BYD at ENCODE; https://www.encodeproject.org/ENCBS489BYD/


title: RN319 C

source_name: Kidney sample_Nephrectomie

tag: gender

value: male

tag: age (yrs)

tag: fuhrman grade

value: kidney

value: Nephrectomie


title: total RNA-seq from forebrain (ENCLB026UUS)

description:
https://www.encodeproject.org/experiments/ENCSR080EVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR080EVZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB026UUS
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: forebrain

value: tissue

value: Forebrain from 41 embyonic 16.5 day mice

value: ENCBS512LKA at ENCODE; https://www.encodeproject.org/ENCBS512LKA/

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


title: RN319 H

tag: t stage

tag: m stage

tag: warm ischemia time* (mins)

value: Biopsie


title: total RNA-seq from neural tube (ENCLB302GKB)

description:
https://www.encodeproject.org/experiments/ENCSR115TWD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR115TWD
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB302GKB
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: neural tube

value: Neural tube from embryonic 13.5 day mice

value: ENCBS956BQY at ENCODE; https://www.encodeproject.org/ENCBS956BQY/


title: RN319 A

tag: previous treatment

tag: tissue

tag: tissue type


title: RN318 H

value: 3 cycles of Sunitinib 50mg once daily. Nephrectomy 4 days following cessation.


title: RN318 G


title: RN318 C


title: RN318 A


title: RN318 B


title: RN318 F


title: total RNA-seq from heart (ENCLB696ITY)

description:
https://www.encodeproject.org/experiments/ENCSR020DGG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR020DGG
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB696ITY
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

value: heart

tag: description

value: Heart pooled from embyonic 16.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS955JPC at ENCODE; https://www.encodeproject.org/ENCBS955JPC/


title: polyA depleted RNA-seq from neural cell (ENCLB930MEM)

description:
https://www.encodeproject.org/experiments/ENCSR995JXE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq of H1-neuron cellular RNA greater than 200 bp depleted in polyadenlated mRNA
experiment encode accession: ENCSR995JXE
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB930MEM
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens neural in vitro differentiated cells male embryo

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c26f62ae-3bde-4efe-99cf-4e2db5694f02/@@download/attachment/SID29906.pdf

value: neural cell

value: in vitro differentiated cells

value: neurons derived from H1 embryonic stem cells, newly promoted to tier 2:not in 2011 analysis

tag: biosample encode accession

value: unknown

value: male

value: Thomas Gingeras, CSHL

value: ENCBS513ENC at ENCODE; https://www.encodeproject.org/ENCBS513ENC/

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

value: ENCODE dbxrefs H1-neurons; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-neurons

value: Cellular Dynamics sample source; http://www.cellulardynamics.com/index.html


title: polyA depleted RNA-seq from neural cell (ENCLB196RDD)

description:
https://www.encodeproject.org/experiments/ENCSR995JXE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of H1-neuron cellular RNA greater than 200 bp depleted in polyadenlated mRNA
experiment encode accession: ENCSR995JXE
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB196RDD
size range: >200
spikeins used: /references/ENCSR470JZL/

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/25073202-c125-44ad-8c91-6026f1f644aa/@@download/attachment/SID29904.pdf

value: neurons derived from H1 embryonic stem cells

tag: age

value: ENCBS512ENC at ENCODE; https://www.encodeproject.org/ENCBS512ENC/