title: shRNA RNA-seq from K562 (ENCLB053XKI)

description:
https://www.encodeproject.org/experiments/ENCSR660ETT/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF3D in K562 cells followed by RNA-seq. (EIF3D_BGKLV19)
experiment encode accession: ENCSR660ETT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB053XKI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF3D

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

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF3D. (EIF3D_BGKLV19_25B)

value: adult

value: ENCBS380NDS at ENCODE; https://www.encodeproject.org/ENCBS380NDS/


title: shRNA RNA-seq from K562 (ENCLB656PUU)

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/ENCSR092WKG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-B_repeat)
experiment encode accession: ENCSR092WKG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB656PUU
size range: >200
spikeins used: /references/ENCSR449DXG/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5673dd05-0885-4ef3-b0eb-3b5b27f24601/@@download/attachment/L-NT_BGKLV19-1B_repeat.pdf

tag: antibody

value: Control

tag: line

value: immortalized cell line

tag: description

value: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-1B_repeat)

tag: biosample encode accession

tag: dev stage

tag: Sex

value: female

tag: age

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

value: Brenton Graveley, UConn

tag: link

value: ENCBS967BUS at ENCODE; https://www.encodeproject.org/ENCBS967BUS/

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 (ENCLB757KTB)

description:
https://www.encodeproject.org/experiments/ENCSR656DQV/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PKM2 in HepG2 cells followed by RNA-seq. (PKM2_BGHLV16)
experiment encode accession: ENCSR656DQV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB757KTB
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/320d1549-9496-4ef6-9c17-cdbc6c8a84eb/@@download/attachment/L-PKM2_BGHLV16_40.pdf

value: PKM

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PKM2. (PKM2_BGHLV16_40)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS421OZB at ENCODE; https://www.encodeproject.org/ENCBS421OZB/

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 omental fat pad (ENCLB848VDG)

description:
https://www.encodeproject.org/experiments/ENCSR080HPT/
***************
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 omentum (but likely more precisely, the adipose tissue of omentum) 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: ENCSR080HPT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB848VDG
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens omental fat pad tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2a06a599-5122-4797-8750-7ae5e18892e3/@@download/attachment/296315.pdf

value: omental fat pad

value: tissue

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

value: adult

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS889JOH at ENCODE; https://www.encodeproject.org/ENCBS889JOH/

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


title: shRNA RNA-seq from HepG2 (ENCLB666MBB)

description:
https://www.encodeproject.org/experiments/ENCSR081IAO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGHLV20)
experiment encode accession: ENCSR081IAO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR135LXL
encode release date: 2016-08-01
lab: Brenton Graveley, UConn
library encode accession: ENCLB666MBB
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CCAR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/656bdef7-fa7f-4888-b777-603e771b6c05/@@download/attachment/L-CCAR1_BGHLV20-5B.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGHLV20-5B)

value: Brenton Graveley, UConn

value: ENCBS145YLE at ENCODE; https://www.encodeproject.org/ENCBS145YLE/


title: shRNA RNA-seq from K562 (ENCLB464FAM)

description:
https://www.encodeproject.org/experiments/ENCSR092WKG/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-B_repeat)
experiment encode accession: ENCSR092WKG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB464FAM
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/5322e483-2b44-441b-9500-37f244fd683c/@@download/attachment/L-NT_BGKLV19-2B_repeat.pdf

value: Control

value: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-2B_repeat)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS177FZX at ENCODE; https://www.encodeproject.org/ENCBS177FZX/

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 (ENCLB492PLL)

description:
https://www.encodeproject.org/experiments/ENCSR648BSC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUF60. (PUF60-BGHLV23)
experiment encode accession: ENCSR648BSC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB492PLL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PUF60

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/946c8035-16c5-41c0-8569-d3a7ac31163c/@@download/attachment/L-PUF60-BGHLV23-32.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUF60. (PUF60-BGHLV23-32)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS976TOE at ENCODE; https://www.encodeproject.org/ENCBS976TOE/

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 (ENCLB247QIA)

description:
https://www.encodeproject.org/experiments/ENCSR656DQV/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PKM2 in HepG2 cells followed by RNA-seq. (PKM2_BGHLV16)
experiment encode accession: ENCSR656DQV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB247QIA
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/372671e0-18a5-4d3b-961f-16319f0ae6da/@@download/attachment/L-PKM2_BGHLV16_39.pdf

value: PKM

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PKM2. (PKM2_BGHLV16_39)

value: Brenton Graveley, UConn

value: ENCBS039DPC at ENCODE; https://www.encodeproject.org/ENCBS039DPC/


title: shRNA RNA-seq from HepG2 (ENCLB209SSI)

description:
https://www.encodeproject.org/experiments/ENCSR648BSC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUF60. (PUF60-BGHLV23)
experiment encode accession: ENCSR648BSC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB209SSI
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/2e812bb1-748d-4138-a0f5-671b08070e71/@@download/attachment/L-PUF60-BGHLV23-31.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUF60. (PUF60-BGHLV23-31)

value: ENCBS136HQP at ENCODE; https://www.encodeproject.org/ENCBS136HQP/


title: shRNA RNA-seq from HepG2 (ENCLB920YRO)

description:
https://www.encodeproject.org/experiments/ENCSR647NYX/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against NONO in HepG2 cells followed by RNA-seq. (NONO_BGHLV17)
experiment encode accession: ENCSR647NYX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB920YRO
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/98a70504-3beb-4044-8fc7-34e20e52ea8b/@@download/attachment/L-NONO_BGHLV17_62.pdf

value: NONO

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NONO. (NONO_BGHLV17_62)

value: ENCBS431NPJ at ENCODE; https://www.encodeproject.org/ENCBS431NPJ/


title: siRNA RNA-seq from K562 (ENCLB261PHJ)

description:
https://www.encodeproject.org/experiments/ENCSR640PVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAFK.
experiment encode accession: ENCSR640PVZ
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR128HAQ
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB261PHJ
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: MAFK

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

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS559WMP at ENCODE; https://www.encodeproject.org/ENCBS559WMP/

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


title: shRNA RNA-seq from K562 (ENCLB883OFC)

description:
https://www.encodeproject.org/experiments/ENCSR077BPR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ESF1. (ESF1_BGKLV29)
experiment encode accession: ENCSR077BPR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB883OFC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting ESF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ed384d5c-fb80-44d4-b314-8550bd56cd02/@@download/attachment/L-ESF1_BGKLV29-31.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against ESF1. (ESF1_BGKLV29-31)

value: ENCBS905KZI at ENCODE; https://www.encodeproject.org/ENCBS905KZI/

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


title: siRNA RNA-seq from K562 (ENCLB455YTE)

description:
https://www.encodeproject.org/experiments/ENCSR656ZOI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting LMNB1.
experiment encode accession: ENCSR656ZOI
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB455YTE
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting LMNB1

value: K562 cells treated with a siRNA knockdown against LMNB1, used in RNA-seq experiments.

value: ENCBS286AYB at ENCODE; https://www.encodeproject.org/ENCBS286AYB/


title: siRNA RNA-seq from K562 (ENCLB244MUL)

description:
https://www.encodeproject.org/experiments/ENCSR640PVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAFK.
experiment encode accession: ENCSR640PVZ
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR128HAQ
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB244MUL
size range: >200
spikeins used: /references/ENCSR866KGS/

value: ENCBS674PFP at ENCODE; https://www.encodeproject.org/ENCBS674PFP/


title: shRNA RNA-seq from HepG2 (ENCLB693YJG)

description:
https://www.encodeproject.org/experiments/ENCSR647NYX/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against NONO in HepG2 cells followed by RNA-seq. (NONO_BGHLV17)
experiment encode accession: ENCSR647NYX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB693YJG
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/ba394f4f-14d2-4c0a-a6dc-dd3ffe7b9534/@@download/attachment/L-NONO_BGHLV17_61.pdf

value: NONO

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NONO. (NONO_BGHLV17_61)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS282XVK at ENCODE; https://www.encodeproject.org/ENCBS282XVK/

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 (ENCLB472HTP)

description:
https://www.encodeproject.org/experiments/ENCSR076PMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGKLV29-B)
experiment encode accession: ENCSR076PMZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR118EFE
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB472HTP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF2S2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1e461d5d-668a-4647-9e78-bd84980f9067/@@download/attachment/L-EIF2S2_BGKLV29-28B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGKLV29-28B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS400MFJ at ENCODE; https://www.encodeproject.org/ENCBS400MFJ/

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


title: shRNA RNA-seq from K562 (ENCLB098TBC)

description:
https://www.encodeproject.org/experiments/ENCSR660ETT/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF3D in K562 cells followed by RNA-seq. (EIF3D_BGKLV19)
experiment encode accession: ENCSR660ETT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB098TBC
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/e3b8e19e-0431-4c26-a3a7-e4150e67bec0/@@download/attachment/L-EIF3D_BGKLV19_26B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF3D. (EIF3D_BGKLV19_26B)

value: ENCBS422KVR at ENCODE; https://www.encodeproject.org/ENCBS422KVR/

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


title: shRNA RNA-seq from K562 (ENCLB818MIA)

description:
https://www.encodeproject.org/experiments/ENCSR076PMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGKLV29-B)
experiment encode accession: ENCSR076PMZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR118EFE
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB818MIA
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/de824c59-1c46-401d-8111-5fa2b8e8ac10/@@download/attachment/L-EIF2S2_BGKLV29-27B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGKLV29-27B)

value: ENCBS681CCH at ENCODE; https://www.encodeproject.org/ENCBS681CCH/


title: shRNA RNA-seq from HepG2 (ENCLB274NOL)

description:
https://www.encodeproject.org/experiments/ENCSR643UFV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NOL12. (NOL12-BGHLV23)
experiment encode accession: ENCSR643UFV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB274NOL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NOL12

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4e57e5b9-e424-4f55-87e1-de4836996d6c/@@download/attachment/L-NOL12-BGHLV23-26.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NOL12. (NOL12-BGHLV23-26)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS077NMC at ENCODE; https://www.encodeproject.org/ENCBS077NMC/


title: shRNA RNA-seq from K562 (ENCLB189QZQ)

description:
https://www.encodeproject.org/experiments/ENCSR077BPR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ESF1. (ESF1_BGKLV29)
experiment encode accession: ENCSR077BPR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB189QZQ
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/814596b0-a585-4607-9e7a-ba7107aeb081/@@download/attachment/L-ESF1_BGKLV29-32.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against ESF1. (ESF1_BGKLV29-32)

value: 53 year

value: adult

value: ENCBS200VZF at ENCODE; https://www.encodeproject.org/ENCBS200VZF/


title: total RNA-seq from uterus (ENCLB929UGW)

description:
https://www.encodeproject.org/experiments/ENCSR071ZLM/
***************
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 uterus 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: ENCSR071ZLM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB929UGW
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0836e1fe-b257-4569-accf-2da13c5ef119/@@download/attachment/296672.pdf

value: uterus

value: tissue

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

value: female

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS887WTT at ENCODE; https://www.encodeproject.org/ENCBS887WTT/

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


title: shRNA RNA-seq from HepG2 (ENCLB604INW)

description:
https://www.encodeproject.org/experiments/ENCSR067GHD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV30)
experiment encode accession: ENCSR067GHD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB604INW
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2519da2c-3a22-48e5-9a54-578a5b95853d/@@download/attachment/L-NT_BGHLV30-1.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (NT_BGHLV30-1)

value: 15 year

value: child

value: male

value: ENCBS672UJA at ENCODE; https://www.encodeproject.org/ENCBS672UJA/

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 (ENCLB498TIQ)

description:
https://www.encodeproject.org/experiments/ENCSR081IAO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGHLV20)
experiment encode accession: ENCSR081IAO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR135LXL
encode release date: 2016-08-01
lab: Brenton Graveley, UConn
library encode accession: ENCLB498TIQ
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/22c18436-01ff-4034-9b4b-dbefccc32e4c/@@download/attachment/L-CCAR1_BGHLV20-6B.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGHLV20-6B)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS779XEH at ENCODE; https://www.encodeproject.org/ENCBS779XEH/


title: shRNA RNA-seq from HepG2 (ENCLB359FBF)

description:
https://www.encodeproject.org/experiments/ENCSR639LKS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FKBP4 in HepG2 cells followed by RNA-seq. (FKBP4_BGHLV17)
experiment encode accession: ENCSR639LKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB359FBF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting FKBP4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2f0509a9-2c76-48b2-bcc8-58933c78b857/@@download/attachment/L-FKBP4_BGHLV17_15.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FKBP4. (FKBP4_BGHLV17_15)

value: ENCBS143EIV at ENCODE; https://www.encodeproject.org/ENCBS143EIV/


title: shRNA RNA-seq from K562 (ENCLB949HRJ)

description:
https://www.encodeproject.org/experiments/ENCSR634KBO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPC. (HNRNPC_BGKLV21)
experiment encode accession: ENCSR634KBO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB949HRJ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0bfec8f7-e3e7-42e7-b4a8-97afba3ff57b/@@download/attachment/L-HNRNPC_BGKLV21_19_17567.pdf

value: HNRNPC

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPC. (HNRNPC_BGKLV21_19_17567)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS220ZHX at ENCODE; https://www.encodeproject.org/ENCBS220ZHX/

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 (ENCLB392MHJ)

description:
https://www.encodeproject.org/experiments/ENCSR067GHD/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV30)
experiment encode accession: ENCSR067GHD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB392MHJ
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/60141a9c-5579-4473-aef1-992c07bf8164/@@download/attachment/L-NT_BGHLV30-2.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (NT_BGHLV30-2)

value: 15 year

value: child

value: male

value: ENCBS781BOJ at ENCODE; https://www.encodeproject.org/ENCBS781BOJ/

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 (ENCLB771DYJ)

description:
https://www.encodeproject.org/experiments/ENCSR639LKS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FKBP4 in HepG2 cells followed by RNA-seq. (FKBP4_BGHLV17)
experiment encode accession: ENCSR639LKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB771DYJ
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/1751269a-3c1f-46ef-87df-a9609e11a960/@@download/attachment/L-FKBP4_BGHLV17_16.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FKBP4. (FKBP4_BGHLV17_16)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS375JNA at ENCODE; https://www.encodeproject.org/ENCBS375JNA/


title: shRNA RNA-seq from K562 (ENCLB398LOI)

description:
https://www.encodeproject.org/experiments/ENCSR060KRD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TROVE2. (TROVE2_BGKLV19-B_rpt)
experiment encode accession: ENCSR060KRD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR092WKG
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB398LOI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TROVE2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e7bcdc12-9046-487e-a6f2-b41d6efaedf8/@@download/attachment/L-TROVE2_BGKLV19-58B_rpt.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown againstTROVE2. (TROVE2_BGKLV19-58B_rpt)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS498NIQ at ENCODE; https://www.encodeproject.org/ENCBS498NIQ/


title: shRNA RNA-seq from K562 (ENCLB788OTZ)

description:
https://www.encodeproject.org/experiments/ENCSR060KRD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TROVE2. (TROVE2_BGKLV19-B_rpt)
experiment encode accession: ENCSR060KRD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR092WKG
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB788OTZ
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/f8bbd70f-e472-42c1-8ad1-86b4cb4d2edd/@@download/attachment/L-TROVE2_BGKLV19-57B_rpt.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown againstTROVE2. (TROVE2_BGKLV19-57B_rpt)

value: ENCBS599BAS at ENCODE; https://www.encodeproject.org/ENCBS599BAS/

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 (ENCLB069LKF)

description:
https://www.encodeproject.org/experiments/ENCSR060IWW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ESF1. (ESF1_BGHLV30)
experiment encode accession: ENCSR060IWW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB069LKF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ESF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fcfc335e-8a08-49d3-ada9-8ab84270cdd9/@@download/attachment/L-ESF1_BGHLV30-36.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ESF1. (ESF1_BGHLV30-36)

value: 15 year

value: child

value: male

value: ENCBS803IPJ at ENCODE; https://www.encodeproject.org/ENCBS803IPJ/

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


title: shRNA RNA-seq from HepG2 (ENCLB025FPR)

description:
https://www.encodeproject.org/experiments/ENCSR643UFV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NOL12. (NOL12-BGHLV23)
experiment encode accession: ENCSR643UFV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB025FPR
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/5047e34e-a5d3-4112-8dd9-cb2cdeba41c1/@@download/attachment/L-NOL12-BGHLV23-25.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NOL12. (NOL12-BGHLV23-25)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS816PYX at ENCODE; https://www.encodeproject.org/ENCBS816PYX/

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


title: shRNA RNA-seq from HepG2 (ENCLB716EZT)

description:
https://www.encodeproject.org/experiments/ENCSR060IWW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ESF1. (ESF1_BGHLV30)
experiment encode accession: ENCSR060IWW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB716EZT
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/06657650-a06e-4ab1-b018-e696c96b4e19/@@download/attachment/L-ESF1_BGHLV30-35.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ESF1. (ESF1_BGHLV30-35)

value: ENCBS930FIG at ENCODE; https://www.encodeproject.org/ENCBS930FIG/


title: shRNA RNA-seq from K562 (ENCLB041EOH)

description:
https://www.encodeproject.org/experiments/ENCSR634KBO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPC. (HNRNPC_BGKLV21)
experiment encode accession: ENCSR634KBO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB041EOH
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/a5627501-a09c-4345-b52d-a86b46b277b0/@@download/attachment/L-HNRNPC_BGKLV21_20_17568.pdf

value: HNRNPC

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPC. (HNRNPC_BGKLV21_20_17568)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS346YOL at ENCODE; https://www.encodeproject.org/ENCBS346YOL/


title: RAMPAGE from thoracic aorta (ENCLB783LSE)

description:
https://www.encodeproject.org/experiments/ENCSR632GYF/
***************
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 aorta 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: ENCSR632GYF
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR429EWK
encode release date: 2016-05-09
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB783LSE
size range: >200

source_name: Homo sapiens thoracic aorta 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/db4fd5dc-145b-44a7-b3ea-0cddb5b458cb/@@download/attachment/296007.pdf

value: thoracic aorta

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS636GUU at ENCODE; https://www.encodeproject.org/ENCBS636GUU/

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


title: RAMPAGE from subcutaneous adipose tissue (ENCLB573WQK)

description:
https://www.encodeproject.org/experiments/ENCSR053ZMS/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human female adipose tissue tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR053ZMS
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR708VVE
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB573WQK
size range: >200

source_name: Homo sapiens subcutaneous adipose 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/e0eadc10-c13c-4a3c-8b98-991815ac32a7/@@download/attachment/296817.pdf

value: subcutaneous adipose tissue

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

value: ENCBS171DKK at ENCODE; https://www.encodeproject.org/ENCBS171DKK/


title: siRNA RNA-seq from K562 (ENCLB860WHO)

description:
https://www.encodeproject.org/experiments/ENCSR631RKH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MXI1.
experiment encode accession: ENCSR631RKH
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR401RKW, ENCSR608CVU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB860WHO
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting MXI1

value: immortalized cell line

value: K562 cells treated with a siRNA knockdown against MXI1, used in RNA-seq experiments.

value: Sherman Weissman, Yale

value: ENCBS421TJJ at ENCODE; https://www.encodeproject.org/ENCBS421TJJ/

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


title: siRNA RNA-seq from K562 (ENCLB080YFO)

description:
https://www.encodeproject.org/experiments/ENCSR631RKH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MXI1.
experiment encode accession: ENCSR631RKH
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR401RKW, ENCSR608CVU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB080YFO
size range: >200
spikeins used: /references/ENCSR866KGS/

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS060ZRJ at ENCODE; https://www.encodeproject.org/ENCBS060ZRJ/


title: RAMPAGE from thoracic aorta (ENCLB994VHP)

description:
https://www.encodeproject.org/experiments/ENCSR632GYF/
***************
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 aorta 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: ENCSR632GYF
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR429EWK
encode release date: 2016-05-09
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB994VHP
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/3713919c-b7ec-4ddf-a45d-5f7a15aed0c0/@@download/attachment/296006.pdf

value: thoracic aorta

value: tissue

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

value: 37 year

value: male


title: shRNA RNA-seq from K562 (ENCLB015DKN)

description:
https://www.encodeproject.org/experiments/ENCSR628JYB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SF1. (K-SF1)
experiment encode accession: ENCSR628JYB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB015DKN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SF1

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/b46d3b75-6890-4203-8ae7-a6c2081ec10f/@@download/attachment/L-K-SF1-2.pdf

value: K562 cells treated with an shRNA knockdown against SF1, used in RNA-seq experiments. (K-SF1-2)

value: Brenton Graveley, UConn

value: ENCBS356NKY at ENCODE; https://www.encodeproject.org/ENCBS356NKY/

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


title: shRNA RNA-seq from K562 (ENCLB012ERH)

description:
https://www.encodeproject.org/experiments/ENCSR048BWH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA1. (HNRNPA1_BGKLV21-B)
experiment encode accession: ENCSR048BWH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR438MDN
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB012ERH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting HNRNPA1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9afd34d0-e9a7-47a1-8c9a-4485e680ab5b/@@download/attachment/L-HNRNPA1_BGKLV21-17B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA1. (HNRNPA1_BGKLV21-17B)

value: ENCBS058XGI at ENCODE; https://www.encodeproject.org/ENCBS058XGI/


title: shRNA RNA-seq from K562 (ENCLB795OFL)

description:
https://www.encodeproject.org/experiments/ENCSR048BWH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA1. (HNRNPA1_BGKLV21-B)
experiment encode accession: ENCSR048BWH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR438MDN
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB795OFL
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/62a01c11-1d57-4cd4-81c6-bf05fa552793/@@download/attachment/L-HNRNPA1_BGKLV21-18B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA1. (HNRNPA1_BGKLV21-18B)

value: 53 year

value: ENCBS026DNX at ENCODE; https://www.encodeproject.org/ENCBS026DNX/

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


title: total RNA-seq from ovary (ENCLB038BJJ)

description:
https://www.encodeproject.org/experiments/ENCSR042GYH/
***************
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 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: ENCSR042GYH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB038BJJ
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e99bdd3e-95c6-4f4a-ae48-6d20791e2de0/@@download/attachment/296343.pdf

value: ovary

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

value: 51 year

value: adult

value: female

value: Thomas Gingeras, CSHL

value: ENCBS711CPB at ENCODE; https://www.encodeproject.org/ENCBS711CPB/

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


title: shRNA RNA-seq from HepG2 (ENCLB031PEX)

description:
https://www.encodeproject.org/experiments/ENCSR040WAK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CALR. (CALR_BGHLV23)
experiment encode accession: ENCSR040WAK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR364GRM
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB031PEX
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/255f9d1a-3bd1-4b55-a9f7-4245e0a8e215/@@download/attachment/L-CALR_BGHLV23-6B.pdf

value: CALR

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CALR. (CALR_BGHLV23-6B)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS550RQC at ENCODE; https://www.encodeproject.org/ENCBS550RQC/

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 (ENCLB388UHT)

description:
https://www.encodeproject.org/experiments/ENCSR624FBY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against LARP7 in HepG2 cells followed by RNA-seq. (LARP7_BGHLV18)
experiment encode accession: ENCSR624FBY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB388UHT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting LARP7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/954d5509-b85e-4b88-a922-997f6177bc74/@@download/attachment/L-LARP7_BGHLV18_20.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against LARP7. (LARP7_BGHLV18_20)

value: ENCBS608OON at ENCODE; https://www.encodeproject.org/ENCBS608OON/


title: shRNA RNA-seq from K562 (ENCLB911SLK)

description:
https://www.encodeproject.org/experiments/ENCSR047IUS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPU. (HNRNPU_BGKLV21-B)
experiment encode accession: ENCSR047IUS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR438MDN
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB911SLK
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/64daf9b6-f997-4f8f-ba41-3c0796d22fb1/@@download/attachment/L-HNRNPU_BGKLV21-24B.pdf

value: HNRNPU

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPU. (HNRNPU_BGKLV21-24B)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS872JXE at ENCODE; https://www.encodeproject.org/ENCBS872JXE/

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 (ENCLB133OFF)

description:
https://www.encodeproject.org/experiments/ENCSR628JYB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SF1. (K-SF1)
experiment encode accession: ENCSR628JYB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB133OFF
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/c08ddb9b-51a2-41d9-8656-724f9c2fe059/@@download/attachment/L-K-SF1-1.pdf

value: K562 cells treated with an shRNA knockdown against SF1, used in RNA-seq experiments. (K-SF1-1)

value: ENCBS731WGV at ENCODE; https://www.encodeproject.org/ENCBS731WGV/


title: shRNA RNA-seq from HepG2 (ENCLB741WUL)

description:
https://www.encodeproject.org/experiments/ENCSR040WAK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CALR. (CALR_BGHLV23)
experiment encode accession: ENCSR040WAK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR364GRM
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB741WUL
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/4e88a068-0b1b-4de7-9eee-b6d775df9ee2/@@download/attachment/L-CALR_BGHLV23-5B.pdf

value: CALR

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CALR. (CALR_BGHLV23-5B)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS260QIN at ENCODE; https://www.encodeproject.org/ENCBS260QIN/


title: shRNA RNA-seq from K562 (ENCLB130ONU)

description:
https://www.encodeproject.org/experiments/ENCSR047IUS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPU. (HNRNPU_BGKLV21-B)
experiment encode accession: ENCSR047IUS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR438MDN
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB130ONU
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/ad304b51-078a-4d90-bfc5-fe101fc074c1/@@download/attachment/L-HNRNPU_BGKLV21-23B.pdf

value: HNRNPU

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPU. (HNRNPU_BGKLV21-23B)

value: adult

value: ENCBS013BQD at ENCODE; https://www.encodeproject.org/ENCBS013BQD/


title: total RNA-seq from gastroesophageal sphincter (ENCLB442XEX)

description:
https://www.encodeproject.org/experiments/ENCSR035SKV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the esophagogastric junction obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR035SKV
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB442XEX
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens gastroesophageal sphincter tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/59ad4a78-4cfa-4460-8815-477c18b86ba3/@@download/attachment/296191.pdf

value: gastroesophageal sphincter

value: tissue

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

value: female

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS874HID at ENCODE; https://www.encodeproject.org/ENCBS874HID/

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


title: shRNA RNA-seq from HepG2 (ENCLB715ZDT)

description:
https://www.encodeproject.org/experiments/ENCSR624FBY/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against LARP7 in HepG2 cells followed by RNA-seq. (LARP7_BGHLV18)
experiment encode accession: ENCSR624FBY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB715ZDT
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/e97ae29c-ed2f-4473-9b2e-b6ee3e549a94/@@download/attachment/L-LARP7_BGHLV18_19.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against LARP7. (LARP7_BGHLV18_19)

value: 15 year

value: child

value: male

value: ENCBS471EIZ at ENCODE; https://www.encodeproject.org/ENCBS471EIZ/

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 neural cell (ENCLB009TMB)

description:
https://www.encodeproject.org/experiments/ENCSR612EAO/
***************
biological replicate number: 1
technical replicate number: 1
description: RAMPAGE H1-neuron
experiment encode accession: ENCSR612EAO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR995JXE
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB009TMB
size range: >200

source_name: Homo sapiens neural in vitro differentiated cells male embryo

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/21e31dd6-9ee1-405d-bc39-f8735205c340/@@download/attachment/SID30045.pdf

value: neural cell

value: in vitro differentiated cells

value: neurons derived from H1 embryonic stem cells

value: unknown

value: embryonic

value: healthy

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

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

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

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


title: shRNA RNA-seq from K562 (ENCLB258JXF)

description:
https://www.encodeproject.org/experiments/ENCSR034VBA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGKLV28)
experiment encode accession: ENCSR034VBA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB258JXF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting HNRNPUL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/41c28466-dc0e-4925-b6bc-0a748ee47470/@@download/attachment/L-HNRNPUL1_BGKLV28-24.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGKLV28-24)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS997MUA at ENCODE; https://www.encodeproject.org/ENCBS997MUA/

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 neural cell (ENCLB290ORE)

description:
https://www.encodeproject.org/experiments/ENCSR612EAO/
***************
biological replicate number: 2
technical replicate number: 1
description: RAMPAGE H1-neuron
experiment encode accession: ENCSR612EAO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR995JXE
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB290ORE
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/9c9042bc-0864-4e10-8a82-734fe16b4e37/@@download/attachment/SID30046.pdf

value: neural cell

value: in vitro differentiated cells

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

value: unknown

value: male

value: Thomas Gingeras, CSHL

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


title: shRNA RNA-seq from K562 (ENCLB402IYO)

description:
https://www.encodeproject.org/experiments/ENCSR032YMP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV29)
experiment encode accession: ENCSR032YMP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB402IYO
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5c1b5424-e740-45b1-b68b-7526614d4522/@@download/attachment/L-NT_BGKLV29-1.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (NT_BGKLV29-1)

value: ENCBS975JQF at ENCODE; https://www.encodeproject.org/ENCBS975JQF/


title: shRNA RNA-seq from K562 (ENCLB395QPL)

description:
https://www.encodeproject.org/experiments/ENCSR032YMP/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV29)
experiment encode accession: ENCSR032YMP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB395QPL
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/d563cbaf-597d-457b-8153-2c884392c689/@@download/attachment/L-NT_BGKLV29-2.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (NT_BGKLV29-2)

value: adult

value: female

value: 53 year

value: ENCBS854WQM at ENCODE; https://www.encodeproject.org/ENCBS854WQM/


title: shRNA RNA-seq from K562 (ENCLB454ECB)

description:
https://www.encodeproject.org/experiments/ENCSR620PUP/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV25)
experiment encode accession: ENCSR620PUP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB454ECB
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/c89649a1-540f-4adf-91d8-be56651176ea/@@download/attachment/L-NT_BGKLV25-2.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (NT_BGKLV25-2)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS217DFO at ENCODE; https://www.encodeproject.org/ENCBS217DFO/

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 (ENCLB027DNU)

description:
https://www.encodeproject.org/experiments/ENCSR620OKS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EFTUD2 in HepG2 cells followed by RNA-seq. (EFTUD2_BGHLV16)
experiment encode accession: ENCSR620OKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB027DNU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EFTUD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/baa56cc8-bc02-4af2-b251-c82807282a23/@@download/attachment/L-EFTUD2_BGHLV16_22.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EFTUD2. (EFTUD2_BGHLV16_22)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS306CIA at ENCODE; https://www.encodeproject.org/ENCBS306CIA/

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 (ENCLB256QBT)

description:
https://www.encodeproject.org/experiments/ENCSR620PUP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV25)
experiment encode accession: ENCSR620PUP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB256QBT
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/f6a6fd37-7dc9-4169-9459-be44488892b5/@@download/attachment/L-NT_BGKLV25-1.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (NT_BGKLV25-1)

value: adult

value: female

value: ENCBS262OLW at ENCODE; https://www.encodeproject.org/ENCBS262OLW/


title: shRNA RNA-seq from K562 (ENCLB796OAN)

description:
https://www.encodeproject.org/experiments/ENCSR031RRO/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV25B)
experiment encode accession: ENCSR031RRO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB796OAN
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/78453be4-627e-4381-993c-efbb7f29a2f6/@@download/attachment/L-NT_BGKLV25-2B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV25-2B)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS140NYG at ENCODE; https://www.encodeproject.org/ENCBS140NYG/


title: RAMPAGE from lower leg skin (ENCLB490QQO)

description:
https://www.encodeproject.org/experiments/ENCSR030CKH/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human lower leg skin tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR030CKH
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR551NII
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB490QQO
size range: >200

source_name: Homo sapiens lower leg skin 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/0979ab70-6209-4d56-b1bc-2cfd72325264/@@download/attachment/296847.pdf

value: lower leg skin

value: tissue

value: Skin of the lower leg aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS836VES at ENCODE; https://www.encodeproject.org/ENCBS836VES/

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


title: shRNA RNA-seq from K562 (ENCLB492QKR)

description:
https://www.encodeproject.org/experiments/ENCSR611LQB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PSIP1. (PSIP1_BGKLV21)
experiment encode accession: ENCSR611LQB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB492QKR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PSIP1

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

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PSIP1. (PSIP1_BGKLV21_46_17583)

value: ENCBS972KMH at ENCODE; https://www.encodeproject.org/ENCBS972KMH/

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 (ENCLB780WVH)

description:
https://www.encodeproject.org/experiments/ENCSR620OKS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EFTUD2 in HepG2 cells followed by RNA-seq. (EFTUD2_BGHLV16)
experiment encode accession: ENCSR620OKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB780WVH
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/10cbd1dc-d1ad-4b7c-91df-de883ef24c44/@@download/attachment/L-EFTUD2_BGHLV16_21.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EFTUD2. (EFTUD2_BGHLV16_21)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS252ZVH at ENCODE; https://www.encodeproject.org/ENCBS252ZVH/

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 (ENCLB901CBE)

description:
https://www.encodeproject.org/experiments/ENCSR611LQB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PSIP1. (PSIP1_BGKLV21)
experiment encode accession: ENCSR611LQB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB901CBE
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/e798ed70-4d11-47cb-91b3-22efad203f79/@@download/attachment/L-PSIP1_BGKLV21_45_17582.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PSIP1. (PSIP1_BGKLV21_45_17582)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS878WRC at ENCODE; https://www.encodeproject.org/ENCBS878WRC/


title: shRNA RNA-seq from K562 (ENCLB778LQL)

description:
https://www.encodeproject.org/experiments/ENCSR031RRO/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV25B)
experiment encode accession: ENCSR031RRO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB778LQL
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/eeca353a-7d52-43b5-b323-a0f23ed03d07/@@download/attachment/L-NT_BGKLV25-1B.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV25-1B)

value: ENCBS745CIF at ENCODE; https://www.encodeproject.org/ENCBS745CIF/

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


title: shRNA RNA-seq from K562 (ENCLB926ODV)

description:
https://www.encodeproject.org/experiments/ENCSR034VBA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGKLV28)
experiment encode accession: ENCSR034VBA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB926ODV
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/6ad06355-2565-469f-9ee9-1735e787f39a/@@download/attachment/L-HNRNPUL1_BGKLV28-23.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGKLV28-23)

value: ENCBS511UGF at ENCODE; https://www.encodeproject.org/ENCBS511UGF/

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


title: RAMPAGE from gastroesophageal sphincter (ENCLB006UWR)

description:
https://www.encodeproject.org/experiments/ENCSR028GEI/
***************
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 esophagogastric junction 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: ENCSR028GEI
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR740YMS
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB006UWR
size range: >200

source_name: Homo sapiens gastroesophageal sphincter 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/204b4dfb-8a3a-4d68-b526-843bb608ab07/@@download/attachment/296725.pdf

value: gastroesophageal sphincter

value: tissue

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

value: Thomas Gingeras, CSHL

value: ENCBS616IQR at ENCODE; https://www.encodeproject.org/ENCBS616IQR/

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


title: shRNA RNA-seq from K562 (ENCLB407USL)

description:
https://www.encodeproject.org/experiments/ENCSR608IAI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FASTKD2 in K562 cells followed by RNA-seq. (FASTKD2 BGKLV13)
experiment encode accession: ENCSR608IAI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB407USL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting FASTKD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/92bacdc8-1f11-4d56-9dd1-a206d805efc3/@@download/attachment/L-FASTKD2_BGKLV13_54.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FASTKD2.(FASTKD2_BGKLV13_54)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS164AGP at ENCODE; https://www.encodeproject.org/ENCBS164AGP/


title: siRNA RNA-seq from K562 (ENCLB987KYJ)

description:
https://www.encodeproject.org/experiments/ENCSR608CVU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR608CVU
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB987KYJ
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: Control

value: immortalized cell line

value: K562 cells treated with siRNA knockdown using a human non-targeting control.

value: Sherman Weissman, Yale

value: ENCBS664VZE at ENCODE; https://www.encodeproject.org/ENCBS664VZE/


title: RAMPAGE from suprapubic skin (ENCLB690AYN)

description:
https://www.encodeproject.org/experiments/ENCSR026WQO/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human suprapubic skin tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR026WQO
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR480SLD
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB690AYN
size range: >200

source_name: Homo sapiens suprapubic skin 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/b30fe863-fd51-441e-a744-a79f9c9a3f4d/@@download/attachment/296779.pdf

value: suprapubic skin

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

value: 51 year

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

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


title: shRNA RNA-seq from K562 (ENCLB678CBV)

description:
https://www.encodeproject.org/experiments/ENCSR608IAI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FASTKD2 in K562 cells followed by RNA-seq. (FASTKD2 BGKLV13)
experiment encode accession: ENCSR608IAI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB678CBV
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/b91e97db-8d82-4926-a89b-b3960b8fcd8d/@@download/attachment/L-FASTKD2_BGKLV13_53.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FASTKD2.(FASTKD2_BGKLV13_53)

value: Brenton Graveley, UConn

value: ENCBS278LNR at ENCODE; https://www.encodeproject.org/ENCBS278LNR/

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 bipolar spindle neuron (ENCLB228SAY)

description:
https://www.encodeproject.org/experiments/ENCSR023VVO/
***************
biological replicate number: 2
technical replicate number: 1
description: bipolar spindle neuron
experiment encode accession: ENCSR023VVO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB228SAY
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: bipolar spindle neuron

value: in vitro differentiated cells

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

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from K562 (ENCLB258KUH)

description:
https://www.encodeproject.org/experiments/ENCSR606QIX/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against BCCIP in K562 cells followed by RNA-seq. (BCCIP_BGKLV19)
experiment encode accession: ENCSR606QIX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR245BNJ
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB258KUH
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9e6deee3-1877-48ce-b247-6c2c80927306/@@download/attachment/L-BCCIP_BGKLV19_6A.pdf

value: BCCIP

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against BCCIP. (BCCIP_BGKLV19_6A)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS257PZA at ENCODE; https://www.encodeproject.org/ENCBS257PZA/


title: total RNA-seq from bipolar spindle neuron (ENCLB444LRG)

description:
https://www.encodeproject.org/experiments/ENCSR023VVO/
***************
biological replicate number: 1
technical replicate number: 1
description: bipolar spindle neuron
experiment encode accession: ENCSR023VVO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB444LRG
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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


title: shRNA RNA-seq from HepG2 (ENCLB462IFC)

description:
https://www.encodeproject.org/experiments/ENCSR016XPB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NPM1. (NPM1_BGHLV26)
experiment encode accession: ENCSR016XPB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB462IFC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NPM1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9d208747-57ba-4aee-88ff-ec15ab9a1476/@@download/attachment/L-NPM1_BGHLV26_27.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against NPM1 (NPM1_BGHLV26_27)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS024EHA at ENCODE; https://www.encodeproject.org/ENCBS024EHA/

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 neural progenitor cell (ENCLB725QAM)

description:
https://www.encodeproject.org/experiments/ENCSR602PHV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of H9 embryonic stem cells that were differentiated down a neuronal pathway. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR602PHV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR244ISQ
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB725QAM
size range: >200

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

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/c4751b45-0758-4aa3-921c-8588b57daff7/@@download/attachment/LID294715.pdf

value: neural progenitor cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

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

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


title: total RNA-seq from testis (ENCLB611FHB)

description:
https://www.encodeproject.org/experiments/ENCSR029KNZ/
***************
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 testis 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: ENCSR029KNZ
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB611FHB
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0eb9d48e-2a81-4984-89d3-d290d07bd3ae/@@download/attachment/296606.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: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from K562 (ENCLB896EZC)

description:
https://www.encodeproject.org/experiments/ENCSR605MFS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1_BGKLV25)
experiment encode accession: ENCSR605MFS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB896EZC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CELF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2212c313-beaa-4109-b50d-38f1dd0fcf1e/@@download/attachment/L-CUGBP1_BGKLV25-9.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1_BGKLV25-9)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS651RVZ at ENCODE; https://www.encodeproject.org/ENCBS651RVZ/

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 (ENCLB762JVP)

description:
https://www.encodeproject.org/experiments/ENCSR606QIX/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against BCCIP in K562 cells followed by RNA-seq. (BCCIP_BGKLV19)
experiment encode accession: ENCSR606QIX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR245BNJ
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB762JVP
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/4a0dc8a1-1075-47a9-8a3a-ab8da1cbf959/@@download/attachment/L-BCCIP_BGKLV19_5A.pdf

value: BCCIP

value: RNA-seq on K562 cells treated with an shRNA knockdown against BCCIP. (BCCIP_BGKLV19_5A)

value: ENCBS155KGP at ENCODE; https://www.encodeproject.org/ENCBS155KGP/


title: 400nM_4_Rep2

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

library_source: genomic

data_processing:
Library strategy: COSMIC-seq
Base pairs were called with Casava v.1.8.2 (Illumina).
Reads were de-multiplexed with the barcode to yield only the 51 bp genomic fragment. Reads were filtered and trimmed to eliminate low-quality reads and adapter sequences, and mapped to the human genome (hg19) with Bowtie v 1.0 (best -m 1) to yield unique alignments.
HOMER (http://biowhat.ucsd.edu/homer/) was used to produce a signal track. The tag density for each factor was normalized to 10^7 tags and Input DNA. Peaks were called with SPP v 1.10.1 with the default parameters of the IDR methodology according to ENCODE guidelines (Landt et al Genome Res. 2012, 22, 1813).
Genome_build: hg19
Supplementary_files_format_and_content: *.bed files contain the COSMIC-seq peak locations. *.bedgraph files contain signal tracks.

molecule: genomic DNA

growth_protocol: E8 with Matrigel-coated plates

extract_protocol:
Cells were washed again with PBS, and isolated with Accutase per manufacturer’s directions. COSMIC was performed as described previously (Erwin et al. Angew. Chem. Int. Ed. 2014, 53, 38, 10124).
Sequencing libraries for Input and AP DNA were labeled with a DNA barcode for multiplexing, and prepared for sequencing with the TruSeq ChIP Sample Prep Kit (Illumina, Inc., San Diego, CA) per manufacturer’s directions.

treatment_protocol: H1-hESCs were treated with molecule for 24 h.

tag: cell line

tag: treatment


title: shRNA RNA-seq from K562 (ENCLB704YVS)

description:
https://www.encodeproject.org/experiments/ENCSR599UDS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AARS. (AARS_BGKLV21)
experiment encode accession: ENCSR599UDS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB704YVS
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6c8d8a0d-01f2-4c96-8cf5-e488c1966745/@@download/attachment/L-AARS_BGKLV21_3_17558.pdf

value: AARS

value: RNA-seq on K562 cells treated with an shRNA knockdown against AARS. (AARS_BGKLV21_3_17558)

value: adult

value: ENCBS818EBR at ENCODE; https://www.encodeproject.org/ENCBS818EBR/


title: shRNA RNA-seq from K562 (ENCLB520KOB)

description:
https://www.encodeproject.org/experiments/ENCSR605MFS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1_BGKLV25)
experiment encode accession: ENCSR605MFS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB520KOB
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/c6986e14-272b-49e2-b157-aa4a3d061eda/@@download/attachment/L-CUGBP1_BGKLV25-10.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1_BGKLV25-10)

value: ENCBS737CUP at ENCODE; https://www.encodeproject.org/ENCBS737CUP/


title: 400nM_2_Rep2


title: shRNA RNA-seq from K562 (ENCLB699VYC)

description:
https://www.encodeproject.org/experiments/ENCSR599UDS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AARS. (AARS_BGKLV21)
experiment encode accession: ENCSR599UDS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB699VYC
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/1a579baf-7e26-415e-8cdf-a92879235bd8/@@download/attachment/L-AARS_BGKLV21_4_17559.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against AARS. (AARS_BGKLV21_4_17559)

value: ENCBS946YFO at ENCODE; https://www.encodeproject.org/ENCBS946YFO/


title: 400nM_4_Rep1


title: shRNA RNA-seq from HepG2 (ENCLB623QMU)

description:
https://www.encodeproject.org/experiments/ENCSR016XPB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NPM1. (NPM1_BGHLV26)
experiment encode accession: ENCSR016XPB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB623QMU
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/02fcb53e-2ca8-4334-8891-bed92269fbc7/@@download/attachment/L-NPM1_BGHLV26_28.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against NPM1 (NPM1_BGHLV26_28)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS321SWI at ENCODE; https://www.encodeproject.org/ENCBS321SWI/

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 neural progenitor cell (ENCLB134SCC)

description:
https://www.encodeproject.org/experiments/ENCSR602PHV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of H9 embryonic stem cells that were differentiated down a neuronal pathway. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR602PHV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR244ISQ
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB134SCC
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/0ed47886-1572-4385-bc60-6889ae21626d/@@download/attachment/LID294716.pdf

value: neural progenitor cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/

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


title: polyA mRNA RNA-seq from K562 (ENCLB460RTX)

description:
https://www.encodeproject.org/experiments/ENCSR596ACL/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial membrane fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR596ACL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB460RTX
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line membrane fraction

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

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Eric Lécuyer, IRCM

tag: subcellular fraction term name

value: membrane

value: ENCBS949ESX at ENCODE; https://www.encodeproject.org/ENCBS949ESX/

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

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