title: small RNA-seq from HT-29 (ENCLB454VES)

description:
https://www.encodeproject.org/experiments/ENCSR807KQN/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line, HT-29. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR807KQN
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB454VES
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa354e32-d260-45c1-a09f-47ddb0a0ad96/@@download/attachment/LID288439.pdf

value: female

value: ENCBS605AAA at ENCODE; https://www.encodeproject.org/ENCBS605AAA/


title: single cell RNA-seq from Purkinje cell (ENCLB747ZHK)

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/ENCSR828FPS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR828FPS
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB747ZHK
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens Purkinje primary cell male adult (20 years)

value: Purkinje cell

value: primary cell

tag: description

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

tag: biosample encode accession

tag: age

value: 20 year

tag: dev stage

value: adult

tag: Sex

value: male

tag: health state

value: normal

tag: lab

value: Barbara Wold, Caltech

tag: link

value: ENCBS590NTA at ENCODE; https://www.encodeproject.org/ENCBS590NTA/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: small RNA-seq from OCI-LY7 (ENCLB206AWW)

description:
https://www.encodeproject.org/experiments/ENCSR740DKM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line, Oci-Ly-7. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR740DKM
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB206AWW
size range: <200

source_name: Homo sapiens OCI-LY7 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/72bb2533-b998-41c4-aba9-72b4e1e10b51/@@download/attachment/288452.pdf

tag: line

value: immortalized cell line

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: 48 year

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS865AAA at ENCODE; https://www.encodeproject.org/ENCBS865AAA/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: single cell RNA-seq from Purkinje cell (ENCLB087SVF)

description:
https://www.encodeproject.org/experiments/ENCSR729ENB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR729ENB
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB087SVF
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: ENCBS883XBA at ENCODE; https://www.encodeproject.org/ENCBS883XBA/


title: single cell RNA-seq from GM12878 (ENCLB242XIT)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 9
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB242XIT
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/e3110414-4013-425e-94f6-72c549702bde/@@download/attachment/Supplemental_Material.pdf
extraction method: None

tag: antibody

value: Control

value: 10 homogenized GM12878 cells prepared for a pool-split experiment

value: unknown

value: adult

value: female

value: ENCBS356XKT at ENCODE; https://www.encodeproject.org/ENCBS356XKT/

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

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: single cell RNA-seq from GM12878 (ENCLB720ZUM)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 5
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB720ZUM
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: immortalized cell line

value: Barbara Wold, Caltech


title: single cell RNA-seq from GM12878 (ENCLB476CZO)

description:
https://www.encodeproject.org/experiments/ENCSR767SOH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single GM12878 cell
experiment encode accession: ENCSR767SOH
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR673UIY
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB476CZO
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Single GM12878 cell, part of a set of 10

value: ENCBS913NDQ at ENCODE; https://www.encodeproject.org/ENCBS913NDQ/


title: single cell RNA-seq from GM12878 (ENCLB283IJI)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 4
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB283IJI
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent


title: single cell RNA-seq from GM12878 (ENCLB146LAW)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB146LAW
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent


title: single cell RNA-seq from GM12878 (ENCLB211FCW)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 3
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB211FCW
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent


title: small RNA-seq from induced pluripotent stem cell (ENCLB204CIK)

description:
https://www.encodeproject.org/experiments/ENCSR722POQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of an induced pluripotent cell line, iPSC. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR722POQ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB204CIK
size range: <200

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ec0f8eac-a115-478e-803c-205eb1e1294a/@@download/attachment/LID290638.pdf

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: small RNA-seq from induced pluripotent stem cell (ENCLB011LRE)

description:
https://www.encodeproject.org/experiments/ENCSR722POQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of an induced pluripotent cell line, iPSC. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR722POQ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB011LRE
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/19663d95-35c9-44c4-a40e-81adbd51eeee/@@download/attachment/LID290639.pdf

value: adult

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/


title: small RNA-seq from neural progenitor cell (ENCLB090HYB)

description:
https://www.encodeproject.org/experiments/ENCSR828LSC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from H9-derived embryonic stem cells that were differentiated down a neuronal pathway. They are stranded SE101 length reads from rRNA-depleted Total RNA <200 nucleotides in size that was pretreated with Tobacco Acid Pyrophosphatase prior to cloning.
experiment encode accession: ENCSR828LSC
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB090HYB
size range: <200

source_name: Homo sapiens neural progenitor in vitro differentiated cells female embryo (5 days) derived from H9

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/eaf9f045-30f1-4e8b-9ddd-ccd755dc5b6b/@@download/attachment/LID294105.pdf

value: neural progenitor cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: small RNA-seq from hepatocyte (ENCLB762TSE)

description:
https://www.encodeproject.org/experiments/ENCSR673PND/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from H9-derived embryonic stem cells that were differentiated down a hepatocytic pathway. They are stranded SE101 length reads from rRNA-depleted Total RNA <200 nucleotides in size that was pretreated with Tobacco Acid Pyrophosphatase prior to cloning.
experiment encode accession: ENCSR673PND
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB762TSE
size range: <200

source_name: Homo sapiens hepatocyte in vitro differentiated cells female embryo (5 days) derived from H9

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/58a75fb5-b468-498d-9677-f7c1ef6efeeb/@@download/attachment/LID294107.pdf

value: hepatocyte

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/


title: single cell RNA-seq from GM12878 (ENCLB882HPA)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 7
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB882HPA
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: immortalized cell line

value: 10 homogenized GM12878 cells prepared for a pool-split experiment

value: unknown

value: Barbara Wold, Caltech

value: ENCBS356XKT at ENCODE; https://www.encodeproject.org/ENCBS356XKT/

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

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: small RNA-seq from OCI-LY7 (ENCLB188SKA)

description:
https://www.encodeproject.org/experiments/ENCSR740DKM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line, Oci-Ly-7. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR740DKM
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB188SKA
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0f1981c6-57eb-4109-91c5-32688545eba3/@@download/attachment/288453.pdf

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: 48 year

value: adult

value: male

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS866AAA at ENCODE; https://www.encodeproject.org/ENCBS866AAA/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: single cell RNA-seq from Purkinje cell (ENCLB257OVB)

description:
https://www.encodeproject.org/experiments/ENCSR659QHV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR659QHV
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB257OVB
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: normal

value: ENCBS589TAT at ENCODE; https://www.encodeproject.org/ENCBS589TAT/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: single cell RNA-seq from GM12878 (ENCLB187EEQ)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB187EEQ
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: immortalized cell line

value: 10 homogenized GM12878 cells prepared for a pool-split experiment

value: unknown

value: female

value: Barbara Wold, Caltech

value: ENCBS356XKT at ENCODE; https://www.encodeproject.org/ENCBS356XKT/

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

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: single cell RNA-seq from GM12878 (ENCLB108EAP)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 6
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB108EAP
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: adult


title: small RNA-seq from hepatocyte (ENCLB884TCK)

description:
https://www.encodeproject.org/experiments/ENCSR673PND/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from H9-derived embryonic stem cells that were differentiated down a hepatocytic pathway. They are stranded SE101 length reads from rRNA-depleted Total RNA <200 nucleotides in size that was pretreated with Tobacco Acid Pyrophosphatase prior to cloning.
experiment encode accession: ENCSR673PND
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB884TCK
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5e9e41e1-ed49-40f6-a4a9-def2691c74a4/@@download/attachment/LID294108.pdf

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: small RNA-seq from SK-N-DZ (ENCLB162IIY)

description:
https://www.encodeproject.org/experiments/ENCSR626WAX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR626WAX
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB162IIY
size range: <200

source_name: Homo sapiens SK-N-DZ immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/374159a4-3217-4b3c-ab64-64afff9c488b/@@download/attachment/LID293643.pdf

value: SK-N-DZ

value: immortalized cell line

value: An immortalized neuroblastoma (brain) cell line derived from a metastatic site in the bone marrow of a 2 year old female.

value: 2 year

value: child

value: Thomas Gingeras, CSHL

tag: subcellular fraction term name

value: nucleus

value: ENCBS707BMT at ENCODE; https://www.encodeproject.org/ENCBS707BMT/

value: Derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2149.aspx


title: single cell RNA-seq from Purkinje cell (ENCLB509KSM)

description:
https://www.encodeproject.org/experiments/ENCSR672QFA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR672QFA
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB509KSM
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: adult

value: male

value: normal

value: Barbara Wold, Caltech

value: ENCBS792VYU at ENCODE; https://www.encodeproject.org/ENCBS792VYU/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: small RNA-seq from SK-N-DZ (ENCLB951VDG)

description:
https://www.encodeproject.org/experiments/ENCSR626WAX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR626WAX
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB951VDG
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/783bafe4-6854-4f60-9c1b-a69b860bd2a3/@@download/attachment/LID293642.pdf

value: SK-N-DZ

value: immortalized cell line

value: An immortalized neuroblastoma (brain) cell line derived from a metastatic site in the bone marrow of a 2 year old female.

value: 2 year

value: child

value: female

value: ENCBS514GVM at ENCODE; https://www.encodeproject.org/ENCBS514GVM/


title: single cell RNA-seq from GM12878 (ENCLB402YMB)

description:
https://www.encodeproject.org/experiments/ENCSR625DPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single GM12878 cell
experiment encode accession: ENCSR625DPZ
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR673UIY
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB402YMB
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Single GM12878 cell, part of a set of 10

value: unknown

value: ENCBS135VMF at ENCODE; https://www.encodeproject.org/ENCBS135VMF/

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

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: small RNA-seq from SK-N-DZ (ENCLB636BID)

description:
https://www.encodeproject.org/experiments/ENCSR610CDO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR610CDO
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB636BID
size range: <200

source_name: Homo sapiens SK-N-DZ immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d3208f58-1e20-453a-84c6-9f30173d13fe/@@download/attachment/LID293640.pdf

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS715HTH at ENCODE; https://www.encodeproject.org/ENCBS715HTH/

value: Derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2149.aspx


title: single cell RNA-seq from GM12878 (ENCLB804XTY)

description:
https://www.encodeproject.org/experiments/ENCSR673UIY/
***************
biological replicate number: 1
technical replicate number: 8
description: RNA-seq on single cell equivalents of 10 isolated and homogenized GM12878 cells
experiment encode accession: ENCSR673UIY
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB804XTY
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: immortalized cell line

value: 10 homogenized GM12878 cells prepared for a pool-split experiment

value: adult

value: Barbara Wold, Caltech

value: ENCBS356XKT at ENCODE; https://www.encodeproject.org/ENCBS356XKT/


title: small RNA-seq from SK-N-DZ (ENCLB661KZL)

description:
https://www.encodeproject.org/experiments/ENCSR610CDO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR610CDO
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB661KZL
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a9cda4cd-6942-4357-b5ac-2934df0aa49c/@@download/attachment/LID293641.pdf

value: SK-N-DZ

value: An immortalized neuroblastoma (brain) cell line derived from a metastatic site in the bone marrow of a 2 year old female.

value: 2 year

value: child

value: female

value: ENCBS580YYW at ENCODE; https://www.encodeproject.org/ENCBS580YYW/


title: single cell RNA-seq from Purkinje cell (ENCLB617JJG)

description:
https://www.encodeproject.org/experiments/ENCSR610BAM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR610BAM
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB617JJG
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: male

value: normal

value: ENCBS938ALS at ENCODE; https://www.encodeproject.org/ENCBS938ALS/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: polyA depleted RNA-seq from keratinocyte (ENCLB555ANK)

description:
https://www.encodeproject.org/experiments/ENCSR000CQO/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary nuclear extracts, NHEK. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQO
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANK
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens keratinocyte primary cell nuclear fraction female

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c32fba3a-93ab-48a5-9181-2495ab9b20da/@@download/attachment/LID9204.pdf

value: keratinocyte

value: epidermal keratinocytes

value: unknown

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS566ENC at ENCODE; https://www.encodeproject.org/ENCBS566ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/

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

value: Lonza  sample source; http://www.lonza.com/public/select-keratinocyte-product-changes.aspx


title: polyA depleted RNA-seq from endothelial cell of umbilical vein (ENCLB555AUU)

description:
https://www.encodeproject.org/experiments/ENCSR000CQH/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on human HUVEC nucleus long polyA- RNA
experiment encode accession: ENCSR000CQH
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AUU
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens endothelial of umbilical vein primary cell nuclear fraction male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5e6c5ae4-6ae8-419a-acd9-c9cd145dd493/@@download/attachment/LID9207.pdf

value: endothelial cell of umbilical vein

value: umbilical vein endothelial cells

value: newborn

value: ENCBS533ENC at ENCODE; https://www.encodeproject.org/ENCBS533ENC/

value: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/

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


title: small RNA-seq from bipolar spindle neuron (ENCLB056HVD)

description:
https://www.encodeproject.org/experiments/ENCSR603RPC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of bipolar neurons that were differentiated from induced pluripotent stem cells. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR603RPC
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB056HVD
size range: <200

source_name: Homo sapiens bipolar spindle neuron in vitro differentiated cells male adult (53 years) derived from induced pluripotent stem cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2585f6f0-b4d8-4041-af3d-2b4c5f55bff8/@@download/attachment/LID291736.pdf

value: bipolar spindle neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: ENCBS369AAA at ENCODE; https://www.encodeproject.org/ENCBS369AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: small RNA-seq from bipolar spindle neuron (ENCLB395ZGN)

description:
https://www.encodeproject.org/experiments/ENCSR603RPC/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of bipolar neurons that were differentiated from induced pluripotent stem cells. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR603RPC
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB395ZGN
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1063f650-718e-43f6-8019-f77a70cd339d/@@download/attachment/LID291737.pdf

value: Thomas Gingeras, CSHL

value: ENCBS374AAA at ENCODE; https://www.encodeproject.org/ENCBS374AAA/


title: polyA depleted RNA-seq from keratinocyte (ENCLB555ALZ)

description:
https://www.encodeproject.org/experiments/ENCSR000CQN/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary cytoplasmic extracts, NHEK.  They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQN
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALZ
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens keratinocyte primary cell cytosolic fraction female

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1bdff925-424f-4644-b5a9-09c7d9d9ad57/@@download/attachment/LID18554.pdf

value: keratinocyte

value: primary cell

value: epidermal keratinocytes

value: unknown

value: female

value: cytosol

value: ENCBS565ENC at ENCODE; https://www.encodeproject.org/ENCBS565ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/

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

value: Lonza  sample source; http://www.lonza.com/public/select-keratinocyte-product-changes.aspx


title: single cell RNA-seq from Purkinje cell (ENCLB228BIT)

description:
https://www.encodeproject.org/experiments/ENCSR561KFF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR561KFF
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB228BIT
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: normal

value: Barbara Wold, Caltech

value: ENCBS602IDT at ENCODE; https://www.encodeproject.org/ENCBS602IDT/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: polyA depleted RNA-seq from fibroblast of lung (ENCLB555AQS)

description:
https://www.encodeproject.org/experiments/ENCSR000CPW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from lung fibroblast primary whole cells, NHLF  isolated from independent donors. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPW
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQS
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens fibroblast of lung primary cell male adult (45 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a17dd801-4390-42b1-9922-43c382d8ff64/@@download/attachment/LID8828.pdf

value: fibroblast of lung

value: lung fibroblasts

value: 45 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS612ENC at ENCODE; https://www.encodeproject.org/ENCBS612ENC/

value: Derived from ENCODE donor ENCDO269AAA; https://www.encodeproject.org/ENCDO269AAA/

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


title: polyA depleted RNA-seq from fibroblast of lung (ENCLB555APF)

description:
https://www.encodeproject.org/experiments/ENCSR000CPX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line AG04450. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPX
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APF
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens fibroblast of lung primary cell male fetal (12 weeks)

extract_protocol:
extraction method: see document
spike-in concentrations: https://www.encodeproject.org/documents/34e684ee-8e9a-4b4e-9708-4a0bc5ae9811/@@download/attachment/wgEncodeCshlSpikeinsConcentrations.txt

value: primary cell

value: fetal lung fibroblast

value: 12 week

value: fetal

value: apparently healthy

value: Unknown Lab

value: ENCBS008ENC at ENCODE; https://www.encodeproject.org/ENCBS008ENC/

value: Derived from ENCODE donor ENCDO001AAA; https://www.encodeproject.org/ENCDO001AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F486; http://web.expasy.org/cellosaurus/CVCL_F486

value: ENCODE dbxrefs AG04450; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=AG04450


title: small RNA-seq from SK-MEL-5 (ENCLB263FZA)

description:
https://www.encodeproject.org/experiments/ENCSR571FTT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR571FTT
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB263FZA
size range: <200

source_name: Homo sapiens SK-MEL-5 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/409e94a6-abd4-46bf-b6ab-bdd593de231d/@@download/attachment/LID294017.pdf

value: immortalized cell line

value: An immortalized malignant melanoma cell line derived from a metastatic axillary node of a 24 year old female.

value: 24 year

value: female

value: cytosol

value: ENCBS324XRL at ENCODE; https://www.encodeproject.org/ENCBS324XRL/

value: Derived from ENCODE donor ENCDO338AAA; https://www.encodeproject.org/ENCDO338AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0527; http://web.expasy.org/cellosaurus/CVCL_0527

value: ATCC sample source; http://www.atcc.org/products/all/HTB-70.aspx


title: polyA depleted RNA-seq from fibroblast of lung (ENCLB555APE)

description:
https://www.encodeproject.org/experiments/ENCSR000CPX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line AG04450. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPX
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APE
size range: >200
spikeins used: /references/ENCSR402QNO/

value: fibroblast of lung

value: primary cell

value: fetal lung fibroblast

value: 12 week

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS004ENC at ENCODE; https://www.encodeproject.org/ENCBS004ENC/

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=AG04450


title: small RNA-seq from SK-MEL-5 (ENCLB642ALL)

description:
https://www.encodeproject.org/experiments/ENCSR571FTT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted TAP pretreated Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR571FTT
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB642ALL
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/900dc1de-695b-4d0f-9034-34da83198b43/@@download/attachment/LID294018.pdf

value: immortalized cell line

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS697RNA at ENCODE; https://www.encodeproject.org/ENCBS697RNA/


title: polyA depleted RNA-seq from fibroblast of lung (ENCLB555AQR)

description:
https://www.encodeproject.org/experiments/ENCSR000CPW/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from lung fibroblast primary whole cells, NHLF  isolated from independent donors. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPW
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQR
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5449fd01-1ede-4ef7-9d93-cd366751209b/@@download/attachment/LID8829.pdf

value: lung fibroblasts

value: 45 year

value: unknown

value: ENCBS613ENC at ENCODE; https://www.encodeproject.org/ENCBS613ENC/

value: Derived from ENCODE donor ENCDO269AAA; https://www.encodeproject.org/ENCDO269AAA/

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


title: polyA depleted RNA-seq from mammary epithelial cell (ENCLB555APX)

description:
https://www.encodeproject.org/experiments/ENCSR000CPU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from mammary gland epithelial primary whole cells, HMEC isolated from independent donors. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DNS normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPU
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APX
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens mammary epithelial primary cell female

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1402bdc4-8260-4613-a1d8-16d384dea3a6/@@download/attachment/LID8831.pdf

value: mammary epithelial cell

value: primary cell

value: mammary epithelial cells

value: female

value: ENCBS552ENC at ENCODE; https://www.encodeproject.org/ENCBS552ENC/

value: Derived from ENCODE donor ENCDO331AAA; https://www.encodeproject.org/ENCDO331AAA/

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


title: polyA depleted RNA-seq from endothelial cell of umbilical vein (ENCLB555ALG)

description:
https://www.encodeproject.org/experiments/ENCSR000CQG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human HUVEC whole cell long polyA- RNA
experiment encode accession: ENCSR000CQG
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALG
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens endothelial of umbilical vein primary cell male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6f82c8cc-0021-4f73-b50d-9bfd39a8658c/@@download/attachment/LID8788.pdf

value: endothelial cell of umbilical vein

value: umbilical vein endothelial cells

value: newborn

value: male

value: ENCBS528ENC at ENCODE; https://www.encodeproject.org/ENCBS528ENC/

value: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/

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


title: polyA depleted RNA-seq from endothelial cell of umbilical vein (ENCLB555AUV)

description:
https://www.encodeproject.org/experiments/ENCSR000CQH/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on human HUVEC nucleus long polyA- RNA
experiment encode accession: ENCSR000CQH
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AUV
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7f78d7f7-e0ad-48f8-9f26-2c380db50964/@@download/attachment/LID9206.pdf

value: unknown

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS531ENC at ENCODE; https://www.encodeproject.org/ENCBS531ENC/


title: polyA depleted RNA-seq from skeletal muscle myoblast (ENCLB555ATG)

description:
https://www.encodeproject.org/experiments/ENCSR000CPV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human HSMM whole cell long polyA- RNA
experiment encode accession: ENCSR000CPV
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATG
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens skeletal muscle myoblast primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c5a8403b-a37e-4499-9fc1-b68e4385287d/@@download/attachment/LID8826.pdf

value: skeletal muscle myoblast

value: primary cell

value: skeletal muscle myoblasts

value: not collected

value: ENCBS469ENC at ENCODE; https://www.encodeproject.org/ENCBS469ENC/

value: Derived from ENCODE donor ENCDO094AAA; https://www.encodeproject.org/ENCDO094AAA/

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


title: small RNA-seq from fibroblast of arm (ENCLB639PKP)

description:
https://www.encodeproject.org/experiments/ENCSR489KNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin fibroblasts. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR489KNQ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB639PKP
size range: <200

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5db8ce45-f789-47a7-937c-a811dfa7596c/@@download/attachment/LID290636.pdf

value: fibroblast of arm

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: polyA mRNA RNA-seq from fibroblast of lung (ENCLB555AVD)

description:
https://www.encodeproject.org/experiments/ENCSR000CPM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from lung fibroblast primary whole cells, NHLF  isolated from independent donors. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPM
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVD
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dc46874c-3424-4b1a-baf7-b93e3a6dc2a1/@@download/attachment/LID8692.pdf

value: fibroblast of lung

value: lung fibroblasts

value: 45 year

value: male

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS612ENC at ENCODE; https://www.encodeproject.org/ENCBS612ENC/

value: Derived from ENCODE donor ENCDO269AAA; https://www.encodeproject.org/ENCDO269AAA/

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


title: polyA depleted RNA-seq from endothelial cell of umbilical vein (ENCLB555AKJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CQG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human HUVEC whole cell long polyA- RNA
experiment encode accession: ENCSR000CQG
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKJ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ff48a976-aa6b-42e3-adcf-cdbb0c77a9e2/@@download/attachment/LID8789.pdf

value: endothelial cell of umbilical vein

value: primary cell

value: umbilical vein endothelial cells

value: newborn

value: ENCBS529ENC at ENCODE; https://www.encodeproject.org/ENCBS529ENC/

value: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/

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


title: single cell RNA-seq from Purkinje cell (ENCLB331AUZ)

description:
https://www.encodeproject.org/experiments/ENCSR558LHB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR558LHB
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB331AUZ
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

source_name: Homo sapiens Purkinje primary cell male adult (20 years)

value: Purkinje cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: adult

value: normal

value: Barbara Wold, Caltech

value: ENCBS456HUG at ENCODE; https://www.encodeproject.org/ENCBS456HUG/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: single cell RNA-seq from Purkinje cell (ENCLB462FVS)

description:
https://www.encodeproject.org/experiments/ENCSR888LYA/
***************
biological replicate number: 1
technical replicate number: 12
description: RNA-seq on single cell equivalents of 20 excised and homogenized Purkinje cells from a 20 year old human male
experiment encode accession: ENCSR888LYA
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB462FVS
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: 20 homogenized Purkinje cells from a 20 year old male brain prepared for a pool-split experiment

value: male

value: ENCBS135VDR at ENCODE; https://www.encodeproject.org/ENCBS135VDR/


title: polyA mRNA RNA-seq from keratinocyte (ENCLB555APT)

description:
https://www.encodeproject.org/experiments/ENCSR000CPL/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary whole cells, NHEK. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APT
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens keratinocyte primary cell female

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a8ee67e6-4d0d-4294-a354-37e6d761cdf3/@@download/attachment/LID16631.pdf

value: keratinocyte

value: primary cell

value: epidermal keratinocytes

value: unknown

value: female

value: Thomas Gingeras, CSHL

value: ENCBS563ENC at ENCODE; https://www.encodeproject.org/ENCBS563ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/

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

value: Lonza  sample source; http://www.lonza.com/public/select-keratinocyte-product-changes.aspx


title: polyA mRNA RNA-seq from fibroblast of lung (ENCLB555AVL)

description:
https://www.encodeproject.org/experiments/ENCSR000CPM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from lung fibroblast primary whole cells, NHLF  isolated from independent donors. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPM
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVL
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bcff11c0-9cf8-4465-942d-bbd8d6c22d91/@@download/attachment/LID8701.pdf

value: fibroblast of lung

value: lung fibroblasts

value: 45 year

value: adult

value: ENCBS613ENC at ENCODE; https://www.encodeproject.org/ENCBS613ENC/

value: Derived from ENCODE donor ENCDO269AAA; https://www.encodeproject.org/ENCDO269AAA/

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


title: polyA mRNA RNA-seq from keratinocyte (ENCLB555APU)

description:
https://www.encodeproject.org/experiments/ENCSR000CPL/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary whole cells, NHEK. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APU
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fccc463d-7572-4980-a01c-d78ab078cbf8/@@download/attachment/LID16632.pdf

value: keratinocyte

value: ENCBS564ENC at ENCODE; https://www.encodeproject.org/ENCBS564ENC/


title: small RNA-seq from fibroblast of arm (ENCLB513JYD)

description:
https://www.encodeproject.org/experiments/ENCSR489KNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin fibroblasts. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR489KNQ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB513JYD
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/230fd101-fd7e-4f19-9ff5-a54f28cd7ac6/@@download/attachment/LID290637.pdf

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: polyA mRNA RNA-seq from keratinocyte (ENCLB555AKK)

description:
https://www.encodeproject.org/experiments/ENCSR000CPL/
***************
biological replicate number: 5
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary whole cells, NHEK. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKK
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/90a86afe-d57e-43fc-9d7a-8c6cfb61e205/@@download/attachment/LID8694.pdf

value: epidermal keratinocytes

value: unknown

value: female

value: Thomas Gingeras, CSHL

value: ENCBS569ENC at ENCODE; https://www.encodeproject.org/ENCBS569ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/

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

value: Lonza  sample source; http://www.lonza.com


title: polyA depleted RNA-seq from keratinocyte (ENCLB555ANJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CQO/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary nuclear extracts, NHEK. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CQO
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANJ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4c75ccd2-d980-4eac-9690-a8d7b584b8a4/@@download/attachment/LID9205.pdf

value: keratinocyte

value: nucleus

value: ENCBS568ENC at ENCODE; https://www.encodeproject.org/ENCBS568ENC/

value: Lonza  sample source; http://www.lonza.com/public/select-keratinocyte-product-changes.aspx


title: single cell RNA-seq from Purkinje cell (ENCLB211OUD)

description:
https://www.encodeproject.org/experiments/ENCSR435ROA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR435ROA
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB211OUD
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: primary cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: adult

value: male

value: normal

value: Barbara Wold, Caltech

value: ENCBS869ANE at ENCODE; https://www.encodeproject.org/ENCBS869ANE/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: polyA depleted RNA-seq from skeletal muscle myoblast (ENCLB555ATF)

description:
https://www.encodeproject.org/experiments/ENCSR000CPV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human HSMM whole cell long polyA- RNA
experiment encode accession: ENCSR000CPV
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATF
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7347789c-fa11-4e7d-956b-52522a06882f/@@download/attachment/LID8827.pdf

value: skeletal muscle myoblast

value: skeletal muscle myoblasts

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

value: ENCBS470ENC at ENCODE; https://www.encodeproject.org/ENCBS470ENC/

value: Derived from ENCODE donor ENCDO094AAA; https://www.encodeproject.org/ENCDO094AAA/

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


title: polyA mRNA RNA-seq from keratinocyte (ENCLB555AKW)

description:
https://www.encodeproject.org/experiments/ENCSR000CPK/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary cytoplasmic extracts, NHEK.  They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPK
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKW
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3f4b315a-770a-4b69-8ad8-4e7a771c412c/@@download/attachment/LID8795.pdf

value: keratinocyte

value: primary cell

value: epidermal keratinocytes

value: female

value: cytosol

value: ENCBS565ENC at ENCODE; https://www.encodeproject.org/ENCBS565ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/

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

value: Lonza  sample source; http://www.lonza.com/public/select-keratinocyte-product-changes.aspx


title: single cell RNA-seq from Purkinje cell (ENCLB804XKW)

description:
https://www.encodeproject.org/experiments/ENCSR724XFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR724XFQ
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB804XKW
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: adult

value: male

value: normal

value: Barbara Wold, Caltech

value: ENCBS931OHT at ENCODE; https://www.encodeproject.org/ENCBS931OHT/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: polyA mRNA RNA-seq from keratinocyte (ENCLB555AKX)

description:
https://www.encodeproject.org/experiments/ENCSR000CPK/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary cytoplasmic extracts, NHEK.  They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPK
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKX
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1ac7e264-b10f-4d21-8335-4b9d0df2ebbc/@@download/attachment/LID8796.pdf

value: keratinocyte

value: primary cell

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS567ENC at ENCODE; https://www.encodeproject.org/ENCBS567ENC/


title: polyA mRNA RNA-seq from keratinocyte (ENCLB555ATM)

description:
https://www.encodeproject.org/experiments/ENCSR000CPJ/
***************
biological replicate number: 4
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary nuclear extracts, NHEK.  They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPJ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATM
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/58a8081a-6755-498c-9e79-9301b1818d2a/@@download/attachment/LID8798.pdf

value: epidermal keratinocytes

value: female

value: nucleus

value: ENCBS568ENC at ENCODE; https://www.encodeproject.org/ENCBS568ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/


title: polyA mRNA RNA-seq from keratinocyte (ENCLB555ATL)

description:
https://www.encodeproject.org/experiments/ENCSR000CPJ/
***************
biological replicate number: 3
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary nuclear extracts, NHEK.  They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPJ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATL
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/51f3fd08-ee1e-4fc7-a4f3-47203bafa87b/@@download/attachment/LID8797.pdf

value: ENCBS566ENC at ENCODE; https://www.encodeproject.org/ENCBS566ENC/

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

value: Lonza  sample source; http://www.lonza.com/public/select-keratinocyte-product-changes.aspx


title: polyA depleted RNA-seq from keratinocyte (ENCLB555AVO)

description:
https://www.encodeproject.org/experiments/ENCSR000CPI/
***************
biological replicate number: 5
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary whole cells, NHEK. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPI
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVO
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/847e574c-a20e-44fa-8059-30e8cfb471ad/@@download/attachment/LID8830.pdf

value: ENCBS569ENC at ENCODE; https://www.encodeproject.org/ENCBS569ENC/

value: Lonza  sample source; http://www.lonza.com


title: single cell RNA-seq from cerebellar granule cell (ENCLB386HBI)

description:
https://www.encodeproject.org/experiments/ENCSR415JJO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on excised cerebellar granule cells from a 20 year old human male
experiment encode accession: ENCSR415JJO
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB386HBI
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 30
nucleic acid starting quantity units: cell-equivalent

source_name: Homo sapiens cerebellar granule primary cell male adult (20 years)

value: Control

value: cerebellar granule cell

value: Granule cells from a 20 year old male brain

value: 20 year

value: adult

value: male

value: normal

value: Barbara Wold, Caltech

value: ENCBS188JNJ at ENCODE; https://www.encodeproject.org/ENCBS188JNJ/


title: single cell RNA-seq from pyramidal cell (ENCLB621DLJ)

description:
https://www.encodeproject.org/experiments/ENCSR423XRG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on 30 cell pools of excised pyramidal cells from a 20 year old human male
experiment encode accession: ENCSR423XRG
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB621DLJ
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 30
nucleic acid starting quantity units: cells

source_name: Homo sapiens pyramidal primary cell male adult (20 years)

value: pyramidal cell

value: primary cell

value: 30 pyramid cells from a 20 year old male brain

value: ENCBS651ADZ at ENCODE; https://www.encodeproject.org/ENCBS651ADZ/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: polyA depleted RNA-seq from keratinocyte (ENCLB555AVQ)

description:
https://www.encodeproject.org/experiments/ENCSR000CPI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary whole cells, NHEK. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPI
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVQ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/278dd7be-7749-4370-ae7e-f0f150454469/@@download/attachment/LID8665.pdf

value: keratinocyte

value: epidermal keratinocytes

value: unknown

value: female

value: Thomas Gingeras, CSHL

value: ENCBS563ENC at ENCODE; https://www.encodeproject.org/ENCBS563ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/

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

value: Lonza  sample source; http://www.lonza.com/public/select-keratinocyte-product-changes.aspx


title: single cell RNA-seq from Purkinje cell (ENCLB632SOL)

description:
https://www.encodeproject.org/experiments/ENCSR417EDR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR417EDR
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB632SOL
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: adult

value: male

value: normal

value: ENCBS346VWP at ENCODE; https://www.encodeproject.org/ENCBS346VWP/


title: polyA mRNA RNA-seq from endothelial cell of umbilical vein (ENCLB555ATW)

description:
https://www.encodeproject.org/experiments/ENCSR000CPB/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on human HUVEC nucleus long polyA+ RNA
experiment encode accession: ENCSR000CPB
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATW
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dc2b619a-3e03-4157-9caa-389b38053452/@@download/attachment/LID8690.pdf

value: endothelial cell of umbilical vein

value: primary cell

value: umbilical vein endothelial cells

value: newborn

value: nucleus

value: ENCBS531ENC at ENCODE; https://www.encodeproject.org/ENCBS531ENC/

value: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/

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


title: polyA mRNA RNA-seq from skeletal muscle myoblast (ENCLB555AWI)

description:
https://www.encodeproject.org/experiments/ENCSR000COY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human HSMM whole cell long polyA+ RNA
experiment encode accession: ENCSR000COY
assay title: polyA mRNA RNA-seq
assembly: hg19, GRCh38
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWI
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bb363deb-8e79-4d8a-bdaa-4030df8d70e8/@@download/attachment/LID8710.pdf

value: skeletal muscle myoblast

value: skeletal muscle myoblasts

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

value: ENCBS469ENC at ENCODE; https://www.encodeproject.org/ENCBS469ENC/

value: Derived from ENCODE donor ENCDO094AAA; https://www.encodeproject.org/ENCDO094AAA/

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


title: single cell RNA-seq from Purkinje cell (ENCLB327MTR)

description:
https://www.encodeproject.org/experiments/ENCSR376KFF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR376KFF
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB327MTR
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: 20 year

value: adult

value: male

value: normal

value: Barbara Wold, Caltech

value: ENCBS122ZLM at ENCODE; https://www.encodeproject.org/ENCBS122ZLM/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: polyA mRNA RNA-seq from endothelial cell of umbilical vein (ENCLB555ASE)

description:
https://www.encodeproject.org/experiments/ENCSR000CPA/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on human HUVEC cytosol long polyA+ RNA
experiment encode accession: ENCSR000CPA
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASE
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens endothelial of umbilical vein primary cell cytosolic fraction male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6be83773-e8ef-41c1-be44-d8ee3b4ee2f9/@@download/attachment/LID8689.pdf

value: endothelial cell of umbilical vein

value: primary cell

value: umbilical vein endothelial cells

value: newborn

value: cytosol

value: ENCBS532ENC at ENCODE; https://www.encodeproject.org/ENCBS532ENC/

value: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/

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


title: polyA mRNA RNA-seq from fibroblast of lung (ENCLB555AKO)

description:
https://www.encodeproject.org/experiments/ENCSR000COO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line AG04450. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKO
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d2ce0eac-56b4-4954-8b3a-6b8591624bed/@@download/attachment/LID8966.pdf

value: fibroblast of lung

value: fetal lung fibroblast

value: 12 week

value: fetal

value: apparently healthy

value: Unknown Lab

value: ENCBS008ENC at ENCODE; https://www.encodeproject.org/ENCBS008ENC/

value: Derived from ENCODE donor ENCDO001AAA; https://www.encodeproject.org/ENCDO001AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F486; http://web.expasy.org/cellosaurus/CVCL_F486

value: ENCODE dbxrefs AG04450; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=AG04450


title: polyA mRNA RNA-seq from mammary epithelial cell (ENCLB555AWZ)

description:
https://www.encodeproject.org/experiments/ENCSR000COX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from mammary gland epithelial primary whole cells, HMEC isolated from independent donors. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ > 200 nucleotides in size.
experiment encode accession: ENCSR000COX
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWZ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/125eb2e5-a9b4-40f5-b6fc-4e80cdf47c40/@@download/attachment/LID8695.pdf

value: mammary epithelial cell

value: primary cell

value: mammary epithelial cells

value: unknown

value: female

value: Thomas Gingeras, CSHL

value: ENCBS552ENC at ENCODE; https://www.encodeproject.org/ENCBS552ENC/

value: Derived from ENCODE donor ENCDO331AAA; https://www.encodeproject.org/ENCDO331AAA/

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


title: small RNA-seq from A375 (ENCLB462UUM)

description:
https://www.encodeproject.org/experiments/ENCSR376XXO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line, A375. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR376XXO
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB462UUM
size range: <200

source_name: Homo sapiens A375 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e759d849-fd5f-4e10-85c3-2ff69a7a8b1f/@@download/attachment/LID288441.pdf

value: immortalized cell line

value: Epithelial cells, malignant melanoma

value: 54 year

value: adult

tag: passage number

value: malignant melanoma

value: Bradley Bernstein, Broad

value: ENCBS607AAA at ENCODE; https://www.encodeproject.org/ENCBS607AAA/

value: Derived from ENCODE donor ENCDO348AAA; https://www.encodeproject.org/ENCDO348AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0132; http://web.expasy.org/cellosaurus/CVCL_0132

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1619.aspx


title: polyA mRNA RNA-seq from endothelial cell of umbilical vein (ENCLB555AVJ)

description:
https://www.encodeproject.org/experiments/ENCSR000COZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human HUVEC whole cell long polyA+ RNA
experiment encode accession: ENCSR000COZ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVJ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cc485a8e-bb54-4ab8-931f-1b5d877b62a2/@@download/attachment/LID8463.pdf

value: endothelial cell of umbilical vein

value: primary cell

value: umbilical vein endothelial cells

value: newborn

value: male

value: ENCBS528ENC at ENCODE; https://www.encodeproject.org/ENCBS528ENC/

value: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/

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


title: polyA mRNA RNA-seq from endothelial cell of umbilical vein (ENCLB555AOY)

description:
https://www.encodeproject.org/experiments/ENCSR000CPB/
***************
biological replicate number: 4
technical replicate number: 1
description: RNA-seq on human HUVEC nucleus long polyA+ RNA
experiment encode accession: ENCSR000CPB
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AOY
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/622d600c-02be-4479-b128-b9f6fa31b47a/@@download/attachment/LID8691.pdf

value: unknown

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS533ENC at ENCODE; https://www.encodeproject.org/ENCBS533ENC/


title: polyA mRNA RNA-seq from endothelial cell of umbilical vein (ENCLB555ASD)

description:
https://www.encodeproject.org/experiments/ENCSR000CPA/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on human HUVEC cytosol long polyA+ RNA
experiment encode accession: ENCSR000CPA
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASD
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6f6f43c9-50aa-47a2-a462-9178495277f8/@@download/attachment/LID8688.pdf

value: cytosol

value: ENCBS530ENC at ENCODE; https://www.encodeproject.org/ENCBS530ENC/


title: polyA mRNA RNA-seq from skeletal muscle myoblast (ENCLB555AWH)

description:
https://www.encodeproject.org/experiments/ENCSR000COY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human HSMM whole cell long polyA+ RNA
experiment encode accession: ENCSR000COY
assay title: polyA mRNA RNA-seq
assembly: hg19, GRCh38
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWH
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/12c0b3ea-b018-4cc2-b9f7-c7a037ada0e7/@@download/attachment/LID8711.pdf

value: skeletal muscle myoblast

value: skeletal muscle myoblasts

value: not collected

value: ENCBS470ENC at ENCODE; https://www.encodeproject.org/ENCBS470ENC/

value: Derived from ENCODE donor ENCDO094AAA; https://www.encodeproject.org/ENCDO094AAA/

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


title: small RNA-seq from A375 (ENCLB833UTL)

description:
https://www.encodeproject.org/experiments/ENCSR376XXO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line, A375. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning.
experiment encode accession: ENCSR376XXO
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB833UTL
size range: <200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/14f05b53-9f99-48a5-81f8-d3e9439aa512/@@download/attachment/LID288440.pdf

value: immortalized cell line

value: Epithelial cells, malignant melanoma

value: 54 year

value: adult

value: female

value: malignant melanoma

value: Bradley Bernstein, Broad

value: ENCBS606AAA at ENCODE; https://www.encodeproject.org/ENCBS606AAA/

value: Derived from ENCODE donor ENCDO348AAA; https://www.encodeproject.org/ENCDO348AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0132; http://web.expasy.org/cellosaurus/CVCL_0132

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1619.aspx


title: single cell RNA-seq from pyramidal cell (ENCLB164LQL)

description:
https://www.encodeproject.org/experiments/ENCSR423XRG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on 30 cell pools of excised pyramidal cells from a 20 year old human male
experiment encode accession: ENCSR423XRG
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB164LQL
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 30
nucleic acid starting quantity units: cells

value: Control

value: pyramidal cell

value: primary cell

value: 30 pyramid cells from a 20 year old male brain

value: 20 year

value: male

value: normal

value: Barbara Wold, Caltech

value: ENCBS590LDH at ENCODE; https://www.encodeproject.org/ENCBS590LDH/

value: Derived from ENCODE donor ENCDO377OGA; https://www.encodeproject.org/ENCDO377OGA/


title: single cell RNA-seq from Purkinje cell (ENCLB350NUB)

description:
https://www.encodeproject.org/experiments/ENCSR366QZI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single Purkinje cell from a 20 year old human male
experiment encode accession: ENCSR366QZI
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR888LYA
encode release date: 2014-07-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB350NUB
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

value: Purkinje cell

value: Single Purkinje cell from a 20 year old male brain, part of a set of 20 cells

value: adult

value: ENCBS982VXC at ENCODE; https://www.encodeproject.org/ENCBS982VXC/


title: total RNA-seq from GMP (ENCLB418HNR)

description:
https://www.encodeproject.org/experiments/ENCSR833HPM/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse GMP RNA 100 cells RNA-seq
experiment encode accession: ENCSR833HPM
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Ross Hardison, PennState
library encode accession: ENCLB418HNR
size range: >200
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 100
nucleic acid starting quantity units: cells

organism: Mus musculus

source_name: Mus musculus strain C57BL/6J GMP primary cell male adult (5-6 weeks)

value: GMP

value: granulocyte monocyte progenitor

value: 5-6 week

value: unknown

value: Ross Hardison, PennState

value: ENCBS883TUU at ENCODE; https://www.encodeproject.org/ENCBS883TUU/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: total RNA-seq from G1E (ENCLB473JWP)

description:
https://www.encodeproject.org/experiments/ENCSR826IXR/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse G1E RNA 1ng RNA-seq
experiment encode accession: ENCSR826IXR
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Ross Hardison, PennState
library encode accession: ENCLB473JWP
size range: >200
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

source_name: Mus musculus strain C57BL/6J G1E immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/73547e04-fa47-41ac-8f6e-6b2664621dfd/@@download/attachment/IsolationOfTotalRnaAndLibraryPrepFromG1eAndEr4.pdf

value: immortalized cell line

value: Gata1- erythroid progenitor

value: 0 day

value: postnatal

value: ENCBS602TAQ at ENCODE; https://www.encodeproject.org/ENCBS602TAQ/

value: ENCODE dbxrefs Cellosaurus CVCL_D046; http://web.expasy.org/cellosaurus/CVCL_D046


title: polyA depleted RNA-seq from keratinocyte (ENCLB555AVP)

description:
https://www.encodeproject.org/experiments/ENCSR000CPI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin keratinocytes primary whole cells, NHEK. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPI
assay title: polyA depleted RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVP
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c91d490f-7fc5-4404-9441-b6d9c19f7bb1/@@download/attachment/LID8666.pdf

value: keratinocyte

value: primary cell

value: epidermal keratinocytes

value: female

value: Thomas Gingeras, CSHL

value: ENCBS564ENC at ENCODE; https://www.encodeproject.org/ENCBS564ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/

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

value: Lonza  sample source; http://www.lonza.com/public/select-keratinocyte-product-changes.aspx


title: polyA mRNA RNA-seq from fibroblast of lung (ENCLB555AKP)

description:
https://www.encodeproject.org/experiments/ENCSR000COO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line AG04450. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKP
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2b98c64a-9dfe-49f6-8984-efb0f60bd64a/@@download/attachment/LID8965.pdf

value: fibroblast of lung

value: fetal lung fibroblast

value: 12 week

value: fetal

value: male

value: apparently healthy

value: John Stamatoyannopoulos, UW

value: ENCBS004ENC at ENCODE; https://www.encodeproject.org/ENCBS004ENC/

value: Derived from ENCODE donor ENCDO001AAA; https://www.encodeproject.org/ENCDO001AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F486; http://web.expasy.org/cellosaurus/CVCL_F486

value: ENCODE dbxrefs AG04450; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=AG04450

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=AG04450


title: total RNA-seq from G1E (ENCLB038MNH)

description:
https://www.encodeproject.org/experiments/ENCSR826IXR/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse G1E RNA 1ng RNA-seq
experiment encode accession: ENCSR826IXR
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-11-20
lab: Ross Hardison, PennState
library encode accession: ENCLB038MNH
size range: >200
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: ng

value: immortalized cell line

value: Gata1- erythroid progenitor

value: 0 day

value: postnatal

value: Ross Hardison, PennState

value: ENCBS807UWB at ENCODE; https://www.encodeproject.org/ENCBS807UWB/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_D046; http://web.expasy.org/cellosaurus/CVCL_D046


title: total RNA-seq from GMP (ENCLB479SFD)

description:
https://www.encodeproject.org/experiments/ENCSR833HPM/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse GMP RNA 100 cells RNA-seq
experiment encode accession: ENCSR833HPM
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-09-29
lab: Ross Hardison, PennState
library encode accession: ENCLB479SFD
size range: >200
spikeins used: /references/ENCSR156CIL/, /references/ENCSR013YHQ/
nucleic acid starting quantity: 100
nucleic acid starting quantity units: cells

value: GMP

value: primary cell

value: granulocyte monocyte progenitor

value: 5-6 week

value: adult

value: unknown

value: ENCBS917EVE at ENCODE; https://www.encodeproject.org/ENCBS917EVE/