title: shRNA RNA-seq from K562 (ENCLB049RPS)

description:
https://www.encodeproject.org/experiments/ENCSR936VPP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (k562-shC)
experiment encode accession: ENCSR936VPP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB049RPS
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/47fcf64f-61d7-4ba6-a6cd-b89a47076fbf/@@download/attachment/L-k562-shC-2.pdf

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (k562-shC-2)

value: female

value: ENCBS031YPZ at ENCODE; https://www.encodeproject.org/ENCBS031YPZ/


title: RAMPAGE from cardiac atrium fibroblast (ENCLB558CTT)

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/ENCSR936TYP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of cardiac atrium fibroblast primary cell type (HCF-aa). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR936TYP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR110BDY
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB558CTT
size range: >200

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens cardiac atrium fibroblast primary cell male child (2 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/f8bcbd6c-3f36-4d33-9ae8-796e2a169b90/@@download/attachment/295343.pdf

value: cardiac atrium fibroblast

value: primary cell

tag: description

value: Cardiac fibroblast (HCF-aa) from the atrial region of a 2 year old caucasian male.

tag: biosample encode accession

tag: age

value: 2 year

tag: dev stage

value: child

tag: passage number

tag: Sex

value: male

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS958FEK at ENCODE; https://www.encodeproject.org/ENCBS958FEK/

value: Derived from ENCODE donor ENCDO664YBM; https://www.encodeproject.org/ENCDO664YBM/

value: ScienCell sample source; http://sciencellonline.com/human-cardiac-fibroblast-adult-atrial-total-rna.html


title: polyA mRNA RNA-seq from HepG2 (ENCLB716GPJ)

description:
https://www.encodeproject.org/experiments/ENCSR931WGT/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial cytosolic fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR931WGT
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB716GPJ
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line cytosolic fraction

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

tag: line

value: immortalized cell line

value: 15 year

tag: health state

value: hepatocellular carcinoma

value: Eric Lécuyer, IRCM

tag: subcellular fraction term name

value: cytosol

value: ENCBS955ZHF at ENCODE; https://www.encodeproject.org/ENCBS955ZHF/

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: polyA mRNA RNA-seq from HepG2 (ENCLB644EBX)

description:
https://www.encodeproject.org/experiments/ENCSR931WGT/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial cytosolic fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR931WGT
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB644EBX
size range: >200
spikeins used: /references/ENCSR422PLF/

value: ENCBS853NQW at ENCODE; https://www.encodeproject.org/ENCBS853NQW/


title: shRNA RNA-seq from K562 (ENCLB477GKN)

description:
https://www.encodeproject.org/experiments/ENCSR936TED/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against POLR2G. (K-POLR2G-30B)
experiment encode accession: ENCSR936TED
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR942UNX
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB477GKN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting POLR2G

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/d6a71f8f-a437-4973-b501-9831999b671c/@@download/attachment/L-K-POLR2G-30B-2.pdf

tag: antibody

value: K562 cells treated with an shRNA knockdown against POL2RG, used in RNA-seq experiments. (K-POLR2G-30B-2)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS023YVH at ENCODE; https://www.encodeproject.org/ENCBS023YVH/

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

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


title: total RNA-seq from Peyer's patch (ENCLB979JEG)

description:
https://www.encodeproject.org/experiments/ENCSR544SAU/
***************
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 small intestine tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR544SAU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB979JEG
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens Peyer's patch tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/65945347-4140-4302-960f-dccb1bd78586/@@download/attachment/296379.pdf

value: Peyer's patch

value: tissue

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

value: Thomas Gingeras, CSHL

value: ENCBS231DCI at ENCODE; https://www.encodeproject.org/ENCBS231DCI/

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


title: shRNA RNA-seq from HepG2 (ENCLB082QUQ)

description:
https://www.encodeproject.org/experiments/ENCSR542ESY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against KRR1. (KRR1_BGHLV27)
experiment encode accession: ENCSR542ESY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB082QUQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting KRR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2b8e0ddd-cfb5-4b96-839f-6bdb1d3af56e/@@download/attachment/L-KRR1_BGHLV27-28.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against KRR1 (KRR1_BGHLV27-28)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS401LBP at ENCODE; https://www.encodeproject.org/ENCBS401LBP/

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 (ENCLB546PQT)

description:
https://www.encodeproject.org/experiments/ENCSR562CCA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SF1. (SF1_BGKLV28)
experiment encode accession: ENCSR562CCA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB546PQT
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a1153b6b-6ac6-4b34-8835-03da22a751a2/@@download/attachment/L-SF1_BGKLV28-50.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SF1. (SF1_BGKLV28-50)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS013ENT at ENCODE; https://www.encodeproject.org/ENCBS013ENT/

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


title: shRNA RNA-seq from K562 (ENCLB859EBA)

description:
https://www.encodeproject.org/experiments/ENCSR927XBT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGKLV21)
experiment encode accession: ENCSR927XBT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB859EBA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting NUSAP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/24fa3981-9155-46be-bc53-692ad9effee9/@@download/attachment/L-NUSAP1_BGKLV21_37_17578.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGKLV21_37_17578)

value: ENCBS237RBH at ENCODE; https://www.encodeproject.org/ENCBS237RBH/

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


title: shRNA RNA-seq from K562 (ENCLB009EQT)

description:
https://www.encodeproject.org/experiments/ENCSR927XBT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGKLV21)
experiment encode accession: ENCSR927XBT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB009EQT
size range: >200
spikeins used: /references/ENCSR449DXG/
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cb14040a-ea25-4fe1-9b9d-f34d8c83f04f/@@download/attachment/L-NUSAP1_BGKLV21_38_17579.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGKLV21_38_17579)

value: ENCBS897EVB at ENCODE; https://www.encodeproject.org/ENCBS897EVB/


title: shRNA RNA-seq from K562 (ENCLB291SNE)

description:
https://www.encodeproject.org/experiments/ENCSR927TSP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TIAL1. (TIAL1_BGKLV21)
experiment encode accession: ENCSR927TSP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB291SNE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TIAL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/07dfdee4-c11b-443c-ba1a-e40926e97031/@@download/attachment/L-TIAL1_BGKLV21_62_17589.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TIAL1. (TIAL1_BGKLV21_62_17589)

value: ENCBS973CSB at ENCODE; https://www.encodeproject.org/ENCBS973CSB/


title: shRNA RNA-seq from K562 (ENCLB957HFM)

description:
https://www.encodeproject.org/experiments/ENCSR535YPK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SFPQ. (SFPQ_BGKLV28)
experiment encode accession: ENCSR535YPK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB957HFM
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/895453df-281f-47c4-8fd4-9c5519c50130/@@download/attachment/L-SFPQ_BGKLV28-51.pdf

value: SFPQ

value: RNA-seq on K562 cells treated with an shRNA knockdown against SFPQ. (SFPQ_BGKLV28-51)

value: ENCBS613LBH at ENCODE; https://www.encodeproject.org/ENCBS613LBH/


title: shRNA RNA-seq from HepG2 (ENCLB456FVF)

description:
https://www.encodeproject.org/experiments/ENCSR532ZPP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against EWSR1. (EWSR1_BGHLV31)
experiment encode accession: ENCSR532ZPP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB456FVF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EWSR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/35999a95-a197-497c-baa4-28f0363cc859/@@download/attachment/L-EWSR1_BGHLV31-36.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EWSR1. (EWSR1_BGHLV31-36)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS221OJT at ENCODE; https://www.encodeproject.org/ENCBS221OJT/

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 (ENCLB806XEG)

description:
https://www.encodeproject.org/experiments/ENCSR927TSP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TIAL1. (TIAL1_BGKLV21)
experiment encode accession: ENCSR927TSP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB806XEG
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/33c2fb61-1ae9-4b55-b291-2517b499b360/@@download/attachment/L-TIAL1_BGKLV21_61_17588.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against TIAL1. (TIAL1_BGKLV21_61_17588)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS647KYQ at ENCODE; https://www.encodeproject.org/ENCBS647KYQ/

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


title: shRNA RNA-seq from HepG2 (ENCLB541DUY)

description:
https://www.encodeproject.org/experiments/ENCSR927SLP/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against LIN28B in HepG2 cells followed by RNA-seq. (LIN28B_BGHLV18)
experiment encode accession: ENCSR927SLP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB541DUY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting LIN28B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3660abac-2451-42b5-aa7d-8b57b455228a/@@download/attachment/L-LIN28B_BGHLV18_21.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against LIN28B. (LIN28B_BGHLV18_21)

value: ENCBS487SZV at ENCODE; https://www.encodeproject.org/ENCBS487SZV/


title: shRNA RNA-seq from HepG2 (ENCLB802OBT)

description:
https://www.encodeproject.org/experiments/ENCSR532ZPP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against EWSR1. (EWSR1_BGHLV31)
experiment encode accession: ENCSR532ZPP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB802OBT
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/a4358839-71f3-4115-aa2c-d41022107901/@@download/attachment/L-EWSR1_BGHLV31-35.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EWSR1. (EWSR1_BGHLV31-35)

value: 15 year

value: child

value: ENCBS599QJL at ENCODE; https://www.encodeproject.org/ENCBS599QJL/


title: shRNA RNA-seq from HepG2 (ENCLB097DXK)

description:
https://www.encodeproject.org/experiments/ENCSR542ESY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against KRR1. (KRR1_BGHLV27)
experiment encode accession: ENCSR542ESY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB097DXK
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/36b3e6ea-1c92-496c-9309-cd1677690b99/@@download/attachment/L-KRR1_BGHLV27-27.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against KRR1 (KRR1_BGHLV27-27)

value: male

value: hepatocellular carcinoma

value: ENCBS892VZB at ENCODE; https://www.encodeproject.org/ENCBS892VZB/

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


title: shRNA RNA-seq from K562 (ENCLB682EEI)

description:
https://www.encodeproject.org/experiments/ENCSR530BOP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGKLV28)
experiment encode accession: ENCSR530BOP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB682EEI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SUPT6H

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/87f2bdd5-93e1-4ff7-ae5d-3cb3b492bab1/@@download/attachment/L-SUPT6H_BGKLV28-58.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGKLV28-58)

value: 53 year

value: adult

value: ENCBS590PKD at ENCODE; https://www.encodeproject.org/ENCBS590PKD/

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


title: shRNA RNA-seq from K562 (ENCLB575IMJ)

description:
https://www.encodeproject.org/experiments/ENCSR936TED/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against POLR2G. (K-POLR2G-30B)
experiment encode accession: ENCSR936TED
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR942UNX
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB575IMJ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/460a0427-7737-40f3-ad2a-8eecb37b4a64/@@download/attachment/L-K-POLR2G-30B-1.pdf

value: K562 cells treated with an shRNA knockdown against POL2RG, used in RNA-seq experiments. (K-POLR2G-30B-1)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS865CZC at ENCODE; https://www.encodeproject.org/ENCBS865CZC/

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


title: shRNA RNA-seq from HepG2 (ENCLB720DGG)

description:
https://www.encodeproject.org/experiments/ENCSR927SLP/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against LIN28B in HepG2 cells followed by RNA-seq. (LIN28B_BGHLV18)
experiment encode accession: ENCSR927SLP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB720DGG
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/fc9e18f8-1a80-43d4-b03a-b0226e48861b/@@download/attachment/L-LIN28B_BGHLV18_22.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against LIN28B. (LIN28B_BGHLV18_22)

value: 15 year

value: child

value: ENCBS314VPT at ENCODE; https://www.encodeproject.org/ENCBS314VPT/

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


title: shRNA RNA-seq from K562 (ENCLB479ITK)

description:
https://www.encodeproject.org/experiments/ENCSR529MBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PPIG. (PPIG_BGKLV29)
experiment encode accession: ENCSR529MBZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB479ITK
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c2dbedee-f061-4005-a8ca-cd993d198117/@@download/attachment/L-PPIG_BGKLV29-47.pdf

value: PPIG

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PPIG. (PPIG_BGKLV29-47)

value: ENCBS782UIO at ENCODE; https://www.encodeproject.org/ENCBS782UIO/


title: total RNA-seq from gastroesophageal sphincter (ENCLB317XOT)

description:
https://www.encodeproject.org/experiments/ENCSR528ZKN/
***************
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: ENCSR528ZKN
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB317XOT
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens gastroesophageal sphincter tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/31c88410-ea80-4059-8960-b72fc3c93f45/@@download/attachment/296186.pdf

value: gastroesophageal sphincter

value: tissue

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

value: 37 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS581RWW at ENCODE; https://www.encodeproject.org/ENCBS581RWW/

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


title: shRNA RNA-seq from K562 (ENCLB101LMZ)

description:
https://www.encodeproject.org/experiments/ENCSR529MBZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PPIG. (PPIG_BGKLV29)
experiment encode accession: ENCSR529MBZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB101LMZ
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/1a632454-5547-4b7e-bdf5-22667a205abe/@@download/attachment/L-PPIG_BGKLV29-48.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PPIG. (PPIG_BGKLV29-48)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS442VLY at ENCODE; https://www.encodeproject.org/ENCBS442VLY/

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 (ENCLB580GBV)

description:
https://www.encodeproject.org/experiments/ENCSR925RNE/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SERBP1 in K562 cells followed by RNA-seq. (SERBP1_BGKLV19)
experiment encode accession: ENCSR925RNE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB580GBV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SERBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/723ad565-debc-428f-818e-2bcf25081d21/@@download/attachment/L-SERBP1_BGKLV19_50B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SERBP1. (SERBP1_BGKLV19_50B)

value: ENCBS622KGA at ENCODE; https://www.encodeproject.org/ENCBS622KGA/


title: microRNA-seq from testis (ENCLB955HCC)

description:
https://www.encodeproject.org/experiments/ENCSR915GVH/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human testis
experiment encode accession: ENCSR915GVH
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB955HCC
size range: <30

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

value: testis

value: tissue

value: Testis 1-2

value: 37 year

value: Barbara Wold, Caltech

value: ENCBS653SLC at ENCODE; https://www.encodeproject.org/ENCBS653SLC/


title: microRNA-seq from testis (ENCLB524EML)

description:
https://www.encodeproject.org/experiments/ENCSR915GVH/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human testis
experiment encode accession: ENCSR915GVH
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB524EML
size range: <30

value: adult

value: male

value: ENCBS906LAU at ENCODE; https://www.encodeproject.org/ENCBS906LAU/

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


title: shRNA RNA-seq from K562 (ENCLB073QUH)

description:
https://www.encodeproject.org/experiments/ENCSR925RNE/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SERBP1 in K562 cells followed by RNA-seq. (SERBP1_BGKLV19)
experiment encode accession: ENCSR925RNE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB073QUH
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/4b4c23b5-66c3-45b6-975b-ae9c4987a735/@@download/attachment/L-SERBP1_BGKLV19_49B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SERBP1. (SERBP1_BGKLV19_49B)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS302IGJ at ENCODE; https://www.encodeproject.org/ENCBS302IGJ/


title: shRNA RNA-seq from K562 (ENCLB516HHP)

description:
https://www.encodeproject.org/experiments/ENCSR921KDS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RCC2. (RCC2_BGKLV21)
experiment encode accession: ENCSR921KDS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB516HHP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RCC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/da9f8c24-db72-4bf4-88af-da0790801f30/@@download/attachment/L-RCC2_BGKLV21_50_17585.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RCC2. (RCC2_BGKLV21_50_17585)

value: ENCBS451AJS at ENCODE; https://www.encodeproject.org/ENCBS451AJS/

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 (ENCLB301GFV)

description:
https://www.encodeproject.org/experiments/ENCSR921KDS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RCC2. (RCC2_BGKLV21)
experiment encode accession: ENCSR921KDS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB301GFV
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/1b2390c2-d0cf-4380-99d5-6d8864fe33f6/@@download/attachment/L-RCC2_BGKLV21_49_17584.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RCC2. (RCC2_BGKLV21_49_17584)

value: ENCBS164ITK at ENCODE; https://www.encodeproject.org/ENCBS164ITK/


title: shRNA RNA-seq from HepG2 (ENCLB862NUH)

description:
https://www.encodeproject.org/experiments/ENCSR538QOG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV31)
experiment encode accession: ENCSR538QOG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB862NUH
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/d08bb25f-15f7-4214-8559-30e2c3b6475e/@@download/attachment/L-NT-BGHLV31-1.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (NT-BGHLV31-1)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS590WTW at ENCODE; https://www.encodeproject.org/ENCBS590WTW/

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 (ENCLB860NSC)

description:
https://www.encodeproject.org/experiments/ENCSR527QNC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against TARDBP. (TARDBP_BGHLV35)
experiment encode accession: ENCSR527QNC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB860NSC
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d174832a-d461-410c-9172-1484503b4d33/@@download/attachment/L-TARDBP_BGHLV35-54.pdf

value: TARDBP

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TARDBP. (TARDBP_BGHLV35-54)

value: male

value: Brenton Graveley, UConn

value: ENCBS998LVK at ENCODE; https://www.encodeproject.org/ENCBS998LVK/


title: shRNA RNA-seq from K562 (ENCLB193OXR)

description:
https://www.encodeproject.org/experiments/ENCSR535YPK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SFPQ. (SFPQ_BGKLV28)
experiment encode accession: ENCSR535YPK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB193OXR
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/80e9a51b-33a5-44e5-83c9-2fd3011a27a5/@@download/attachment/L-SFPQ_BGKLV28-52.pdf

value: SFPQ

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SFPQ. (SFPQ_BGKLV28-52)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS162AGB at ENCODE; https://www.encodeproject.org/ENCBS162AGB/

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


title: shRNA RNA-seq from HepG2 (ENCLB489RDA)

description:
https://www.encodeproject.org/experiments/ENCSR527QNC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against TARDBP. (TARDBP_BGHLV35)
experiment encode accession: ENCSR527QNC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB489RDA
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/fab92e50-135c-41fc-a5d0-882db6420698/@@download/attachment/L-TARDBP_BGHLV35-53.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TARDBP. (TARDBP_BGHLV35-53)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS483OZH at ENCODE; https://www.encodeproject.org/ENCBS483OZH/


title: shRNA RNA-seq from K562 (ENCLB697XSQ)

description:
https://www.encodeproject.org/experiments/ENCSR524YXQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SRPK2. (SRPK2_BGKLV34)
experiment encode accession: ENCSR524YXQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB697XSQ
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SRPK2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e76005c6-2ab8-40e4-b31e-09bdd67b67c1/@@download/attachment/L-SRPK2_BGKLV34-39.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRPK2. (SRPK2_BGKLV34-39)

value: ENCBS652FMW at ENCODE; https://www.encodeproject.org/ENCBS652FMW/


title: RAMPAGE from adrenal gland (ENCLB140WPB)

description:
https://www.encodeproject.org/experiments/ENCSR970OWZ/
***************
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 adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR970OWZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR954PZB
encode release date: 2016-03-16
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB140WPB
size range: >200

source_name: Homo sapiens adrenal gland tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/84bf8c92-f70a-4506-ab67-661cfc3e4718/@@download/attachment/295990.pdf

value: adrenal gland

value: tissue

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

value: 54 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS724UYV at ENCODE; https://www.encodeproject.org/ENCBS724UYV/

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


title: shRNA RNA-seq from HepG2 (ENCLB387QPV)

description:
https://www.encodeproject.org/experiments/ENCSR913ZWR/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX52 in HepG2 cells followed by RNA-seq. (DDX52_BGHLV16)
experiment encode accession: ENCSR913ZWR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB387QPV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX52

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/36a6f72d-2ee2-4099-9db4-3c9de1fea2e4/@@download/attachment/L-DDX52_BGHLV16_14.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX52. (DDX52_BGHLV16_14)

value: Brenton Graveley, UConn

value: ENCBS897BFW at ENCODE; https://www.encodeproject.org/ENCBS897BFW/

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 (ENCLB314VYW)

description:
https://www.encodeproject.org/experiments/ENCSR530BOP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGKLV28)
experiment encode accession: ENCSR530BOP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB314VYW
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/6258844c-9c53-457b-a0cc-1d367b08de7f/@@download/attachment/L-SUPT6H_BGKLV28-57.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGKLV28-57)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS218LCA at ENCODE; https://www.encodeproject.org/ENCBS218LCA/

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 (ENCLB563SKV)

description:
https://www.encodeproject.org/experiments/ENCSR524YXQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SRPK2. (SRPK2_BGKLV34)
experiment encode accession: ENCSR524YXQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB563SKV
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/84e460b4-9f31-45bc-925d-7ac122fad595/@@download/attachment/L-SRPK2_BGKLV34-40.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRPK2. (SRPK2_BGKLV34-40)

value: ENCBS773VAN at ENCODE; https://www.encodeproject.org/ENCBS773VAN/


title: shRNA RNA-seq from HepG2 (ENCLB190PXH)

description:
https://www.encodeproject.org/experiments/ENCSR913ZWR/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX52 in HepG2 cells followed by RNA-seq. (DDX52_BGHLV16)
experiment encode accession: ENCSR913ZWR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB190PXH
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/fa77077e-14a8-4122-b977-5df3b86dc9a4/@@download/attachment/L-DDX52_BGHLV16_13.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX52. (DDX52_BGHLV16_13)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS994VIY at ENCODE; https://www.encodeproject.org/ENCBS994VIY/


title: shRNA RNA-seq from HepG2 (ENCLB121KJF)

description:
https://www.encodeproject.org/experiments/ENCSR912EHP/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PES1 in HepG2 cells followed by RNA-seq. (PES1_BGHLV17)
experiment encode accession: ENCSR912EHP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB121KJF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PES1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c1cc6034-5d74-420d-a55d-1a0ada295ee3/@@download/attachment/L-PES1_BGHLV17_19.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PES1. (PES1_BGHLV17_19)

value: Brenton Graveley, UConn

value: ENCBS067QSF at ENCODE; https://www.encodeproject.org/ENCBS067QSF/

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 (ENCLB808NDU)

description:
https://www.encodeproject.org/experiments/ENCSR518JXY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZNF622. (ZNF622_BGHLV33)
experiment encode accession: ENCSR518JXY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB808NDU
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ZNF622

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ffa0bbca-2b66-4609-88f7-adf8592a1273/@@download/attachment/L-ZNF622_BGHLV33-48.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZNF622. (ZNF622_BGHLV33-48)

value: ENCBS081QNQ at ENCODE; https://www.encodeproject.org/ENCBS081QNQ/


title: shRNA RNA-seq from K562 (ENCLB768TAQ)

description:
https://www.encodeproject.org/experiments/ENCSR911DGK/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TFIP11 in K562 cells followed by RNA-seq. (TFIP11_BGKLV19)
experiment encode accession: ENCSR911DGK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB768TAQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TFIP11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a51107eb-0af5-42b2-b350-ca7809a8a50b/@@download/attachment/L-TFIP11_BGKLV19_56B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TFIP11. (TFIP11_BGKLV19_56B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS530DUV at ENCODE; https://www.encodeproject.org/ENCBS530DUV/

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 (ENCLB970WUE)

description:
https://www.encodeproject.org/experiments/ENCSR912EHP/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PES1 in HepG2 cells followed by RNA-seq. (PES1_BGHLV17)
experiment encode accession: ENCSR912EHP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB970WUE
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/4b906015-a775-4cc5-bf57-98910830b0c1/@@download/attachment/L-PES1_BGHLV17_20.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PES1. (PES1_BGHLV17_20)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS287NGC at ENCODE; https://www.encodeproject.org/ENCBS287NGC/


title: shRNA RNA-seq from K562 (ENCLB626TCW)

description:
https://www.encodeproject.org/experiments/ENCSR517JHY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MAK16. (MAK16_BGKLV32)
experiment encode accession: ENCSR517JHY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB626TCW
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting MAK16

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/faa6853e-b22f-43f6-8580-6f220d3b9e68/@@download/attachment/L-MAK16_BGKLV32-37.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against MAK16. (MAK16_BGKLV32-37)

value: Brenton Graveley, UConn

value: ENCBS400IMH at ENCODE; https://www.encodeproject.org/ENCBS400IMH/


title: shRNA RNA-seq from K562 (ENCLB601HEF)

description:
https://www.encodeproject.org/experiments/ENCSR911DGK/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TFIP11 in K562 cells followed by RNA-seq. (TFIP11_BGKLV19)
experiment encode accession: ENCSR911DGK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB601HEF
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/765ea189-b0ef-4ec9-9ad4-e16f8241fbb6/@@download/attachment/L-TFIP11_BGKLV19_55B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TFIP11. (TFIP11_BGKLV19_55B)

value: 53 year

value: ENCBS506VSB at ENCODE; https://www.encodeproject.org/ENCBS506VSB/


title: shRNA RNA-seq from K562 (ENCLB147PAM)

description:
https://www.encodeproject.org/experiments/ENCSR517JHY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MAK16. (MAK16_BGKLV32)
experiment encode accession: ENCSR517JHY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB147PAM
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/52d2e1e8-6e4d-4779-bab3-7c9883eeef68/@@download/attachment/L-MAK16_BGKLV32-38.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against MAK16. (MAK16_BGKLV32-38)

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS590KAM at ENCODE; https://www.encodeproject.org/ENCBS590KAM/


title: shRNA RNA-seq from HepG2 (ENCLB026YCO)

description:
https://www.encodeproject.org/experiments/ENCSR910YNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PABPC1. (PABPC1-BGHLV22)
experiment encode accession: ENCSR910YNJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB026YCO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PABPC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ab9f0f44-426c-426a-89be-bdb872787476/@@download/attachment/L-PABPC1-BGHLV22-34.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PABPC1. (PABPC1-BGHLV22-34)

value: 15 year

value: ENCBS296ABO at ENCODE; https://www.encodeproject.org/ENCBS296ABO/

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 (ENCLB999FKH)

description:
https://www.encodeproject.org/experiments/ENCSR518JXY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZNF622. (ZNF622_BGHLV33)
experiment encode accession: ENCSR518JXY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB999FKH
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/fc0c2cbe-3da5-44e8-aef6-12888a76e5d4/@@download/attachment/L-ZNF622_BGHLV33-47.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZNF622. (ZNF622_BGHLV33-47)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS141CQG at ENCODE; https://www.encodeproject.org/ENCBS141CQG/


title: shRNA RNA-seq from HepG2 (ENCLB752SNL)

description:
https://www.encodeproject.org/experiments/ENCSR910YNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PABPC1. (PABPC1-BGHLV22)
experiment encode accession: ENCSR910YNJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB752SNL
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/eec7dea2-cd91-436a-adc9-4d60fd927c41/@@download/attachment/L-PABPC1-BGHLV22-33.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PABPC1. (PABPC1-BGHLV22-33)

value: Brenton Graveley, UConn

value: ENCBS315MGA at ENCODE; https://www.encodeproject.org/ENCBS315MGA/


title: shRNA RNA-seq from K562 (ENCLB639AXF)

description:
https://www.encodeproject.org/experiments/ENCSR907UTB/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DAZAP1 in K562 cells followed by RNA-seq. (DAZAP1 BGKLV13)
experiment encode accession: ENCSR907UTB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB639AXF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DAZAP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/234f2a3a-112a-457f-a727-41fc6d16eb05/@@download/attachment/L-DAZAP1_BGKLV13_38.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DAZAP1.(DAZAP1_BGKLV13_38)

value: 53 year

value: adult

value: female

value: ENCBS808ZQB at ENCODE; https://www.encodeproject.org/ENCBS808ZQB/

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 (ENCLB128IHE)

description:
https://www.encodeproject.org/experiments/ENCSR511BNY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGKLV29)
experiment encode accession: ENCSR511BNY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB128IHE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting FIP1L1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bf4f5c89-12c3-47e2-9ee3-33466a14831c/@@download/attachment/L-FIP1L1_BGKLV29-33.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGKLV29-33)

value: chronic myelogenous leukemia (CML)

value: ENCBS690NWI at ENCODE; https://www.encodeproject.org/ENCBS690NWI/


title: shRNA RNA-seq from HepG2 (ENCLB986ZDR)

description:
https://www.encodeproject.org/experiments/ENCSR511SYK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ACO1. (ACO1_BGHLV31)
experiment encode accession: ENCSR511SYK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB986ZDR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ACO1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/519e0d01-4eee-44d4-9391-0adfa9ff11d0/@@download/attachment/L-ACO1_BGHLV31-6.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ACO1. (ACO1_BGHLV31-6)

value: 15 year

value: child

value: ENCBS266IRW at ENCODE; https://www.encodeproject.org/ENCBS266IRW/

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 (ENCLB376AEJ)

description:
https://www.encodeproject.org/experiments/ENCSR511SYK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ACO1. (ACO1_BGHLV31)
experiment encode accession: ENCSR511SYK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB376AEJ
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/95b4c17b-9328-4b3c-bfb1-633465e59d1d/@@download/attachment/L-ACO1_BGHLV31-5.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ACO1. (ACO1_BGHLV31-5)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS339GWD at ENCODE; https://www.encodeproject.org/ENCBS339GWD/


title: total RNA-seq from fibroblast of arm (ENCLB851MTT)

description:
https://www.encodeproject.org/experiments/ENCSR510QZW/
***************
biological replicate number: 2
technical replicate number: 1
description: fibroblast of arm
experiment encode accession: ENCSR510QZW
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB851MTT
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

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

value: fibroblast of arm

value: primary cell

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

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

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

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

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

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


title: shRNA RNA-seq from HepG2 (ENCLB061ZSN)

description:
https://www.encodeproject.org/experiments/ENCSR905HID/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FMR1. (FMR1-BGHLV23)
experiment encode accession: ENCSR905HID
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB061ZSN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting FMR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b3545661-5d8d-4b13-a21c-8716375d8183/@@download/attachment/L-FMR1-BGHLV23-18.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FMR1. (FMR1-BGHLV23-18)

value: child

value: 15 year

value: ENCBS901YOY at ENCODE; https://www.encodeproject.org/ENCBS901YOY/

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


title: shRNA RNA-seq from HepG2 (ENCLB552FZS)

description:
https://www.encodeproject.org/experiments/ENCSR517JDK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NKRF. (NKRF_BGHLV27)
experiment encode accession: ENCSR517JDK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB552FZS
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f444d683-65d3-4b84-ba5a-eee8ddeac6da/@@download/attachment/L-NKRF_BGHLV27-37.pdf

value: NKRF

value: RNA-seq on HepG2 cells treated with an Control shRNA against NKRF (NKRF_BGHLV27-37)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS696KRJ at ENCODE; https://www.encodeproject.org/ENCBS696KRJ/

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


title: shRNA RNA-seq from HepG2 (ENCLB793URP)

description:
https://www.encodeproject.org/experiments/ENCSR905HID/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FMR1. (FMR1-BGHLV23)
experiment encode accession: ENCSR905HID
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB793URP
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/e9c01f17-a252-4eaf-93a1-e1d2fcd68299/@@download/attachment/L-FMR1-BGHLV23-17.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FMR1. (FMR1-BGHLV23-17)

value: ENCBS130RRG at ENCODE; https://www.encodeproject.org/ENCBS130RRG/


title: shRNA RNA-seq from K562 (ENCLB380KQV)

description:
https://www.encodeproject.org/experiments/ENCSR898NWE/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq
experiment encode accession: ENCSR898NWE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB380KQV
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: Trizol (LifeTech cat#: 15596-018)

value: Control

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. This K562 growth has been treated with a control shRNA.

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS698ZKR at ENCODE; https://www.encodeproject.org/ENCBS698ZKR/

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

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

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: total RNA-seq from fibroblast of arm (ENCLB956GGO)

description:
https://www.encodeproject.org/experiments/ENCSR510QZW/
***************
biological replicate number: 1
technical replicate number: 1
description: fibroblast of arm
experiment encode accession: ENCSR510QZW
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB956GGO
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: fibroblast of arm

value: primary cell

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

value: male

value: Thomas Gingeras, CSHL

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

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

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

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


title: shRNA RNA-seq from K562 (ENCLB752PAC)

description:
https://www.encodeproject.org/experiments/ENCSR898NWE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq
experiment encode accession: ENCSR898NWE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB752PAC
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/0609b5c0-f2d3-4772-a5ab-b54fb3717ee9/@@download/attachment/L-K-non-target-1.pdf

value: Control

value: immortalized cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. This K562 growth has been treated with a control shRNA.

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS322JPK at ENCODE; https://www.encodeproject.org/ENCBS322JPK/


title: total RNA-seq from right lobe of liver (ENCLB381PQE)

description:
https://www.encodeproject.org/experiments/ENCSR504QMK/
***************
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 liver 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: ENCSR504QMK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB381PQE
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5abfbc82-cc27-4781-83f4-4c975bd3b178/@@download/attachment/296325.pdf

value: right lobe of liver

value: tissue

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

value: adult

value: female

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

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


title: shRNA RNA-seq from K562 (ENCLB517VKB)

description:
https://www.encodeproject.org/experiments/ENCSR511BNY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGKLV29)
experiment encode accession: ENCSR511BNY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB517VKB
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/23a75814-d3b3-4a85-9a01-a1c93dcce546/@@download/attachment/L-FIP1L1_BGKLV29-34.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGKLV29-34)

value: chronic myelogenous leukemia (CML)

value: ENCBS029GNW at ENCODE; https://www.encodeproject.org/ENCBS029GNW/

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 esophagus squamous epithelium (ENCLB736YFJ)

description:
https://www.encodeproject.org/experiments/ENCSR510MIA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the mucosa of the esophagus obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR510MIA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB736YFJ
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/24be2f2d-f5d1-4b7f-9231-d078bbba5a92/@@download/attachment/296192.pdf

value: esophagus squamous epithelium

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

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS842VSS at ENCODE; https://www.encodeproject.org/ENCBS842VSS/

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


title: shRNA RNA-seq from HepG2 (ENCLB950ZAG)

description:
https://www.encodeproject.org/experiments/ENCSR517JDK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NKRF. (NKRF_BGHLV27)
experiment encode accession: ENCSR517JDK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB950ZAG
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/4fafb939-77a0-4b3c-a01f-1062d064816b/@@download/attachment/L-NKRF_BGHLV27-38.pdf

value: NKRF

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against NKRF (NKRF_BGHLV27-38)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS114MFP at ENCODE; https://www.encodeproject.org/ENCBS114MFP/

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 (ENCLB236SEZ)

description:
https://www.encodeproject.org/experiments/ENCSR891DYO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PES1 in K562 cells followed by RNA-seq. (PES1_BGKLV19)
experiment encode accession: ENCSR891DYO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB236SEZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PES1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a0d33612-a058-4465-a502-dacd8ddcc24b/@@download/attachment/L-PES1_BGKLV19_40B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PES1. (PES1_BGKLV19_40B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS588YDJ at ENCODE; https://www.encodeproject.org/ENCBS588YDJ/

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 subcutaneous adipose tissue (ENCLB439GZV)

description:
https://www.encodeproject.org/experiments/ENCSR504NIU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's adipose tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR504NIU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB439GZV
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7854fc11-b6d5-4f61-bdaa-a0ac0d4a3514/@@download/attachment/296164.pdf

value: subcutaneous adipose tissue

value: tissue

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

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from K562 (ENCLB654XKK)

description:
https://www.encodeproject.org/experiments/ENCSR891DYO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PES1 in K562 cells followed by RNA-seq. (PES1_BGKLV19)
experiment encode accession: ENCSR891DYO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB654XKK
size range: >200
spikeins used: /references/ENCSR449DXG/

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 PES1. (PES1_BGKLV19_39B)

value: Brenton Graveley, UConn

value: ENCBS891EMR at ENCODE; https://www.encodeproject.org/ENCBS891EMR/


title: shRNA RNA-seq from K562 (ENCLB152NIY)

description:
https://www.encodeproject.org/experiments/ENCSR907UTB/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DAZAP1 in K562 cells followed by RNA-seq. (DAZAP1 BGKLV13)
experiment encode accession: ENCSR907UTB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB152NIY
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/3bbb9b78-768b-40c7-8269-3f925ee25210/@@download/attachment/L-DAZAP1_BGKLV13_37.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DAZAP1.(DAZAP1_BGKLV13_37)

value: 53 year

value: ENCBS017YLT at ENCODE; https://www.encodeproject.org/ENCBS017YLT/


title: total RNA-seq from HepG2 (ENCLB180MXK)

description:
https://www.encodeproject.org/experiments/ENCSR887ZSY/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial membrane fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR887ZSY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB180MXK
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line membrane fraction

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: membrane

value: Eric Lécuyer, IRCM

value: ENCBS553PEJ at ENCODE; https://www.encodeproject.org/ENCBS553PEJ/

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 suprapubic skin (ENCLB554UDA)

description:
https://www.encodeproject.org/experiments/ENCSR501EGS/
***************
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: ENCSR501EGS
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR862RGX
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB554UDA
size range: >200

source_name: Homo sapiens suprapubic skin 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/d2ff803b-98d6-4e2a-9bad-ffe7a981360f/@@download/attachment/296810.pdf

value: suprapubic skin

value: tissue

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

value: 37 year

value: adult

value: Thomas Gingeras, CSHL

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

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


title: RAMPAGE from uterus (ENCLB761CYN)

description:
https://www.encodeproject.org/experiments/ENCSR502DKA/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human uterus tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR502DKA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR113HQM
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB761CYN
size range: >200

source_name: Homo sapiens uterus 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/142e6abb-1fab-42c1-bb0b-bc50527daa0c/@@download/attachment/296814.pdf

value: uterus

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

value: 53 year

value: female

value: ENCBS210YNQ at ENCODE; https://www.encodeproject.org/ENCBS210YNQ/

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


title: total RNA-seq from HepG2 (ENCLB962WGJ)

description:
https://www.encodeproject.org/experiments/ENCSR887ZSY/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial membrane fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR887ZSY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB962WGJ
size range: >200
spikeins used: /references/ENCSR422PLF/

value: immortalized cell line

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: membrane

value: Eric Lécuyer, IRCM

value: ENCBS433UJJ at ENCODE; https://www.encodeproject.org/ENCBS433UJJ/


title: RAMPAGE from stomach (ENCLB532BYE)

description:
https://www.encodeproject.org/experiments/ENCSR497BYB/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human stomach tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR497BYB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR853WOM
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB532BYE
size range: >200

source_name: Homo sapiens stomach 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/67a2987a-df69-4d9a-a984-da0f5e80f745/@@download/attachment/296848.pdf

value: stomach

value: tissue

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

value: 51 year

value: adult

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from K562 (ENCLB850WBY)

description:
https://www.encodeproject.org/experiments/ENCSR891AXF/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SSB in K562 cells followed by RNA-seq. (SSB BGKLV13)
experiment encode accession: ENCSR891AXF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB850WBY
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2d04d681-fad9-4a19-849d-5d30e27f5dcc/@@download/attachment/L-SSB_BGKLV13_67.pdf

value: SSB

value: RNA-seq on K562 cells treated with an shRNA knockdown against SSB.(SSB_BGKLV13_67)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS326ULG at ENCODE; https://www.encodeproject.org/ENCBS326ULG/

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 K562 (ENCLB728XIS)

description:
https://www.encodeproject.org/experiments/ENCSR885DVH/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial total fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR885DVH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB728XIS
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: Eric Lécuyer, IRCM

value: ENCBS036OIX at ENCODE; https://www.encodeproject.org/ENCBS036OIX/


title: shRNA RNA-seq from K562 (ENCLB793RBS)

description:
https://www.encodeproject.org/experiments/ENCSR885YOI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against CSTF2 in K562 cells followed by RNA-seq. (CSTF2_BGKLV19)
experiment encode accession: ENCSR885YOI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR245BNJ
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB793RBS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CSTF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b989f456-ebc8-4040-8c35-5f8e3b2b2507/@@download/attachment/L-CSTF2_BGKLV19_10A.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CSTF2. (CSTF2_BGKLV19_10A)

value: ENCBS731EBS at ENCODE; https://www.encodeproject.org/ENCBS731EBS/


title: shRNA RNA-seq from K562 (ENCLB123EUR)

description:
https://www.encodeproject.org/experiments/ENCSR891AXF/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SSB in K562 cells followed by RNA-seq. (SSB BGKLV13)
experiment encode accession: ENCSR891AXF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB123EUR
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/a425321f-b79f-45ab-af2c-c63acbbcaa34/@@download/attachment/L-SSB_BGKLV13_68.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SSB.(SSB_BGKLV13_68)

value: adult

value: ENCBS886PEW at ENCODE; https://www.encodeproject.org/ENCBS886PEW/


title: total RNA-seq from K562 (ENCLB381UET)

description:
https://www.encodeproject.org/experiments/ENCSR885DVH/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial total fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR885DVH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB381UET
size range: >200
spikeins used: /references/ENCSR866KGS/

value: ENCBS403VZZ at ENCODE; https://www.encodeproject.org/ENCBS403VZZ/


title: total RNA-seq from prostate gland (ENCLB016VKQ)

description:
https://www.encodeproject.org/experiments/ENCSR495HDM/
***************
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 prostate 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: ENCSR495HDM
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB016VKQ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens prostate gland tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f69a7821-86cb-4409-9c52-64033e09a4d6/@@download/attachment/296600.pdf

value: prostate gland

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS656EUB at ENCODE; https://www.encodeproject.org/ENCBS656EUB/

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


title: shRNA RNA-seq from HepG2 (ENCLB808TWB)

description:
https://www.encodeproject.org/experiments/ENCSR496ETJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PES1. (PES1_BGHLV31)
experiment encode accession: ENCSR496ETJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB808TWB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PES1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/458f58ef-182a-42fb-b62a-dfc1ae85ad72/@@download/attachment/L-PES1_BGHLV31-46.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PES1. (PES1_BGHLV31-46)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS502FPQ at ENCODE; https://www.encodeproject.org/ENCBS502FPQ/

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 (ENCLB991SXF)

description:
https://www.encodeproject.org/experiments/ENCSR496ETJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PES1. (PES1_BGHLV31)
experiment encode accession: ENCSR496ETJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB991SXF
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/274b46d6-f518-4bd3-86c6-4115a2372058/@@download/attachment/L-PES1_BGHLV31-45.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PES1. (PES1_BGHLV31-45)

value: ENCBS484TBT at ENCODE; https://www.encodeproject.org/ENCBS484TBT/


title: shRNA RNA-seq from K562 (ENCLB203XEC)

description:
https://www.encodeproject.org/experiments/ENCSR885YOI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against CSTF2 in K562 cells followed by RNA-seq. (CSTF2_BGKLV19)
experiment encode accession: ENCSR885YOI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR245BNJ
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB203XEC
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/3bedbd60-9951-4483-84ee-c8524b7868b5/@@download/attachment/L-CSTF2_BGKLV19_9A.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CSTF2. (CSTF2_BGKLV19_9A)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS745UXY at ENCODE; https://www.encodeproject.org/ENCBS745UXY/

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 (ENCLB785FWS)

description:
https://www.encodeproject.org/experiments/ENCSR883BXR/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against LSM11 in HepG2 cells followed by RNA-seq. (LSM11_BGHLV18)
experiment encode accession: ENCSR883BXR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB785FWS
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ece1c434-50f7-4152-947a-d1ba89112582/@@download/attachment/L-LSM11_BGHLV18_23.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against LSM11. (LSM11_BGHLV18_23)

value: 15 year

value: male

value: ENCBS508YFO at ENCODE; https://www.encodeproject.org/ENCBS508YFO/


title: shRNA RNA-seq from K562 (ENCLB652AJP)

description:
https://www.encodeproject.org/experiments/ENCSR494UDF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DKC1. (DKC1_BGKLV32)
experiment encode accession: ENCSR494UDF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB652AJP
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4c769ead-8108-4367-b012-539827004a24/@@download/attachment/L-DKC1_BGKLV32-30.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DKC1. (DKC1_BGKLV32-30)

value: Brenton Graveley, UConn

value: ENCBS732XZP at ENCODE; https://www.encodeproject.org/ENCBS732XZP/


title: shRNA RNA-seq from HepG2 (ENCLB383KND)

description:
https://www.encodeproject.org/experiments/ENCSR538QOG/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV31)
experiment encode accession: ENCSR538QOG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB383KND
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/0fd2dc62-eab4-4ea9-bdeb-d69aba91dc37/@@download/attachment/L-NT-BGHLV31-2.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (NT-BGHLV31-2)

value: child

value: hepatocellular carcinoma

value: ENCBS734KAG at ENCODE; https://www.encodeproject.org/ENCBS734KAG/

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 glomerular endothelial cell (ENCLB608FPN)

description:
https://www.encodeproject.org/experiments/ENCSR878EUT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of primary renal glomerular endothelial cells (HGC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR878EUT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB608FPN
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4423e21e-9b63-4113-9673-d13ea45dd5f0/@@download/attachment/295116.pdf

value: glomerular endothelial cell

value: primary cell

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

value: fetal

value: female

value: 22 week

value: Thomas Gingeras, CSHL

value: ENCBS889CYK at ENCODE; https://www.encodeproject.org/ENCBS889CYK/

value: Derived from ENCODE donor ENCDO778HJK; https://www.encodeproject.org/ENCDO778HJK/