title: shRNA RNA-seq from K562 (ENCLB313YDO)

description:
https://www.encodeproject.org/experiments/ENCSR945GUR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NAA15. (NAA15_BGKLV32)
experiment encode accession: ENCSR945GUR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB313YDO
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/00d69bdd-bc7d-4b0b-bb66-fb57351789cb/@@download/attachment/L-NAA15_BGKLV32-42.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against NAA15. (NAA15_BGKLV32-42)

value: Brenton Graveley, UConn

value: ENCBS331OZE at ENCODE; https://www.encodeproject.org/ENCBS331OZE/


title: shRNA RNA-seq from HepG2 (ENCLB124CFU)

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/ENCSR960MSV/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV27B)
experiment encode accession: ENCSR960MSV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB124CFU
size range: >200
spikeins used: /references/ENCSR358OMW/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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/72832a1d-8e38-4e2a-aa1e-e4c6a0ad5a24/@@download/attachment/L-NT_BGHLV27-2B.pdf

tag: antibody

value: Control

tag: line

tag: description

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV27-2B)

tag: biosample encode accession

tag: age

value: 15 year

tag: dev stage

value: child

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

tag: lab

tag: link

value: ENCBS611WLI at ENCODE; https://www.encodeproject.org/ENCBS611WLI/

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 (ENCLB698ECG)

description:
https://www.encodeproject.org/experiments/ENCSR958KSY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP8. (AKAP8_BGHLV27)
experiment encode accession: ENCSR958KSY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB698ECG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting AKAP8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c276f049-6b69-453e-9100-d2c54b60f997/@@download/attachment/L-AKAP8_BGHLV27-6.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against AKAP8 (AKAP8_BGHLV27-6)

value: ENCBS818CDN at ENCODE; https://www.encodeproject.org/ENCBS818CDN/


title: shRNA RNA-seq from K562 (ENCLB628ZZW)

description:
https://www.encodeproject.org/experiments/ENCSR943LIB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SNRNP200. (SNRNP200_BGKLV28)
experiment encode accession: ENCSR943LIB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB628ZZW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SNRNP200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4ddb42ab-9d4a-43fc-925a-02a3c3e80725/@@download/attachment/L-SNRNP200_BGKLV28-54.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SNRNP200. (SNRNP200_BGKLV28-54)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS675OVW at ENCODE; https://www.encodeproject.org/ENCBS675OVW/

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 (ENCLB364ROA)

description:
https://www.encodeproject.org/experiments/ENCSR958KSY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP8. (AKAP8_BGHLV27)
experiment encode accession: ENCSR958KSY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB364ROA
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/67d8e9e6-f99f-4a15-a911-3562f3592924/@@download/attachment/L-AKAP8_BGHLV27-5.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against AKAP8 (AKAP8_BGHLV27-5)

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS089VZP at ENCODE; https://www.encodeproject.org/ENCBS089VZP/


title: RAMPAGE from right lobe of liver (ENCLB064JHN)

description:
https://www.encodeproject.org/experiments/ENCSR941SAZ/
***************
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 right lobe of liver 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: ENCSR941SAZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR504QMK
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB064JHN
size range: >200

source_name: Homo sapiens right lobe of liver 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/b5209ff1-4e7b-4e11-a344-cc96fba6bbd6/@@download/attachment/296701.pdf

value: right lobe of liver

value: tissue

value: Liver tissue from a 53 year old female received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: Thomas Gingeras, CSHL

value: ENCBS796JPW at ENCODE; https://www.encodeproject.org/ENCBS796JPW/

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


title: RAMPAGE from adrenal gland (ENCLB950ZIH)

description:
https://www.encodeproject.org/experiments/ENCSR930XIH/
***************
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 adrenal gland 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: ENCSR930XIH
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR754WLW
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB950ZIH
size range: >200

source_name: Homo sapiens adrenal gland 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/c71ee04e-c2f5-49de-b95a-a335b608e7be/@@download/attachment/296723.pdf

value: adrenal gland

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

value: 53 year

value: adult

value: ENCBS006KAW at ENCODE; https://www.encodeproject.org/ENCBS006KAW/


title: RAMPAGE from esophagus squamous epithelium (ENCLB156IZG)

description:
https://www.encodeproject.org/experiments/ENCSR930RDW/
***************
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 esophagus mucosa 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: ENCSR930RDW
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR351OTL
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB156IZG
size range: >200

source_name: Homo sapiens esophagus squamous epithelium 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/dd7ce6e0-5237-44dc-85b3-e76161debac4/@@download/attachment/296726.pdf

value: esophagus squamous epithelium

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

value: female

value: ENCBS504VDB at ENCODE; https://www.encodeproject.org/ENCBS504VDB/


title: shRNA RNA-seq from HepG2 (ENCLB516RRN)

description:
https://www.encodeproject.org/experiments/ENCSR929PXS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CEBPZ. (CEBPZ_BGHLV30)
experiment encode accession: ENCSR929PXS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB516RRN
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6f297267-a28c-480f-858f-a603cc3cdeaa/@@download/attachment/L-CEBPZ_BGHLV30-19.pdf

value: CEBPZ

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CEBPZ. (CEBPZ_BGHLV30-19)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS686ZOG at ENCODE; https://www.encodeproject.org/ENCBS686ZOG/

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 (ENCLB917OAO)

description:
https://www.encodeproject.org/experiments/ENCSR943LIB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SNRNP200. (SNRNP200_BGKLV28)
experiment encode accession: ENCSR943LIB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB917OAO
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/c9383f72-8e71-4239-bd5b-db7c579823ed/@@download/attachment/L-SNRNP200_BGKLV28-53.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SNRNP200. (SNRNP200_BGKLV28-53)

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS982AOH at ENCODE; https://www.encodeproject.org/ENCBS982AOH/

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 (ENCLB168TMK)

description:
https://www.encodeproject.org/experiments/ENCSR968YWY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGHLV35)
experiment encode accession: ENCSR968YWY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB168TMK
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bc868782-2434-4340-9ea3-e1a0a167dc11/@@download/attachment/L-GPKOW_BGHLV35-21.pdf

value: GPKOW

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGHLV35-21)

value: ENCBS095YKY at ENCODE; https://www.encodeproject.org/ENCBS095YKY/


title: shRNA RNA-seq from HepG2 (ENCLB644YDC)

description:
https://www.encodeproject.org/experiments/ENCSR929PXS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CEBPZ. (CEBPZ_BGHLV30)
experiment encode accession: ENCSR929PXS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB644YDC
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/97e1398d-3e5a-4bd9-a2c9-ae4a0e958a37/@@download/attachment/L-CEBPZ_BGHLV30-20.pdf

value: CEBPZ

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CEBPZ. (CEBPZ_BGHLV30-20)

value: 15 year

value: child

value: male

value: ENCBS236NEP at ENCODE; https://www.encodeproject.org/ENCBS236NEP/


title: shRNA RNA-seq from HepG2 (ENCLB908ZJN)

description:
https://www.encodeproject.org/experiments/ENCSR968YWY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGHLV35)
experiment encode accession: ENCSR968YWY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB908ZJN
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/0967665b-a0bb-4304-9529-47cedbfb46c7/@@download/attachment/L-GPKOW_BGHLV35-22.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GPKOW. (GPKOW_BGHLV35-22)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS014HHE at ENCODE; https://www.encodeproject.org/ENCBS014HHE/

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


title: shRNA RNA-seq from HepG2 (ENCLB330IUF)

description:
https://www.encodeproject.org/experiments/ENCSR925SYZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against BOP1. (BOP1_BGHLV35)
experiment encode accession: ENCSR925SYZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB330IUF
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting BOP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3a0b2ad3-83a7-4f0d-8cc9-20a8f2b2dc06/@@download/attachment/L-BOP1_BGHLV35-10.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against BOP1. (BOP1_BGHLV35-10)

value: ENCBS622TME at ENCODE; https://www.encodeproject.org/ENCBS622TME/


title: shRNA RNA-seq from HepG2 (ENCLB165TOO)

description:
https://www.encodeproject.org/experiments/ENCSR910ECL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP3. (UTP3_BGHLV33)
experiment encode accession: ENCSR910ECL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB165TOO
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting UTP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bbae7806-1a88-4d99-bd09-d9cf8333a845/@@download/attachment/L-UTP3_BGHLV33-38.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP3. (UTP3_BGHLV33-38)

value: ENCBS117URM at ENCODE; https://www.encodeproject.org/ENCBS117URM/


title: shRNA RNA-seq from K562 (ENCLB562NRU)

description:
https://www.encodeproject.org/experiments/ENCSR902WSK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SSRP1. (SSRP1_BGKLV29)
experiment encode accession: ENCSR902WSK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB562NRU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 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/c9e68a42-0e98-4788-bd10-48057de7cc2a/@@download/attachment/L-SSRP1_BGKLV29-55.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SSRP1. (SSRP1_BGKLV29-55)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS969AZO at ENCODE; https://www.encodeproject.org/ENCBS969AZO/

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 spleen (ENCLB088AOF)

description:
https://www.encodeproject.org/experiments/ENCSR900SGE/
***************
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 spleen 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: ENCSR900SGE
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB088AOF
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens spleen tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cac03959-192d-4043-9a9c-2e1a479dc9b3/@@download/attachment/296575.pdf

value: spleen

value: tissue

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

value: Thomas Gingeras, CSHL

value: ENCBS213OJV at ENCODE; https://www.encodeproject.org/ENCBS213OJV/

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


title: shRNA RNA-seq from K562 (ENCLB576JOX)

description:
https://www.encodeproject.org/experiments/ENCSR902WSK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SSRP1. (SSRP1_BGKLV29)
experiment encode accession: ENCSR902WSK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB576JOX
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/0c58aca7-36b9-4875-8ed9-054b6477264c/@@download/attachment/L-SSRP1_BGKLV29-56.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SSRP1. (SSRP1_BGKLV29-56)

value: Brenton Graveley, UConn

value: ENCBS638OEZ at ENCODE; https://www.encodeproject.org/ENCBS638OEZ/


title: shRNA RNA-seq from HepG2 (ENCLB452BSZ)

description:
https://www.encodeproject.org/experiments/ENCSR925SYZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against BOP1. (BOP1_BGHLV35)
experiment encode accession: ENCSR925SYZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB452BSZ
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/e7087683-c03f-4ce2-a197-ec200aeddde7/@@download/attachment/L-BOP1_BGHLV35-9.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against BOP1. (BOP1_BGHLV35-9)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS838BWA at ENCODE; https://www.encodeproject.org/ENCBS838BWA/

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


title: shRNA RNA-seq from HepG2 (ENCLB419UML)

description:
https://www.encodeproject.org/experiments/ENCSR896MMU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against MSI2. (MSI2_BGHLV30)
experiment encode accession: ENCSR896MMU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB419UML
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting MSI2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/68af9e3f-c444-4076-b924-269fa530c3ec/@@download/attachment/L-MSI2_BGHLV30-43.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MSI2. (MSI2_BGHLV30-43)

value: ENCBS810BDN at ENCODE; https://www.encodeproject.org/ENCBS810BDN/

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


title: shRNA RNA-seq from HepG2 (ENCLB027HHT)

description:
https://www.encodeproject.org/experiments/ENCSR896MMU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against MSI2. (MSI2_BGHLV30)
experiment encode accession: ENCSR896MMU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB027HHT
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/5d7a37a0-3897-413f-b5f0-6a08eed99c9d/@@download/attachment/L-MSI2_BGHLV30-44.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MSI2. (MSI2_BGHLV30-44)

value: ENCBS862LXP at ENCODE; https://www.encodeproject.org/ENCBS862LXP/


title: shRNA RNA-seq from K562 (ENCLB674KGB)

description:
https://www.encodeproject.org/experiments/ENCSR898OPN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBM17. (RBM17_BGKLV29-B)
experiment encode accession: ENCSR898OPN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR118EFE
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB674KGB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RBM17

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d395205f-e014-4185-a70c-9022c882a117/@@download/attachment/L-RBM17_BGKLV29-54B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM17. (RBM17_BGKLV29-54B)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS934FPI at ENCODE; https://www.encodeproject.org/ENCBS934FPI/

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 esophagus muscularis mucosa (ENCLB448KNY)

description:
https://www.encodeproject.org/experiments/ENCSR883KJV/
***************
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: ENCSR883KJV
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR182CBU
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB448KNY
size range: >200

source_name: Homo sapiens esophagus muscularis mucosa tissue male adult (37 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/81486b84-49ad-4220-941e-d97dccd16e1a/@@download/attachment/296744.pdf

value: esophagus muscularis mucosa

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS146EHL at ENCODE; https://www.encodeproject.org/ENCBS146EHL/

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


title: shRNA RNA-seq from HepG2 (ENCLB468SBU)

description:
https://www.encodeproject.org/experiments/ENCSR910ECL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP3. (UTP3_BGHLV33)
experiment encode accession: ENCSR910ECL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB468SBU
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/f2b70b3c-7e7c-41b6-a851-2a59f3151f39/@@download/attachment/L-UTP3_BGHLV33-37.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP3. (UTP3_BGHLV33-37)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS049AMV at ENCODE; https://www.encodeproject.org/ENCBS049AMV/

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


title: shRNA RNA-seq from K562 (ENCLB824XXA)

description:
https://www.encodeproject.org/experiments/ENCSR898OPN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBM17. (RBM17_BGKLV29-B)
experiment encode accession: ENCSR898OPN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR118EFE
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB824XXA
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/6d3eda0b-4103-404d-8161-e6ea6fdb4cde/@@download/attachment/L-RBM17_BGKLV29-53B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM17. (RBM17_BGKLV29-53B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS730QNJ at ENCODE; https://www.encodeproject.org/ENCBS730QNJ/

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 (ENCLB474XTL)

description:
https://www.encodeproject.org/experiments/ENCSR896CFV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGHLV35)
experiment encode accession: ENCSR896CFV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB474XTL
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SF3B1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3b7e1cd1-3d95-4c4a-83de-4ead8db08e65/@@download/attachment/L-SF3B1_BGHLV35-42.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGHLV35-42)

value: male

value: ENCBS873YWS at ENCODE; https://www.encodeproject.org/ENCBS873YWS/


title: RAMPAGE from spleen (ENCLB243VWA)

description:
https://www.encodeproject.org/experiments/ENCSR887SSW/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human spleen tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR887SSW
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR194HVU
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB243VWA
size range: >200

source_name: Homo sapiens spleen 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/b0a894d7-6987-4f27-b623-3788d8c3e3e4/@@download/attachment/296786.pdf

value: spleen

value: tissue

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

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS253SDK at ENCODE; https://www.encodeproject.org/ENCBS253SDK/

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


title: total RNA-seq from GM12878 (ENCLB360EJW)

description:
https://www.encodeproject.org/experiments/ENCSR889TRN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of GM12878 bulk prep 10 ng
experiment encode accession: ENCSR889TRN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB360EJW
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

value: GM12878 growth

value: unknown

value: Barbara Wold, Caltech

value: ENCBS195IGI at ENCODE; https://www.encodeproject.org/ENCBS195IGI/

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

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

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


title: RAMPAGE from adrenal gland (ENCLB449WOT)

description:
https://www.encodeproject.org/experiments/ENCSR880BIV/
***************
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 adrenal gland 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: ENCSR880BIV
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR276MMH
encode release date: 2016-05-09
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB449WOT
size range: >200

source_name: Homo sapiens adrenal gland tissue male adult (37 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/d839c9fc-d6e9-43b9-81eb-e9d8aec5ac86/@@download/attachment/295973.pdf

value: adrenal gland

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

value: 37 year

value: adult

value: male

value: ENCBS227VDO at ENCODE; https://www.encodeproject.org/ENCBS227VDO/

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


title: shRNA RNA-seq from HepG2 (ENCLB546ADR)

description:
https://www.encodeproject.org/experiments/ENCSR896CFV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGHLV35)
experiment encode accession: ENCSR896CFV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB546ADR
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/f90fc77a-4d72-40b9-8cdf-bfacbffa2d91/@@download/attachment/L-SF3B1_BGHLV35-41.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGHLV35-41)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS670JAO at ENCODE; https://www.encodeproject.org/ENCBS670JAO/

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


title: RAMPAGE from right atrium auricular region (ENCLB078ODF)

description:
https://www.encodeproject.org/experiments/ENCSR877SCS/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human right cardiac atrium tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR877SCS
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR571RXE
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB078ODF
size range: >200

source_name: Homo sapiens right atrium auricular region 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/59668117-ac3a-4ead-ba16-340b27d2104e/@@download/attachment/296845.pdf

value: right atrium auricular region

value: tissue

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

value: 53 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS357SRJ at ENCODE; https://www.encodeproject.org/ENCBS357SRJ/

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


title: shRNA RNA-seq from K562 (ENCLB596VEK)

description:
https://www.encodeproject.org/experiments/ENCSR874ZLI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CCDC124. (CCDC124_BGKLV32)
experiment encode accession: ENCSR874ZLI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB596VEK
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CCDC124

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c8f0a39d-f240-4f44-9d29-5460272f4023/@@download/attachment/L-CCDC124_BGKLV32-13.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against CCDC124. (CCDC124_BGKLV32-13)

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS540TUC at ENCODE; https://www.encodeproject.org/ENCBS540TUC/

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 adrenal gland (ENCLB012DPP)

description:
https://www.encodeproject.org/experiments/ENCSR880BIV/
***************
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 adrenal gland 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: ENCSR880BIV
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR276MMH
encode release date: 2016-05-09
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB012DPP
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/0b277b1a-62c4-434a-a69a-ca7e38a8e9ad/@@download/attachment/295972.pdf

value: adrenal gland

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

value: 37 year

value: male

value: ENCBS227VDO at ENCODE; https://www.encodeproject.org/ENCBS227VDO/

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


title: shRNA RNA-seq from K562 (ENCLB904YEB)

description:
https://www.encodeproject.org/experiments/ENCSR874ZLI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CCDC124. (CCDC124_BGKLV32)
experiment encode accession: ENCSR874ZLI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB904YEB
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/76430584-6ed2-4b72-8fe9-9e4169e16bfd/@@download/attachment/L-CCDC124_BGKLV32-14.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CCDC124. (CCDC124_BGKLV32-14)

value: 53 year

value: female

value: Brenton Graveley, UConn

value: ENCBS783CHQ at ENCODE; https://www.encodeproject.org/ENCBS783CHQ/


title: total RNA-seq from hepatocyte (ENCLB816UYB)

description:
https://www.encodeproject.org/experiments/ENCSR859HWB/
***************
biological replicate number: 2
technical replicate number: 1
description: hepatocyte
experiment encode accession: ENCSR859HWB
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB816UYB
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.350
nucleic acid starting quantity units: ng

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

value: hepatocyte

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

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

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


title: shRNA RNA-seq from K562 (ENCLB480SPT)

description:
https://www.encodeproject.org/experiments/ENCSR874DVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against GLRX3. (GLRX3_BGKLV34)
experiment encode accession: ENCSR874DVZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB480SPT
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting GLRX3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/14e48681-7772-480c-956e-8017fbd08df5/@@download/attachment/L-GLRX3_BGKLV34-17.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against GLRX3. (GLRX3_BGKLV34-17)

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS147SKA at ENCODE; https://www.encodeproject.org/ENCBS147SKA/

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


title: total RNA-seq from suprapubic skin (ENCLB591IEN)

description:
https://www.encodeproject.org/experiments/ENCSR862RGX/
***************
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 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: ENCSR862RGX
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB591IEN
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens suprapubic skin tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/159cdaf8-a8c3-45aa-8f9e-62eadb824c6c/@@download/attachment/296374.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: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS218MJW at ENCODE; https://www.encodeproject.org/ENCBS218MJW/

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


title: total RNA-seq from tibial nerve (ENCLB464VVH)

description:
https://www.encodeproject.org/experiments/ENCSR858QEL/
***************
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 tibial nerve 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: ENCSR858QEL
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB464VVH
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens tibial nerve tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1f044ca3-ec8a-486c-b6af-5c6e79d7b742/@@download/attachment/296340.pdf

value: tibial nerve

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

value: 53 year

value: female

value: ENCBS358ZMI at ENCODE; https://www.encodeproject.org/ENCBS358ZMI/

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


title: shRNA RNA-seq from K562 (ENCLB196YJS)

description:
https://www.encodeproject.org/experiments/ENCSR866XLI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against LARP4. (LARP4_BGKLV28)
experiment encode accession: ENCSR866XLI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB196YJS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting LARP4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/02dcd1cd-2d8b-4700-bf21-5f560bca67a9/@@download/attachment/L-LARP4_BGKLV28-26.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against LARP4. (LARP4_BGKLV28-26)

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS559ZAU at ENCODE; https://www.encodeproject.org/ENCBS559ZAU/

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


title: shRNA RNA-seq from K562 (ENCLB484IEM)

description:
https://www.encodeproject.org/experiments/ENCSR874DVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against GLRX3. (GLRX3_BGKLV34)
experiment encode accession: ENCSR874DVZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB484IEM
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/56308478-c68a-4c97-a86c-858d3d843c75/@@download/attachment/L-GLRX3_BGKLV34-18.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against GLRX3. (GLRX3_BGKLV34-18)

value: ENCBS736SUI at ENCODE; https://www.encodeproject.org/ENCBS736SUI/

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


title: total RNA-seq from hepatocyte (ENCLB881IUD)

description:
https://www.encodeproject.org/experiments/ENCSR859HWB/
***************
biological replicate number: 1
technical replicate number: 1
description: hepatocyte
experiment encode accession: ENCSR859HWB
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB881IUD
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.350
nucleic acid starting quantity units: ng

value: hepatocyte

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

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

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


title: shRNA RNA-seq from K562 (ENCLB620YWG)

description:
https://www.encodeproject.org/experiments/ENCSR866XLI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against LARP4. (LARP4_BGKLV28)
experiment encode accession: ENCSR866XLI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB620YWG
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/0664d926-52e2-4350-8a0b-032a9ab46b2a/@@download/attachment/L-LARP4_BGKLV28-25.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against LARP4. (LARP4_BGKLV28-25)

value: 53 year

value: adult

value: female

value: ENCBS519VAI at ENCODE; https://www.encodeproject.org/ENCBS519VAI/


title: total RNA-seq from GM12878 (ENCLB855HEY)

description:
https://www.encodeproject.org/experiments/ENCSR889TRN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq of GM12878 bulk prep 10 ng
experiment encode accession: ENCSR889TRN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB855HEY
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: GM12878 growth

value: unknown

value: Barbara Wold, Caltech

value: ENCBS195IGI at ENCODE; https://www.encodeproject.org/ENCBS195IGI/

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

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

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


title: total RNA-seq from sigmoid colon (ENCLB743CLP)

description:
https://www.encodeproject.org/experiments/ENCSR857WJK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the sigmoid colon 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: ENCSR857WJK
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB743CLP
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens sigmoid colon tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/16278ca1-e2ab-4883-93bd-078771646212/@@download/attachment/296139.pdf

value: sigmoid colon

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS516KIQ at ENCODE; https://www.encodeproject.org/ENCBS516KIQ/

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


title: total RNA-seq from stomach (ENCLB456EOR)

description:
https://www.encodeproject.org/experiments/ENCSR853WOM/
***************
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 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: ENCSR853WOM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB456EOR
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens stomach tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6e7d27f1-e025-452b-ab22-348104aa6403/@@download/attachment/296676.pdf

value: stomach

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

value: 51 year

value: adult

value: female

value: ENCBS038PAI at ENCODE; https://www.encodeproject.org/ENCBS038PAI/

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


title: RAMPAGE from transverse colon (ENCLB657IDF)

description:
https://www.encodeproject.org/experiments/ENCSR855GRG/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human transverse colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR855GRG
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR800WIY
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB657IDF
size range: >200

source_name: Homo sapiens transverse colon 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/cb8eeff9-029c-49b5-8415-de15365fc651/@@download/attachment/296821.pdf

value: transverse colon

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

value: 53 year

value: ENCBS974EYF at ENCODE; https://www.encodeproject.org/ENCBS974EYF/

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


title: total RNA-seq from GM12878 (ENCLB919DEB)

description:
https://www.encodeproject.org/experiments/ENCSR843RJV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq of GM12878 bulk prep 100 pg
experiment encode accession: ENCSR843RJV
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB919DEB
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.100
nucleic acid starting quantity units: ng

value: immortalized cell line

value: GM12878 growth

value: unknown

value: Barbara Wold, Caltech

value: ENCBS195IGI at ENCODE; https://www.encodeproject.org/ENCBS195IGI/

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

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

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


title: RAMPAGE from testis (ENCLB813NSM)

description:
https://www.encodeproject.org/experiments/ENCSR866SRG/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human testis tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR866SRG
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR344MQK
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB813NSM
size range: >200

source_name: Homo sapiens testis 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/f3125772-bbde-4f34-b727-628a9491bbad/@@download/attachment/296843.pdf

value: testis

value: tissue

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

value: 54 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS255MJZ at ENCODE; https://www.encodeproject.org/ENCBS255MJZ/

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


title: total RNA-seq from GM12878 (ENCLB518OAU)

description:
https://www.encodeproject.org/experiments/ENCSR843RJV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of GM12878 bulk prep 100 pg
experiment encode accession: ENCSR843RJV
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB518OAU
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.100
nucleic acid starting quantity units: ng

value: immortalized cell line

value: female


title: shRNA RNA-seq from K562 (ENCLB755GKG)

description:
https://www.encodeproject.org/experiments/ENCSR844QNT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PPP1R8. (PPP1R8_BGKLV28)
experiment encode accession: ENCSR844QNT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB755GKG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PPP1R8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9f45cb0c-dfc9-4cc9-ae29-13767966689f/@@download/attachment/L-PPP1R8_BGKLV28-41.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PPP1R8. (PPP1R8_BGKLV28-41)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS731WEZ at ENCODE; https://www.encodeproject.org/ENCBS731WEZ/

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 (ENCLB205YQH)

description:
https://www.encodeproject.org/experiments/ENCSR844QNT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PPP1R8. (PPP1R8_BGKLV28)
experiment encode accession: ENCSR844QNT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB205YQH
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/901032c4-3475-4c27-985c-2d2cbf956419/@@download/attachment/L-PPP1R8_BGKLV28-42.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PPP1R8. (PPP1R8_BGKLV28-42)

value: ENCBS290OFW at ENCODE; https://www.encodeproject.org/ENCBS290OFW/


title: shRNA RNA-seq from K562 (ENCLB387AAL)

description:
https://www.encodeproject.org/experiments/ENCSR843LYF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2_BGKLV28)
experiment encode accession: ENCSR843LYF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB387AAL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting YTHDC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3aa5c06b-bccc-44cc-b428-c8c2f94e2373/@@download/attachment/L-YTHDC2_BGKLV28-64.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2_BGKLV28-64)

value: ENCBS688QTO at ENCODE; https://www.encodeproject.org/ENCBS688QTO/


title: RAMPAGE from testis (ENCLB674WHM)

description:
https://www.encodeproject.org/experiments/ENCSR841EQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human testis tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR841EQJ
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR029KNZ
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB674WHM
size range: >200

source_name: Homo sapiens testis tissue male adult (37 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/653166e8-0cb9-4410-9f49-0b8fd391fd61/@@download/attachment/296809.pdf

value: testis

value: tissue

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

value: 37 year

value: adult

value: male

value: ENCBS315DHM at ENCODE; https://www.encodeproject.org/ENCBS315DHM/

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


title: total RNA-seq from upper lobe of left lung (ENCLB692XZA)

description:
https://www.encodeproject.org/experiments/ENCSR839ZDH/
***************
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 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: ENCSR839ZDH
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB692XZA
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens upper lobe of left lung tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d921255f-4038-4d8e-b5b9-180fb3270361/@@download/attachment/296291.pdf

value: upper lobe of left lung

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

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS271JIM at ENCODE; https://www.encodeproject.org/ENCBS271JIM/

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


title: total RNA-seq from sigmoid colon (ENCLB666FJO)

description:
https://www.encodeproject.org/experiments/ENCSR827IXS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the sigmoid colon 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: ENCSR827IXS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB666FJO
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6a3cef38-bc51-45c2-873b-49a26ebf68c9/@@download/attachment/296142.pdf

value: sigmoid colon

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

value: 51 year

value: female

value: ENCBS214FDP at ENCODE; https://www.encodeproject.org/ENCBS214FDP/

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


title: shRNA RNA-seq from K562 (ENCLB416MCW)

description:
https://www.encodeproject.org/experiments/ENCSR843LYF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2_BGKLV28)
experiment encode accession: ENCSR843LYF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB416MCW
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/07c350a5-6dcd-4512-a1aa-73f405456123/@@download/attachment/L-YTHDC2_BGKLV28-63.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against YTHDC2. (YTHDC2_BGKLV28-63)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS082JRQ at ENCODE; https://www.encodeproject.org/ENCBS082JRQ/

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 sigmoid colon (ENCLB754DEI)

description:
https://www.encodeproject.org/experiments/ENCSR833XGD/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human sigmoid colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR833XGD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR812AKX
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB754DEI
size range: >200

source_name: Homo sapiens sigmoid colon 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/543fcaa0-16af-4198-af18-17b597109b8b/@@download/attachment/296782.pdf

value: tissue

value: adult

value: male

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS894VJJ at ENCODE; https://www.encodeproject.org/ENCBS894VJJ/


title: shRNA RNA-seq from HepG2 (ENCLB331AGB)

description:
https://www.encodeproject.org/experiments/ENCSR837QDN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGHLV27)
experiment encode accession: ENCSR837QDN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB331AGB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SUGP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/97d70ffc-4e42-40da-bf11-be3a30a49a20/@@download/attachment/L-SUGP2_BGHLV27-54.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against SUGP2 (SUGP2_BGHLV27-54)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS551DVZ at ENCODE; https://www.encodeproject.org/ENCBS551DVZ/

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 ovary (ENCLB024MDB)

description:
https://www.encodeproject.org/experiments/ENCSR841ADZ/
***************
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 ovary 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: ENCSR841ADZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB024MDB
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens ovary tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/deceec82-e47d-41f2-ac64-7ae94e9c1bbd/@@download/attachment/296341.pdf

value: ovary

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

value: 53 year

value: female

value: ENCBS688BQS at ENCODE; https://www.encodeproject.org/ENCBS688BQS/

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


title: shRNA RNA-seq from K562 (ENCLB228IHV)

description:
https://www.encodeproject.org/experiments/ENCSR835RMN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against GRSF1. (GRSF1_BGKLV29-B)
experiment encode accession: ENCSR835RMN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR118EFE
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB228IHV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting GRSF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2269c901-b004-403b-974f-c85f27296f1d/@@download/attachment/L-GRSF1_BGKLV29-37B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against GRSF1. (GRSF1_BGKLV29-37B)

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS017IKU at ENCODE; https://www.encodeproject.org/ENCBS017IKU/

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 (ENCLB492NJH)

description:
https://www.encodeproject.org/experiments/ENCSR835RMN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against GRSF1. (GRSF1_BGKLV29-B)
experiment encode accession: ENCSR835RMN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR118EFE
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB492NJH
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/13d69ffb-1d51-4a19-b1ae-67c615a69b5a/@@download/attachment/L-GRSF1_BGKLV29-38B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against GRSF1. (GRSF1_BGKLV29-38B)

value: ENCBS771FYB at ENCODE; https://www.encodeproject.org/ENCBS771FYB/


title: shRNA RNA-seq from HepG2 (ENCLB206KMT)

description:
https://www.encodeproject.org/experiments/ENCSR837QDN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGHLV27)
experiment encode accession: ENCSR837QDN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB206KMT
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/368db7b8-df36-41d2-9bcc-606fe5a87401/@@download/attachment/L-SUGP2_BGHLV27-53.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against SUGP2 (SUGP2_BGHLV27-53)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS313GMZ at ENCODE; https://www.encodeproject.org/ENCBS313GMZ/

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 tibial nerve (ENCLB134BWO)

description:
https://www.encodeproject.org/experiments/ENCSR848OYH/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human tibial nerve tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR848OYH
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR272UNO
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB134BWO
size range: >200

source_name: Homo sapiens tibial nerve 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/c6df370f-23b5-4cff-b865-85abd6e52a82/@@download/attachment/296824.pdf

value: tibial nerve

value: tissue

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

value: 51 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS473HNM at ENCODE; https://www.encodeproject.org/ENCBS473HNM/

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


title: shRNA RNA-seq from K562 (ENCLB774DDS)

description:
https://www.encodeproject.org/experiments/ENCSR823WTA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGKLV32)
experiment encode accession: ENCSR823WTA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB774DDS
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting KIF1C

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1edd57b9-4cce-48e8-a78a-e9c13cd412f3/@@download/attachment/L-KIF1C_BGKLV32-33.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGKLV32-33)

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS923TYZ at ENCODE; https://www.encodeproject.org/ENCBS923TYZ/

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 (ENCLB558DDB)

description:
https://www.encodeproject.org/experiments/ENCSR829EFL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGKLV34)
experiment encode accession: ENCSR829EFL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB558DDB
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting NSUN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1f3826f6-93f8-453c-8c46-7ee440e004bf/@@download/attachment/L-NSUN2_BGKLV34-26.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGKLV34-26)

value: ENCBS060TLT at ENCODE; https://www.encodeproject.org/ENCBS060TLT/


title: shRNA RNA-seq from K562 (ENCLB253JUV)

description:
https://www.encodeproject.org/experiments/ENCSR823WTA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGKLV32)
experiment encode accession: ENCSR823WTA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB253JUV
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/61ced384-a2ba-4af7-9956-cf5eedb113b7/@@download/attachment/L-KIF1C_BGKLV32-34.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGKLV32-34)

value: ENCBS013GDO at ENCODE; https://www.encodeproject.org/ENCBS013GDO/


title: total RNA-seq from sigmoid colon (ENCLB490FBP)

description:
https://www.encodeproject.org/experiments/ENCSR812AKX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the sigmoid colon 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: ENCSR812AKX
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB490FBP
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7e7a1878-f2d3-46be-a28a-337efa06c3c5/@@download/attachment/296140.pdf

value: sigmoid colon

value: tissue

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

value: male

value: 54 year

value: ENCBS894VJJ at ENCODE; https://www.encodeproject.org/ENCBS894VJJ/

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


title: shRNA RNA-seq from K562 (ENCLB836CRX)

description:
https://www.encodeproject.org/experiments/ENCSR829EFL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGKLV34)
experiment encode accession: ENCSR829EFL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB836CRX
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/02aca9e5-36cb-4da8-aa6a-5f0aebffd362/@@download/attachment/L-NSUN2_BGKLV34-25.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGKLV34-25)

value: 53 year

value: adult

value: female

value: ENCBS323XFD at ENCODE; https://www.encodeproject.org/ENCBS323XFD/


title: shRNA RNA-seq from K562 (ENCLB946FHJ)

description:
https://www.encodeproject.org/experiments/ENCSR812TLY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AGGF1. (AGGF1_BGKLV32)
experiment encode accession: ENCSR812TLY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB946FHJ
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting AGGF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/604b1abf-0356-45eb-b236-e73dd4e32e64/@@download/attachment/L-AGGF1_BGKLV32-5.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against AGGF1. (AGGF1_BGKLV32-5)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS268LPU at ENCODE; https://www.encodeproject.org/ENCBS268LPU/

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 (ENCLB678TGU)

description:
https://www.encodeproject.org/experiments/ENCSR810FHY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UPF2. (UPF2_BGKLV21-B)
experiment encode accession: ENCSR810FHY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR438MDN
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB678TGU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting UPF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2537a9c4-445d-4c69-902d-beaf6509b46c/@@download/attachment/L-UPF2_BGKLV21-65B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UPF2. (UPF2_BGKLV21-65B)

value: ENCBS018CRO at ENCODE; https://www.encodeproject.org/ENCBS018CRO/


title: shRNA RNA-seq from K562 (ENCLB367CHS)

description:
https://www.encodeproject.org/experiments/ENCSR810FHY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UPF2. (UPF2_BGKLV21-B)
experiment encode accession: ENCSR810FHY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR438MDN
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB367CHS
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/dad38a20-8bb2-4302-b1da-e23028870a5e/@@download/attachment/L-UPF2_BGKLV21-66B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UPF2. (UPF2_BGKLV21-66B)

value: ENCBS937ULR at ENCODE; https://www.encodeproject.org/ENCBS937ULR/


title: shRNA RNA-seq from K562 (ENCLB117TFZ)

description:
https://www.encodeproject.org/experiments/ENCSR812TLY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AGGF1. (AGGF1_BGKLV32)
experiment encode accession: ENCSR812TLY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB117TFZ
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/ee3085d2-3a46-4fbc-a1d3-605c37017d5e/@@download/attachment/L-AGGF1_BGKLV32-6.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against AGGF1. (AGGF1_BGKLV32-6)

value: ENCBS040EUG at ENCODE; https://www.encodeproject.org/ENCBS040EUG/


title: shRNA RNA-seq from K562 (ENCLB960LAC)

description:
https://www.encodeproject.org/experiments/ENCSR809ISU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGKLV32)
experiment encode accession: ENCSR809ISU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB960LAC
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting AKAP8L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/63a8c1a5-6e1e-4466-a5cd-dd2f7865cfb6/@@download/attachment/L-AKAP8L_BGKLV32-9.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGKLV32-9)

value: ENCBS572YNK at ENCODE; https://www.encodeproject.org/ENCBS572YNK/


title: shRNA RNA-seq from K562 (ENCLB631ELF)

description:
https://www.encodeproject.org/experiments/ENCSR809ISU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGKLV32)
experiment encode accession: ENCSR809ISU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB631ELF
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/245390e5-f95d-43c2-9b86-4540f88c4eca/@@download/attachment/L-AKAP8L_BGKLV32-10.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGKLV32-10)

value: 53 year

value: adult

value: female

value: ENCBS007ZNT at ENCODE; https://www.encodeproject.org/ENCBS007ZNT/


title: shRNA RNA-seq from HepG2 (ENCLB131ZRS)

description:
https://www.encodeproject.org/experiments/ENCSR808FBR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX5. (DDX5_BGHLV30)
experiment encode accession: ENCSR808FBR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR776SXA
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB131ZRS
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/78daab1b-ba9d-48cc-bca2-5fde2faa432c/@@download/attachment/L-DDX5_BGHLV30-26B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX5. (DDX5_BGHLV30-26B)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS866LUZ at ENCODE; https://www.encodeproject.org/ENCBS866LUZ/

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 Peyer's patch (ENCLB272RXA)

description:
https://www.encodeproject.org/experiments/ENCSR802HPM/
***************
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 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: ENCSR802HPM
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB272RXA
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens Peyer's patch tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/61a90203-9b19-4007-aed2-cd6101ad0cf3/@@download/attachment/296375.pdf

value: Peyer's patch

value: tissue

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

value: 37 year

value: Thomas Gingeras, CSHL

value: ENCBS024TYX at ENCODE; https://www.encodeproject.org/ENCBS024TYX/

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


title: shRNA RNA-seq from HepG2 (ENCLB429VYG)

description:
https://www.encodeproject.org/experiments/ENCSR807ODB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGHLV31)
experiment encode accession: ENCSR807ODB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB429VYG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting AKAP8L

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/75ed7e3c-0483-4460-80d6-f77f5d162a5e/@@download/attachment/L-AKAP8L_BGHLV31-10.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGHLV31-10)

value: ENCBS635NSH at ENCODE; https://www.encodeproject.org/ENCBS635NSH/


title: total RNA-seq from transverse colon (ENCLB214XDA)

description:
https://www.encodeproject.org/experiments/ENCSR800WIY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the transverse colon 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: ENCSR800WIY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB214XDA
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens transverse colon tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9d57f879-3f9f-437c-9ebd-8d9115d7e2dc/@@download/attachment/296165.pdf

value: transverse colon

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

value: adult

value: female

value: 53 year

value: ENCBS974EYF at ENCODE; https://www.encodeproject.org/ENCBS974EYF/

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


title: total RNA-seq from tibial nerve (ENCLB478GSY)

description:
https://www.encodeproject.org/experiments/ENCSR796HLX/
***************
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 tibial nerve 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: ENCSR796HLX
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB478GSY
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens tibial nerve tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/93760a19-983b-40cb-8589-c96ff690b54f/@@download/attachment/296337.pdf

value: tibial nerve

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

value: male

value: ENCBS986CBC at ENCODE; https://www.encodeproject.org/ENCBS986CBC/


title: shRNA RNA-seq from K562 (ENCLB397BLR)

description:
https://www.encodeproject.org/experiments/ENCSR795VAK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CPEB4. (CPEB4_BGKLV25)
experiment encode accession: ENCSR795VAK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR031RRO
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB397BLR
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CPEB4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7126cf3c-6474-4110-b455-51a77e82220c/@@download/attachment/L-CPEB4_BGKLV25-8B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CPEB4. (CPEB4_BGKLV25-8B)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS226YIA at ENCODE; https://www.encodeproject.org/ENCBS226YIA/

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 (ENCLB319SSU)

description:
https://www.encodeproject.org/experiments/ENCSR794NUE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1_BGKLV28)
experiment encode accession: ENCSR794NUE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB319SSU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting HNRNPA2B1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4f8efa18-149f-4531-9649-253efbc62140/@@download/attachment/L-HNRNPA2B1_BGKLV28-19.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1_BGKLV28-19)

value: ENCBS865HYV at ENCODE; https://www.encodeproject.org/ENCBS865HYV/


title: shRNA RNA-seq from HepG2 (ENCLB422LCZ)

description:
https://www.encodeproject.org/experiments/ENCSR807ODB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGHLV31)
experiment encode accession: ENCSR807ODB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB422LCZ
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/59777731-c94a-4372-93b5-3a805e9556aa/@@download/attachment/L-AKAP8L_BGHLV31-9.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AKAP8L. (AKAP8L_BGHLV31-9)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS705NHL at ENCODE; https://www.encodeproject.org/ENCBS705NHL/

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 (ENCLB378OAI)

description:
https://www.encodeproject.org/experiments/ENCSR794NUE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1_BGKLV28)
experiment encode accession: ENCSR794NUE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB378OAI
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/252dd8a2-3270-42e1-97e6-aa00d41f727f/@@download/attachment/L-HNRNPA2B1_BGKLV28-20.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1_BGKLV28-20)

value: 53 year

value: adult

value: female

value: ENCBS334VOL at ENCODE; https://www.encodeproject.org/ENCBS334VOL/