title: total RNA-seq from glomerular endothelial cell (ENCLB905CHP)

description:
https://www.encodeproject.org/experiments/ENCSR878EUT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of primary renal glomerular endothelial cells (HGC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR878EUT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB905CHP
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens glomerular endothelial primary cell male fetal (22 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8236f115-4cf9-4bab-828c-01a311da3b75/@@download/attachment/295115.pdf

value: Human Renal Glomerular Endothelial Cell (HGC) from a fetal male kidney at 22 weeks gestation.

value: male

value: ENCBS574ALN at ENCODE; https://www.encodeproject.org/ENCBS574ALN/

value: Derived from ENCODE donor ENCDO611INZ; https://www.encodeproject.org/ENCDO611INZ/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=4005


title: microRNA-seq from right lobe of liver (ENCLB454WLG)

status: Public on Nov 08 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/ENCSR875UFE/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human right lobe of liver
experiment encode accession: ENCSR875UFE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB454WLG
size range: <30

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

value: right lobe of liver

value: tissue

tag: description

value: Liver

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: lab

value: Barbara Wold, Caltech

tag: link

value: ENCBS688NPW at ENCODE; https://www.encodeproject.org/ENCBS688NPW/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: microRNA-seq from right lobe of liver (ENCLB247BIW)

description:
https://www.encodeproject.org/experiments/ENCSR875UFE/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human right lobe of liver
experiment encode accession: ENCSR875UFE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB247BIW
size range: <30

value: ENCBS594VBH at ENCODE; https://www.encodeproject.org/ENCBS594VBH/


title: shRNA RNA-seq from HepG2 (ENCLB733UBP)

description:
https://www.encodeproject.org/experiments/ENCSR883BXR/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against LSM11 in HepG2 cells followed by RNA-seq. (LSM11_BGHLV18)
experiment encode accession: ENCSR883BXR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB733UBP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting LSM11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b6da5440-fa9a-4251-b4ba-5aeb7dab9380/@@download/attachment/L-LSM11_BGHLV18_24.pdf

tag: antibody

tag: line

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against LSM11. (LSM11_BGHLV18_24)

value: 15 year

value: child

tag: health state

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS842MLZ at ENCODE; https://www.encodeproject.org/ENCBS842MLZ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from HepG2 (ENCLB024SPS)

description:
https://www.encodeproject.org/experiments/ENCSR880DEH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGHLV22)
experiment encode accession: ENCSR880DEH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB024SPS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PNPT1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b9f74218-9703-41ab-9a2c-2c08b1d01326/@@download/attachment/L-PNPT1-BGHLV22-37.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGHLV22-37)

value: male

value: ENCBS648DPW at ENCODE; https://www.encodeproject.org/ENCBS648DPW/


title: shRNA RNA-seq from HepG2 (ENCLB183QVD)

description:
https://www.encodeproject.org/experiments/ENCSR880DEH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGHLV22)
experiment encode accession: ENCSR880DEH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB183QVD
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/66f38738-9524-4e23-8830-46f454db9d3e/@@download/attachment/L-PNPT1-BGHLV22-38.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGHLV22-38)

value: ENCBS547FPL at ENCODE; https://www.encodeproject.org/ENCBS547FPL/


title: siRNA RNA-seq from K562 (ENCLB640DQI)

description:
https://www.encodeproject.org/experiments/ENCSR874ZXG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting E2F4.
experiment encode accession: ENCSR874ZXG
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR074DIJ
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB640DQI
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting E2F4

value: K562 cells treated with a siRNA knockdown against E2F4, used in RNA-seq experiments.

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS769PCI at ENCODE; https://www.encodeproject.org/ENCBS769PCI/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: siRNA RNA-seq from K562 (ENCLB915IQT)

description:
https://www.encodeproject.org/experiments/ENCSR874ZXG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting E2F4.
experiment encode accession: ENCSR874ZXG
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR074DIJ
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB915IQT
size range: >200
spikeins used: /references/ENCSR866KGS/

value: immortalized cell line

value: ENCBS543QWH at ENCODE; https://www.encodeproject.org/ENCBS543QWH/


title: shRNA RNA-seq from HepG2 (ENCLB606NKP)

description:
https://www.encodeproject.org/experiments/ENCSR871BXO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against STIP1. (STIP1-BGHLV22)
experiment encode accession: ENCSR871BXO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB606NKP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting STIP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c2b00f9b-ec9b-4450-a4eb-495131dbc95b/@@download/attachment/L-STIP1-BGHLV22-49.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against STIP1. (STIP1-BGHLV22-49)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS697NJJ at ENCODE; https://www.encodeproject.org/ENCBS697NJJ/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: total RNA-seq from HepG2 (ENCLB866JXA)

description:
https://www.encodeproject.org/experiments/ENCSR862HPO/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial cytosolic fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR862HPO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB866JXA
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line cytosolic fraction

extract_protocol: extraction method: Trizol (LifeTech cat#: 15596-018)

value: male

tag: subcellular fraction term name

value: cytosol

value: Eric Lécuyer, IRCM

value: ENCBS719OUD at ENCODE; https://www.encodeproject.org/ENCBS719OUD/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from HepG2 (ENCLB303PMZ)

description:
https://www.encodeproject.org/experiments/ENCSR490DYI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPLL. (HNRNPLL_BGHLV35)
experiment encode accession: ENCSR490DYI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB303PMZ
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting HNRNPLL

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/df39785f-e313-46c2-8c86-f150871a6f6b/@@download/attachment/L-HNRNPLL_BGHLV35-25.pdf

value: HNRNPLL

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPLL. (HNRNPLL_BGHLV35-25)

value: ENCBS471COV at ENCODE; https://www.encodeproject.org/ENCBS471COV/


title: total RNA-seq from stomach (ENCLB005GBM)

description:
https://www.encodeproject.org/experiments/ENCSR471RUK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's stomach tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR471RUK
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB005GBM
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens stomach tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/98819b35-0b09-4bf0-83c8-2a0eef6512d4/@@download/attachment/296673.pdf

value: stomach

value: tissue

value: Stomach aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS085LTC at ENCODE; https://www.encodeproject.org/ENCBS085LTC/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: total RNA-seq from gastroesophageal sphincter (ENCLB816BDO)

description:
https://www.encodeproject.org/experiments/ENCSR485WBR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the esophagogastric junction obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR485WBR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB816BDO
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens gastroesophageal sphincter tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8712493b-2366-4333-93f7-790cc0e7f424/@@download/attachment/296187.pdf

value: gastroesophageal sphincter

value: Esophagogastric junction tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: ENCBS812ZNH at ENCODE; https://www.encodeproject.org/ENCBS812ZNH/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: shRNA RNA-seq from HepG2 (ENCLB512WWM)

description:
https://www.encodeproject.org/experiments/ENCSR490DYI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPLL. (HNRNPLL_BGHLV35)
experiment encode accession: ENCSR490DYI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB512WWM
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6872185d-6d15-4754-a75e-a468820ad9e2/@@download/attachment/L-HNRNPLL_BGHLV35-26.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPLL. (HNRNPLL_BGHLV35-26)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS519IOB at ENCODE; https://www.encodeproject.org/ENCBS519IOB/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: RAMPAGE from omental fat pad (ENCLB873NNR)

description:
https://www.encodeproject.org/experiments/ENCSR472PZH/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human adipose tissue of omentum tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR472PZH
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR645TCG
encode release date: 2016-08-15
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB873NNR
size range: >200

source_name: Homo sapiens omental fat pad tissue female adult (53 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bd62fc04-6ebc-403f-90a2-e141911e38d7/@@download/attachment/296783.pdf

value: omental fat pad

value: tissue

value: Visceral adipose tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 53 year

value: adult

value: female

value: Thomas Gingeras, CSHL

value: ENCBS460FHO at ENCODE; https://www.encodeproject.org/ENCBS460FHO/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: total RNA-seq from right atrium auricular region (ENCLB789RBC)

description:
https://www.encodeproject.org/experiments/ENCSR457ENP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's heart tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR457ENP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB789RBC
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens right atrium auricular region tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dbcf5313-9608-425c-809b-f4bfbc027226/@@download/attachment/296329.pdf

value: right atrium auricular region

value: Atrial appendage tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: 51 year

value: ENCBS269BVG at ENCODE; https://www.encodeproject.org/ENCBS269BVG/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: total RNA-seq from esophagus squamous epithelium (ENCLB561LCS)

description:
https://www.encodeproject.org/experiments/ENCSR474TRG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the mucosa of the esophagus obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR474TRG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB561LCS
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens esophagus squamous epithelium tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bb6357c9-1783-45f5-9889-8ac2b6f76983/@@download/attachment/296188.pdf

value: esophagus squamous epithelium

value: Esophagus mucosa tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: male

value: ENCBS740AHU at ENCODE; https://www.encodeproject.org/ENCBS740AHU/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: RAMPAGE from thyroid gland (ENCLB526SMY)

description:
https://www.encodeproject.org/experiments/ENCSR477JQM/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human female thyroid gland tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR477JQM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR687HJY
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB526SMY
size range: >200

source_name: Homo sapiens thyroid gland tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6e8da311-0fd2-46ec-9773-3d42e6cb4f70/@@download/attachment/296816.pdf

value: thyroid gland

value: tissue

value: Thyroid aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: ENCBS123ACX at ENCODE; https://www.encodeproject.org/ENCBS123ACX/


title: total RNA-seq from HepG2 (ENCLB805ZYQ)

description:
https://www.encodeproject.org/experiments/ENCSR862HPO/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial cytosolic fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR862HPO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB805ZYQ
size range: >200
spikeins used: /references/ENCSR422PLF/

value: immortalized cell line

value: 15 year

value: child

value: hepatocellular carcinoma

value: cytosol

value: Eric Lécuyer, IRCM

value: ENCBS481IVE at ENCODE; https://www.encodeproject.org/ENCBS481IVE/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: RAMPAGE from esophagus muscularis mucosa (ENCLB518BYJ)

description:
https://www.encodeproject.org/experiments/ENCSR454ZQB/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human muscle layer of esophagus tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR454ZQB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR750ETS
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB518BYJ
size range: >200

source_name: Homo sapiens esophagus muscularis mucosa tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/96f802be-d043-409d-abce-f2c9dd230f67/@@download/attachment/296780.pdf

value: esophagus muscularis mucosa

value: Esophagus muscle layer tissue sent from GTEx to the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS730TAX at ENCODE; https://www.encodeproject.org/ENCBS730TAX/


title: total RNA-seq from suprapubic skin (ENCLB504OXA)

description:
https://www.encodeproject.org/experiments/ENCSR480SLD/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's suprapubic skin tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR480SLD
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB504OXA
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens suprapubic skin tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/24b51eab-b2a7-427f-8637-44faedec941f/@@download/attachment/296380.pdf

value: suprapubic skin

value: tissue

value: Suprapubic skin (not sun exposed) aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: female

value: ENCBS375AFE at ENCODE; https://www.encodeproject.org/ENCBS375AFE/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: shRNA RNA-seq from K562 (ENCLB264ZYW)

description:
https://www.encodeproject.org/experiments/ENCSR494UDF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DKC1. (DKC1_BGKLV32)
experiment encode accession: ENCSR494UDF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB264ZYW
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DKC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2cf11c06-d770-407f-95de-5eefbcebed61/@@download/attachment/L-DKC1_BGKLV32-29.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DKC1. (DKC1_BGKLV32-29)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS813JVE at ENCODE; https://www.encodeproject.org/ENCBS813JVE/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: RAMPAGE from heart left ventricle (ENCLB074XNR)

description:
https://www.encodeproject.org/experiments/ENCSR464UVO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's heart left ventricle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR464UVO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR391VGU
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB074XNR
size range: >200

source_name: Homo sapiens heart left ventricle tissue female adult (53 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c7ce6b45-4614-4c93-ae6f-524139ac96d2/@@download/attachment/296702.pdf

value: heart left ventricle

value: Heart (left ventricle) tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS323ATG at ENCODE; https://www.encodeproject.org/ENCBS323ATG/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: shRNA RNA-seq from HepG2 (ENCLB003VQF)

description:
https://www.encodeproject.org/experiments/ENCSR457WBK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NUP35. (NUP35_BGHLV27)
experiment encode accession: ENCSR457WBK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR960MSV
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB003VQF
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NUP35

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bd3b94c8-fbff-4a90-b7c5-bda6d6c3c42d/@@download/attachment/L-NUP35_BGHLV27-39B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NUP35. (NUP35_BGHLV27-39B)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS832ULV at ENCODE; https://www.encodeproject.org/ENCBS832ULV/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: RAMPAGE from epithelial cell of proximal tubule (ENCLB468FOT)

description:
https://www.encodeproject.org/experiments/ENCSR861MQP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from epithelial cells of proximal tubule (HRPTE piC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR861MQP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR118TVR
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB468FOT
size range: >200

source_name: Homo sapiens epithelial of proximal tubule primary cell

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e7d7f1e6-c309-445b-8f49-94702e8ea485/@@download/attachment/LID295137.pdf

value: epithelial cell of proximal tubule

value: primary cell

value: Human Renal Proximal Tubular Epithelial Cells.

value: unknown

value: not collected

tag: passage number

value: ENCBS492GGP at ENCODE; https://www.encodeproject.org/ENCBS492GGP/

value: Derived from ENCODE donor ENCDO771VPD; https://www.encodeproject.org/ENCDO771VPD/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=4105


title: total RNA-seq from K562 (ENCLB756NMR)

description:
https://www.encodeproject.org/experiments/ENCSR860DWK/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial cytosolic fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR860DWK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB756NMR
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line cytosolic fraction

value: immortalized cell line

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: cytosol

value: Eric Lécuyer, IRCM

value: ENCBS039FPC at ENCODE; https://www.encodeproject.org/ENCBS039FPC/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: shRNA RNA-seq from K562 (ENCLB820VAO)

description:
https://www.encodeproject.org/experiments/ENCSR454KYR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGKLV34)
experiment encode accession: ENCSR454KYR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB820VAO
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SF3A3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2e0f3934-586d-4405-b8ba-c3ad221b513a/@@download/attachment/L-SF3A3_BGKLV34-38.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGKLV34-38)

value: Brenton Graveley, UConn

value: ENCBS122QXN at ENCODE; https://www.encodeproject.org/ENCBS122QXN/


title: shRNA RNA-seq from HepG2 (ENCLB446FEV)

description:
https://www.encodeproject.org/experiments/ENCSR457WBK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NUP35. (NUP35_BGHLV27)
experiment encode accession: ENCSR457WBK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR960MSV
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB446FEV
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f84d8267-7b2a-46bc-a6d1-43298aa5c151/@@download/attachment/L-NUP35_BGHLV27-40B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NUP35. (NUP35_BGHLV27-40B)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS696RMN at ENCODE; https://www.encodeproject.org/ENCBS696RMN/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from K562 (ENCLB621RPN)

description:
https://www.encodeproject.org/experiments/ENCSR454KYR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGKLV34)
experiment encode accession: ENCSR454KYR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB621RPN
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bfa5e21a-d58a-4381-b6a9-b7c6bfe2965b/@@download/attachment/L-SF3A3_BGKLV34-37.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGKLV34-37)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS544UHC at ENCODE; https://www.encodeproject.org/ENCBS544UHC/


title: RAMPAGE from epithelial cell of proximal tubule (ENCLB778DCL)

description:
https://www.encodeproject.org/experiments/ENCSR861MQP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from epithelial cells of proximal tubule (HRPTE piC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR861MQP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR118TVR
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB778DCL
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4533e350-f075-4cf0-aa71-792f22689e5e/@@download/attachment/LID295138.pdf

value: epithelial cell of proximal tubule

value: primary cell

value: Human Renal Proximal Tubular Epithelial Cells.

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

value: ENCBS175CMC at ENCODE; https://www.encodeproject.org/ENCBS175CMC/

value: Derived from ENCODE donor ENCDO359WZJ; https://www.encodeproject.org/ENCDO359WZJ/


title: total RNA-seq from suprapubic skin (ENCLB958TEH)

description:
https://www.encodeproject.org/experiments/ENCSR450ENK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's suprapubic skin tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR450ENK
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB958TEH
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens suprapubic skin tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/20c2c1a4-9e10-477e-86d0-d32101c35c53/@@download/attachment/296378.pdf

value: suprapubic skin

value: tissue

value: Suprapubic skin (not sun exposed) aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: ENCBS586YKG at ENCODE; https://www.encodeproject.org/ENCBS586YKG/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: shRNA RNA-seq from K562 (ENCLB647HVA)

description:
https://www.encodeproject.org/experiments/ENCSR453HKS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against XPO5. (XPO5_BGKLV28)
experiment encode accession: ENCSR453HKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB647HVA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting XPO5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c669dd7c-753c-4237-919f-616466ecc46b/@@download/attachment/L-XPO5_BGKLV28-62.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against XPO5. (XPO5_BGKLV28-62)

value: 53 year

value: adult

value: Brenton Graveley, UConn

value: ENCBS751SXP at ENCODE; https://www.encodeproject.org/ENCBS751SXP/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: total RNA-seq from Peyer's patch (ENCLB561KXB)

description:
https://www.encodeproject.org/experiments/ENCSR450BNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's small intestine tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR450BNZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB561KXB
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens Peyer's patch tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ad4ac056-08e7-40be-aa7c-f8bf46517056/@@download/attachment/296381.pdf

value: Peyer's patch

value: Small intestine aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: female

value: ENCBS168WDM at ENCODE; https://www.encodeproject.org/ENCBS168WDM/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: shRNA RNA-seq from HepG2 (ENCLB598ENU)

description:
https://www.encodeproject.org/experiments/ENCSR871BXO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against STIP1. (STIP1-BGHLV22)
experiment encode accession: ENCSR871BXO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB598ENU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting STIP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fb1119aa-b02d-4351-9f2d-7166f0c7841a/@@download/attachment/L-STIP1-BGHLV22-50.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against STIP1. (STIP1-BGHLV22-50)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS020YDI at ENCODE; https://www.encodeproject.org/ENCBS020YDI/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from K562 (ENCLB234FFX)

description:
https://www.encodeproject.org/experiments/ENCSR453HKS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against XPO5. (XPO5_BGKLV28)
experiment encode accession: ENCSR453HKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB234FFX
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d4117eef-2060-4920-b86c-5de84036955f/@@download/attachment/L-XPO5_BGKLV28-61.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against XPO5. (XPO5_BGKLV28-61)

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS627GSN at ENCODE; https://www.encodeproject.org/ENCBS627GSN/


title: total RNA-seq from K562 (ENCLB291DQQ)

description:
https://www.encodeproject.org/experiments/ENCSR860DWK/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial cytosolic fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR860DWK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB291DQQ
size range: >200
spikeins used: /references/ENCSR866KGS/

extract_protocol: extraction method: Trizol (LifeTech cat#: 15596-018)

value: female

value: Eric Lécuyer, IRCM

value: cytosol

value: ENCBS871QLJ at ENCODE; https://www.encodeproject.org/ENCBS871QLJ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: shRNA RNA-seq from HepG2 (ENCLB959OLD)

description:
https://www.encodeproject.org/experiments/ENCSR856ZRV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV17)
experiment encode accession: ENCSR856ZRV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB959OLD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting Non-specific target control

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/56bb5dfe-a55f-450a-b84a-c48f1a8ddeca/@@download/attachment/L-NT_BGHLV17_64.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target. (NT_BGHLV17_64)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS449AIA at ENCODE; https://www.encodeproject.org/ENCBS449AIA/


title: total RNA-seq from heart left ventricle (ENCLB327BGU)

description:
https://www.encodeproject.org/experiments/ENCSR436QDU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's heart tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR436QDU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB327BGU
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens heart left ventricle tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/99a15fa2-2977-45d3-a397-3699fa6cd275/@@download/attachment/296330.pdf

value: heart left ventricle

value: tissue

value: Heart (left ventricle) tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: 51 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS038PFI at ENCODE; https://www.encodeproject.org/ENCBS038PFI/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: shRNA RNA-seq from K562 (ENCLB992TEQ)

description:
https://www.encodeproject.org/experiments/ENCSR856CJK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX55. (DDX55_BGKLV21)
experiment encode accession: ENCSR856CJK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB992TEQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX55

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/40ba2ffb-3492-48a7-8df0-c0f83bded678/@@download/attachment/L-DDX55_BGKLV21_7_17560.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX55. (DDX55_BGKLV21_7_17560)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS111GYT at ENCODE; https://www.encodeproject.org/ENCBS111GYT/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: RAMPAGE from OCI-LY7 (ENCLB809QEF)

description:
https://www.encodeproject.org/experiments/ENCSR855LXJ/
***************
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, a peripherial blood sample from a 48 year old male with Non-Hodgkin lymphoma. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR855LXJ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR001HHK
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB809QEF
size range: >200

source_name: Homo sapiens OCI-LY7 immortalized cell line

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/aa753391-af0a-4da5-91d2-4b9135ac426a/@@download/attachment/289916.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: 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: total RNA-seq from gastrocnemius medialis (ENCLB236RKR)

description:
https://www.encodeproject.org/experiments/ENCSR853BNH/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's skeletal muscle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR853BNH
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB236RKR
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens gastrocnemius medialis tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6887491c-1ffc-4a5c-8298-c58b6acd1acb/@@download/attachment/295876.pdf

value: gastrocnemius medialis

value: tissue

value: Skeletal Muscle GTEx tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS543SZC at ENCODE; https://www.encodeproject.org/ENCBS543SZC/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: RAMPAGE from OCI-LY7 (ENCLB850OBN)

description:
https://www.encodeproject.org/experiments/ENCSR855LXJ/
***************
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, a peripherial blood sample from a 48 year old male with Non-Hodgkin lymphoma. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR855LXJ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR001HHK
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB850OBN
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/51f61065-6bc5-4d98-81af-d33921aac860/@@download/attachment/289915.pdf

value: immortalized cell line

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


title: shRNA RNA-seq from K562 (ENCLB036KZM)

description:
https://www.encodeproject.org/experiments/ENCSR856CJK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX55. (DDX55_BGKLV21)
experiment encode accession: ENCSR856CJK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB036KZM
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol: extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX55. (DDX55_BGKLV21_8_17561)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS144YDQ at ENCODE; https://www.encodeproject.org/ENCBS144YDQ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: shRNA RNA-seq from HepG2 (ENCLB028XKT)

description:
https://www.encodeproject.org/experiments/ENCSR853PBF/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DHX30 in HepG2 cells followed by RNA-seq. (DHX30-32-BGHLV20)
experiment encode accession: ENCSR853PBF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB028XKT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DHX30

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3007d608-27b9-45cf-9159-cf55c389fee4/@@download/attachment/L-DHX30-32-BGHLV20-20_17715.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DHX30. (DHX30-32-BGHLV20-20_17715)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS787BXG at ENCODE; https://www.encodeproject.org/ENCBS787BXG/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from K562 (ENCLB114RXE)

description:
https://www.encodeproject.org/experiments/ENCSR438MDN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV21-B)
experiment encode accession: ENCSR438MDN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB114RXE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting Non-specific target control

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c8c60d10-21cc-4a14-9aa9-035547ac8815/@@download/attachment/L-NT_BGKLV21-2B.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (NT_BGKLV21-2B)

value: adult

value: ENCBS530MLH at ENCODE; https://www.encodeproject.org/ENCBS530MLH/


title: shRNA RNA-seq from K562 (ENCLB101NSC)

description:
https://www.encodeproject.org/experiments/ENCSR438MDN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV21-B)
experiment encode accession: ENCSR438MDN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB101NSC
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4f631480-a86c-4763-adb3-b7037f2bff7e/@@download/attachment/L-NT_BGKLV21-1B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (NT_BGKLV21-1B)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS800RVX at ENCODE; https://www.encodeproject.org/ENCBS800RVX/


title: shRNA RNA-seq from HepG2 (ENCLB634DST)

description:
https://www.encodeproject.org/experiments/ENCSR853PBF/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DHX30 in HepG2 cells followed by RNA-seq. (DHX30-32-BGHLV20)
experiment encode accession: ENCSR853PBF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB634DST
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bb8bd84a-b5e5-4517-955d-368c6d70cdc2/@@download/attachment/L-DHX30-32-BGHLV20-19_17714.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DHX30. (DHX30-32-BGHLV20-19_17714)

value: 15 year

value: child

value: ENCBS402BUA at ENCODE; https://www.encodeproject.org/ENCBS402BUA/


title: total RNA-seq from gastrocnemius medialis (ENCLB011CNK)

description:
https://www.encodeproject.org/experiments/ENCSR853BNH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's skeletal muscle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR853BNH
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB011CNK
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/86ab8389-f77c-44df-b5b4-7351bffaa231/@@download/attachment/295875.pdf

value: gastrocnemius medialis

value: tissue

value: Skeletal Muscle GTEx tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS543SZC at ENCODE; https://www.encodeproject.org/ENCBS543SZC/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: total RNA-seq from breast epithelium (ENCLB197GXK)

description:
https://www.encodeproject.org/experiments/ENCSR438YPF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's adipose tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR438YPF
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB197GXK
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens breast epithelium tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5347ecf9-4def-48be-ac30-e5a84a473dbc/@@download/attachment/296318.pdf

value: breast epithelium

value: Mammary breast tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: adult

value: ENCBS160KYO at ENCODE; https://www.encodeproject.org/ENCBS160KYO/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: total RNA-seq from breast epithelium (ENCLB483RUB)

description:
https://www.encodeproject.org/experiments/ENCSR434TEU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's adipose tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR434TEU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB483RUB
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens breast epithelium tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4b683a2c-935e-49cc-a4d7-586026cb9d04/@@download/attachment/296317.pdf

value: 53 year

value: female

value: ENCBS490RBH at ENCODE; https://www.encodeproject.org/ENCBS490RBH/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: RAMPAGE from SK-N-DZ (ENCLB037CTF)

description:
https://www.encodeproject.org/experiments/ENCSR852KOV/
***************
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 PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR852KOV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR569JKX
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB037CTF
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/448a6b80-2bdd-486d-9646-ffe1706870b6/@@download/attachment/LID294657.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: cytosol

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

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: shRNA RNA-seq from HepG2 (ENCLB921NGP)

description:
https://www.encodeproject.org/experiments/ENCSR856ZRV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV17)
experiment encode accession: ENCSR856ZRV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB921NGP
size range: >200
spikeins used: /references/ENCSR449DXG/
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a7efcb06-68cd-4cc3-8596-ff6e9c41f9bf/@@download/attachment/L-NT_BGHLV17_63.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target. (NT_BGHLV17_63)

value: 15 year

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS224OGG at ENCODE; https://www.encodeproject.org/ENCBS224OGG/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: total RNA-seq from upper lobe of left lung (ENCLB308EJA)

description:
https://www.encodeproject.org/experiments/ENCSR425RGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's lung tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR425RGZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB308EJA
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens upper lobe of left lung tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/da79b00c-e3f4-4a78-b9ff-02340bab044d/@@download/attachment/296296.pdf

value: upper lobe of left lung

value: tissue

value: Lung tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: adult

value: female

value: Thomas Gingeras, CSHL

value: ENCBS711XVO at ENCODE; https://www.encodeproject.org/ENCBS711XVO/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: shRNA RNA-seq from HepG2 (ENCLB669JPP)

description:
https://www.encodeproject.org/experiments/ENCSR851KEX/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PPIL4 in HepG2 cells followed by RNA-seq. (PPIL4-BGHLV20)
experiment encode accession: ENCSR851KEX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB669JPP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PPIL4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f28c54da-81ec-46d5-a32d-9b5b97c110c1/@@download/attachment/L-PPIL4-BGHLV20-51_17732.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PPIL4. (PPIL4-BGHLV20-51_17732)

value: child

value: ENCBS715WYI at ENCODE; https://www.encodeproject.org/ENCBS715WYI/


title: shRNA RNA-seq from HepG2 (ENCLB170JCY)

description:
https://www.encodeproject.org/experiments/ENCSR422JMS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SSRP1. (SSRP1_BGHLV27)
experiment encode accession: ENCSR422JMS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB170JCY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SSRP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f16b95f6-1e23-4d79-9877-662e1d30bbb6/@@download/attachment/L-SSRP1_BGHLV27-52.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against SSRP1 (SSRP1_BGHLV27-52)

value: 15 year

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS101OYY at ENCODE; https://www.encodeproject.org/ENCBS101OYY/


title: shRNA RNA-seq from HepG2 (ENCLB103UVG)

description:
https://www.encodeproject.org/experiments/ENCSR426UUG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF2. (U2AF2_BGHLV26)
experiment encode accession: ENCSR426UUG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB103UVG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting U2AF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/02404dac-d1cd-4069-a7fa-0c931658b4ce/@@download/attachment/L-U2AF2_BGHLV26_63.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA againstU2AF2 (U2AF2_BGHLV26_63)

value: ENCBS835EOX at ENCODE; https://www.encodeproject.org/ENCBS835EOX/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from K562 (ENCLB844MEN)

description:
https://www.encodeproject.org/experiments/ENCSR424QCW/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV36)
experiment encode accession: ENCSR424QCW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB844MEN
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/94e83620-0317-48b8-8b85-b7f3c2b7c8a1/@@download/attachment/L-NT_BGKLV36-2.pdf

value: Control

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV36-2)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS131LFM at ENCODE; https://www.encodeproject.org/ENCBS131LFM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: shRNA RNA-seq from K562 (ENCLB901MPM)

description:
https://www.encodeproject.org/experiments/ENCSR424QCW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV36)
experiment encode accession: ENCSR424QCW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB901MPM
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ea2d1823-60f6-4f05-b81b-c979821d12dd/@@download/attachment/L-NT_BGKLV36-1.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV36-1)

value: ENCBS405CUM at ENCODE; https://www.encodeproject.org/ENCBS405CUM/


title: RAMPAGE from subcutaneous adipose tissue (ENCLB307HTR)

description:
https://www.encodeproject.org/experiments/ENCSR419MZM/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human adipose tissue tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR419MZM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR504NIU
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB307HTR
size range: >200

source_name: Homo sapiens subcutaneous adipose tissue female adult (53 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cd7054eb-88ec-4ff7-8e79-00e39cf325cc/@@download/attachment/296820.pdf

value: subcutaneous adipose tissue

value: tissue

value: Subcutaneous adipose tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: Thomas Gingeras, CSHL

value: ENCBS280PMM at ENCODE; https://www.encodeproject.org/ENCBS280PMM/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: shRNA RNA-seq from HepG2 (ENCLB216TOV)

description:
https://www.encodeproject.org/experiments/ENCSR422JMS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SSRP1. (SSRP1_BGHLV27)
experiment encode accession: ENCSR422JMS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB216TOV
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/89f975d9-8ebc-4044-9f3e-4c917041dcb0/@@download/attachment/L-SSRP1_BGHLV27-51.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against SSRP1 (SSRP1_BGHLV27-51)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS771QGO at ENCODE; https://www.encodeproject.org/ENCBS771QGO/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from HepG2 (ENCLB189KTF)

description:
https://www.encodeproject.org/experiments/ENCSR851KEX/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PPIL4 in HepG2 cells followed by RNA-seq. (PPIL4-BGHLV20)
experiment encode accession: ENCSR851KEX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB189KTF
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e8961dec-5a85-4adb-b961-b208ab4832a6/@@download/attachment/L-PPIL4-BGHLV20-52_17733.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PPIL4. (PPIL4-BGHLV20-52_17733)

value: ENCBS765FVI at ENCODE; https://www.encodeproject.org/ENCBS765FVI/


title: shRNA RNA-seq from K562 (ENCLB140GUC)

description:
https://www.encodeproject.org/experiments/ENCSR850PWM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against ZRANB2 in K562 cells followed by RNA-seq. (ZRANB2 BGKLV13)
experiment encode accession: ENCSR850PWM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB140GUC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting ZRANB2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7772578d-4a07-4d98-aff5-be0349d2375b/@@download/attachment/L-ZRANB2_BGKLV13_11.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ZRANB2.(ZRANB2_BGKLV13_11)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS433WAM at ENCODE; https://www.encodeproject.org/ENCBS433WAM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: shRNA RNA-seq from HepG2 (ENCLB108MYA)

description:
https://www.encodeproject.org/experiments/ENCSR426UUG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF2. (U2AF2_BGHLV26)
experiment encode accession: ENCSR426UUG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB108MYA
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d997602e-2c46-4d5c-b028-4b7103bbcaa2/@@download/attachment/L-U2AF2_BGHLV26_64.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA againstU2AF2 (U2AF2_BGHLV26_64)

value: 15 year

value: child

value: male

value: ENCBS218GVF at ENCODE; https://www.encodeproject.org/ENCBS218GVF/


title: shRNA RNA-seq from K562 (ENCLB013QNK)

description:
https://www.encodeproject.org/experiments/ENCSR850PWM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against ZRANB2 in K562 cells followed by RNA-seq. (ZRANB2 BGKLV13)
experiment encode accession: ENCSR850PWM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB013QNK
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6f083b8c-3779-4d37-a71a-497c2b84eaf7/@@download/attachment/L-ZRANB2_BGKLV13_12.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ZRANB2.(ZRANB2_BGKLV13_12)

value: Brenton Graveley, UConn

value: ENCBS995UMN at ENCODE; https://www.encodeproject.org/ENCBS995UMN/


title: shRNA RNA-seq from K562 (ENCLB280WVM)

description:
https://www.encodeproject.org/experiments/ENCSR416ZJH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PABPN1. (PABPN1_BGKLV28)
experiment encode accession: ENCSR416ZJH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB280WVM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PABPN1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c5550311-bafe-4f3b-918e-84461a68c895/@@download/attachment/L-PABPN1_BGKLV28-35.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PABPN1. (PABPN1_BGKLV28-35)

value: ENCBS753DCN at ENCODE; https://www.encodeproject.org/ENCBS753DCN/


title: total RNA-seq from transverse colon (ENCLB364ORB)

description:
https://www.encodeproject.org/experiments/ENCSR403SZN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's transverse colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR403SZN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB364ORB
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens transverse colon tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/af9390eb-4db6-4992-8c82-c29f4b3349b5/@@download/attachment/296670.pdf

value: transverse colon

value: tissue

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS999VTF at ENCODE; https://www.encodeproject.org/ENCBS999VTF/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: shRNA RNA-seq from K562 (ENCLB528JFY)

description:
https://www.encodeproject.org/experiments/ENCSR416ZJH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PABPN1. (PABPN1_BGKLV28)
experiment encode accession: ENCSR416ZJH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB528JFY
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c99a3ced-84bb-4a84-bbfd-0ca17f2979fe/@@download/attachment/L-PABPN1_BGKLV28-36.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PABPN1. (PABPN1_BGKLV28-36)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS165ART at ENCODE; https://www.encodeproject.org/ENCBS165ART/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: total RNA-seq from upper lobe of left lung (ENCLB837IVL)

description:
https://www.encodeproject.org/experiments/ENCSR406SAW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's lung tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR406SAW
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB837IVL
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa4e0cb7-610b-4841-8e0f-c142699e48f5/@@download/attachment/296293.pdf

value: upper lobe of left lung

value: Lung tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.

value: ENCBS596PXT at ENCODE; https://www.encodeproject.org/ENCBS596PXT/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: shRNA RNA-seq from HepG2 (ENCLB476PQP)

description:
https://www.encodeproject.org/experiments/ENCSR850FEH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against GRWD1 in HepG2 cells followed by RNA-seq. (GRWD1_BGHLV18)
experiment encode accession: ENCSR850FEH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB476PQP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting GRWD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c1cc1f89-de57-4a0a-a97a-606f515cd1a4/@@download/attachment/L-GRWD1_BGHLV18_14.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GRWD1. (GRWD1_BGHLV18_14)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS400CWC at ENCODE; https://www.encodeproject.org/ENCBS400CWC/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: RAMPAGE from H4 (ENCLB248FWG)

description:
https://www.encodeproject.org/experiments/ENCSR850NOP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line H4 isolated from a neuroglioma of a 37 year old caucasian male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR850NOP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR919QJT
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB248FWG
size range: >200

source_name: Homo sapiens H4 immortalized cell line

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1157a644-01ff-4265-a33d-40c3ef58895f/@@download/attachment/293016.pdf

value: 37 year

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS836LDB at ENCODE; https://www.encodeproject.org/ENCBS836LDB/

value: Derived from ENCODE donor ENCDO337AAA; https://www.encodeproject.org/ENCDO337AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1239; http://web.expasy.org/cellosaurus/CVCL_1239


title: shRNA RNA-seq from HepG2 (ENCLB811DNQ)

description:
https://www.encodeproject.org/experiments/ENCSR850FEH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against GRWD1 in HepG2 cells followed by RNA-seq. (GRWD1_BGHLV18)
experiment encode accession: ENCSR850FEH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB811DNQ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/91e885dd-7216-4d60-8ba7-0ad730ae5bde/@@download/attachment/L-GRWD1_BGHLV18_13.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GRWD1. (GRWD1_BGHLV18_13)

value: ENCBS385LUB at ENCODE; https://www.encodeproject.org/ENCBS385LUB/


title: total RNA-seq from thoracic aorta (ENCLB351PPD)

description:
https://www.encodeproject.org/experiments/ENCSR837ZLY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's aorta tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR837ZLY
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB351PPD
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens thoracic aorta tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6564df36-ad2a-4f25-9d76-e72d7cee575d/@@download/attachment/295918.pdf

value: thoracic aorta

value: tissue

value: Aorta tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS560HZX at ENCODE; https://www.encodeproject.org/ENCBS560HZX/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: total RNA-seq from liver (ENCLB420PUQ)

description:
https://www.encodeproject.org/experiments/ENCSR388ZNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on Adult Human Liver Tissue STL010,STL011
experiment encode accession: ENCSR388ZNJ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB420PUQ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Homo sapiens liver tissue male adult (32 years)

value: liver

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: male

value: healthy with non-obstructive CAD (coronary artery disease)

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: RAMPAGE from SK-N-DZ (ENCLB383LUE)

description:
https://www.encodeproject.org/experiments/ENCSR852KOV/
***************
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 PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR852KOV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR569JKX
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB383LUE
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/85105df5-d4ac-4aa6-8588-3f7f68a96cff/@@download/attachment/LID294656.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: 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: shRNA RNA-seq from HepG2 (ENCLB852IWC)

description:
https://www.encodeproject.org/experiments/ENCSR838SMC/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPS5 in HepG2 cells followed by RNA-seq. (RPS5_BGHLV18)
experiment encode accession: ENCSR838SMC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB852IWC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RPS5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b8b31c8b-702d-45c6-ba77-8d0c64c612a6/@@download/attachment/L-RPS5_BGHLV18_57.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS5. (RPS5_BGHLV18_57)

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS644PWW at ENCODE; https://www.encodeproject.org/ENCBS644PWW/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from HepG2 (ENCLB386NMT)

description:
https://www.encodeproject.org/experiments/ENCSR838SMC/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RPS5 in HepG2 cells followed by RNA-seq. (RPS5_BGHLV18)
experiment encode accession: ENCSR838SMC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB386NMT
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5b149f5b-368c-4819-aa48-e3661cbf1d6d/@@download/attachment/L-RPS5_BGHLV18_58.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS5. (RPS5_BGHLV18_58)

value: male

value: ENCBS729TZG at ENCODE; https://www.encodeproject.org/ENCBS729TZG/


title: total RNA-seq from heart left ventricle (ENCLB273VNM)

description:
https://www.encodeproject.org/experiments/ENCSR391VGU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's heart tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR391VGU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB273VNM
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens heart left ventricle tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f7b6fbf1-3ba5-4d58-896f-ee706e9e400c/@@download/attachment/296328.pdf

value: heart left ventricle

value: tissue

value: Heart (left ventricle) tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: 53 year

value: adult

value: female

value: Thomas Gingeras, CSHL

value: ENCBS323ATG at ENCODE; https://www.encodeproject.org/ENCBS323ATG/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: RAMPAGE from Karpas-422 (ENCLB314YJK)

description:
https://www.encodeproject.org/experiments/ENCSR836WAX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line Karpas-422. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR836WAX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR314LXG
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB314YJK
size range: >200

source_name: Homo sapiens Karpas-422 immortalized cell line

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3adee7f0-683f-42f2-aba7-479f20d0cecb/@@download/attachment/289918.pdf

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: human B cell non-Hodgkin's lymphoma

value: Bradley Bernstein, Broad

value: ENCBS870AAA at ENCODE; https://www.encodeproject.org/ENCBS870AAA/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: shRNA RNA-seq from HepG2 (ENCLB155KOE)

description:
https://www.encodeproject.org/experiments/ENCSR389HFU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FTO. (FTO_BGHLV35)
experiment encode accession: ENCSR389HFU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB155KOE
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting FTO

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c6198250-3f2e-4062-b804-3ec51ffb1b54/@@download/attachment/L-FTO_BGHLV35-18.pdf

value: FTO

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FTO. (FTO_BGHLV35-18)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS172JGT at ENCODE; https://www.encodeproject.org/ENCBS172JGT/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: RAMPAGE from Karpas-422 (ENCLB646FZT)

description:
https://www.encodeproject.org/experiments/ENCSR836WAX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line Karpas-422. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR836WAX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR314LXG
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB646FZT
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/eabb2918-73f1-44c7-8564-e27205fea563/@@download/attachment/289917.pdf

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: adult

value: female

value: ENCBS869AAA at ENCODE; https://www.encodeproject.org/ENCBS869AAA/


title: total RNA-seq from liver (ENCLB869UHR)

description:
https://www.encodeproject.org/experiments/ENCSR388ZNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-Seq on Adult Human Liver Tissue STL010,STL011
experiment encode accession: ENCSR388ZNJ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB869UHR
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Homo sapiens liver tissue female child (4 years)

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/