title: shRNA RNA-seq from K562 (ENCLB190YAP)

description:
https://www.encodeproject.org/experiments/ENCSR192BPV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGKLV28)
experiment encode accession: ENCSR192BPV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB190YAP
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/820bca26-45d2-4311-baac-1c0fc36b5ab5/@@download/attachment/L-SUGP2_BGKLV28-56.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGKLV28-56)

value: ENCBS799TLB at ENCODE; https://www.encodeproject.org/ENCBS799TLB/


title: total RNA-seq from K562 (ENCLB798NKH)

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/ENCSR696YIB/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial insoluble fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR696YIB
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB798NKH
size range: >200
spikeins used: /references/ENCSR866KGS/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 immortalized cell line insoluble cytoplasmic fraction

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

tag: line

tag: description

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: subcellular fraction term name

value: insoluble cytoplasmic fraction

tag: lab

value: Eric Lécuyer, IRCM

tag: link

value: ENCBS159UIB at ENCODE; https://www.encodeproject.org/ENCBS159UIB/

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 (ENCLB106DNY)

description:
https://www.encodeproject.org/experiments/ENCSR697GLD/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF4 in K562 cells followed by RNA-seq. (SRSF4 BGKLV13)
experiment encode accession: ENCSR697GLD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB106DNY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SRSF4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2ffd32a7-a754-4496-9800-bebcea1b7bcc/@@download/attachment/L-SRSF4_BGKLV13_50.pdf

tag: antibody

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF4.(SRSF4_BGKLV13_50)

value: Brenton Graveley, UConn

value: ENCBS103HEN at ENCODE; https://www.encodeproject.org/ENCBS103HEN/


title: shRNA RNA-seq from K562 (ENCLB078OFI)

description:
https://www.encodeproject.org/experiments/ENCSR697GLD/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF4 in K562 cells followed by RNA-seq. (SRSF4 BGKLV13)
experiment encode accession: ENCSR697GLD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB078OFI
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/9030dea2-6fa2-45d4-9853-4f7c43b6a037/@@download/attachment/L-SRSF4_BGKLV13_49.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF4.(SRSF4_BGKLV13_49)

value: ENCBS770VHR at ENCODE; https://www.encodeproject.org/ENCBS770VHR/


title: shRNA RNA-seq from HepG2 (ENCLB967GJQ)

description:
https://www.encodeproject.org/experiments/ENCSR706SXN/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RPL23A in HepG2 cells followed by RNA-seq. (RPL23A_BGHLV18)
experiment encode accession: ENCSR706SXN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB967GJQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RPL23A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d4310adf-b2a7-4911-b8a3-399d7d903798/@@download/attachment/L-RPL23A_BGHLV18_52.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPL23A. (RPL23A_BGHLV18_52)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS180AZS at ENCODE; https://www.encodeproject.org/ENCBS180AZS/

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 (ENCLB661HAY)

description:
https://www.encodeproject.org/experiments/ENCSR182GKG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGHLV31)
experiment encode accession: ENCSR182GKG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB661HAY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting KIF1C

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bbf32398-bc9b-4ed4-b978-c1ae85573818/@@download/attachment/L-KIF1C_BGHLV31-41.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGHLV31-41)

value: ENCBS135IEJ at ENCODE; https://www.encodeproject.org/ENCBS135IEJ/


title: total RNA-seq from esophagus muscularis mucosa (ENCLB275IVH)

description:
https://www.encodeproject.org/experiments/ENCSR182CBU/
***************
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 esophagal muscle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR182CBU
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB275IVH
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens esophagus muscularis mucosa tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/90f355e5-afdd-477c-9f94-73511d9c35f3/@@download/attachment/296290.pdf

value: esophagus muscularis mucosa

value: tissue

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

value: 37 year

value: adult

value: Thomas Gingeras, CSHL

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

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


title: RAMPAGE from omental fat pad (ENCLB649NOI)

description:
https://www.encodeproject.org/experiments/ENCSR176WZV/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human female adipose tissue of omentum tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR176WZV
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR729CAZ
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB649NOI
size range: >200

source_name: Homo sapiens omental fat pad 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/3c62bab8-c8a3-4b26-8494-a03f9dd40a51/@@download/attachment/296818.pdf

value: omental fat pad

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

value: ENCBS517FSZ at ENCODE; https://www.encodeproject.org/ENCBS517FSZ/


title: shRNA RNA-seq from K562 (ENCLB112III)

description:
https://www.encodeproject.org/experiments/ENCSR174OYC/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV34)
experiment encode accession: ENCSR174OYC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB112III
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/14c6c5dc-4fbd-4679-81a7-1d26a9bc5e41/@@download/attachment/L-NT_BGKLV34-2.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV34-2)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS645VVV at ENCODE; https://www.encodeproject.org/ENCBS645VVV/

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


title: shRNA RNA-seq from HepG2 (ENCLB924IXA)

description:
https://www.encodeproject.org/experiments/ENCSR696LLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against NIP7 in HepG2 cells followed by RNA-seq. (NIP7_BGHLV18)
experiment encode accession: ENCSR696LLZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB924IXA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NIP7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0ea795d4-47da-4506-be9c-ae39cb343f81/@@download/attachment/L-NIP7_BGHLV18_30.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NIP7. (NIP7_BGHLV18_30)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS755NZH at ENCODE; https://www.encodeproject.org/ENCBS755NZH/

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 (ENCLB687XPH)

description:
https://www.encodeproject.org/experiments/ENCSR174OYC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV34)
experiment encode accession: ENCSR174OYC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB687XPH
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/28ead38a-7cf9-438c-b5bd-13128c10b8df/@@download/attachment/L-NT_BGKLV34-1.pdf

value: Control

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV34-1)

value: adult

value: ENCBS922JMC at ENCODE; https://www.encodeproject.org/ENCBS922JMC/


title: shRNA RNA-seq from HepG2 (ENCLB022WHC)

description:
https://www.encodeproject.org/experiments/ENCSR182GKG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGHLV31)
experiment encode accession: ENCSR182GKG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB022WHC
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/7349032e-5c60-4fbb-a39b-2f782cfd19f7/@@download/attachment/L-KIF1C_BGHLV31-42.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against KIF1C. (KIF1C_BGHLV31-42)

value: ENCBS142FZQ at ENCODE; https://www.encodeproject.org/ENCBS142FZQ/


title: shRNA RNA-seq from HepG2 (ENCLB917FVM)

description:
https://www.encodeproject.org/experiments/ENCSR696LLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against NIP7 in HepG2 cells followed by RNA-seq. (NIP7_BGHLV18)
experiment encode accession: ENCSR696LLZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB917FVM
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/d751a465-1148-4731-b993-990f7c43cef7/@@download/attachment/L-NIP7_BGHLV18_29.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NIP7. (NIP7_BGHLV18_29)

value: Brenton Graveley, UConn

value: ENCBS467XVF at ENCODE; https://www.encodeproject.org/ENCBS467XVF/


title: shRNA RNA-seq from K562 (ENCLB181GSH)

description:
https://www.encodeproject.org/experiments/ENCSR165VBD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UTP18. (UTP18_BGKLV32)
experiment encode accession: ENCSR165VBD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB181GSH
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting UTP18

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fb0450c8-ab17-4178-a5af-ded5cf7d49a4/@@download/attachment/L-UTP18_BGKLV32-62.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UTP18. (UTP18_BGKLV32-62)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS063NCT at ENCODE; https://www.encodeproject.org/ENCBS063NCT/

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 (ENCLB090RXD)

description:
https://www.encodeproject.org/experiments/ENCSR165VBD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UTP18. (UTP18_BGKLV32)
experiment encode accession: ENCSR165VBD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB090RXD
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/6caad31c-9153-4868-bbc0-3d0421e2beac/@@download/attachment/L-UTP18_BGKLV32-61.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UTP18. (UTP18_BGKLV32-61)

value: ENCBS863MAI at ENCODE; https://www.encodeproject.org/ENCBS863MAI/


title: total RNA-seq from omental fat pad (ENCLB851XPG)

description:
https://www.encodeproject.org/experiments/ENCSR158KFO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's adipose tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR158KFO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB851XPG
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens omental fat pad tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5390ce3f-10f0-4b76-967a-bccee1eef17e/@@download/attachment/296319.pdf

value: omental fat pad

value: tissue

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

value: 51 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS689JVM at ENCODE; https://www.encodeproject.org/ENCBS689JVM/

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


title: shRNA RNA-seq from HepG2 (ENCLB426VJX)

description:
https://www.encodeproject.org/experiments/ENCSR693MZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against HNRNPF in HepG2 cells followed by RNA-seq. (HNRNPF-BGHLV20)
experiment encode accession: ENCSR693MZJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB426VJX
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/08032fa8-4d4e-43fe-939e-90e73b772bdb/@@download/attachment/L-HNRNPF-BGHLV20-36_17725.pdf

value: HNRNPF

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPF. (HNRNPF-BGHLV20-36_17725)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS783YSP at ENCODE; https://www.encodeproject.org/ENCBS783YSP/

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 (ENCLB261FZE)

description:
https://www.encodeproject.org/experiments/ENCSR695XOD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1-BGHLV23)
experiment encode accession: ENCSR695XOD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB261FZE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CELF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d40dcfcc-4367-44d5-b267-a53440f42efe/@@download/attachment/L-CUGBP1-BGHLV23-9.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1-BGHLV23-9)

value: ENCBS503ZYE at ENCODE; https://www.encodeproject.org/ENCBS503ZYE/


title: total RNA-seq from K562 (ENCLB212NSR)

description:
https://www.encodeproject.org/experiments/ENCSR696YIB/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial insoluble fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR696YIB
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB212NSR
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: insoluble cytoplasmic fraction

value: Eric Lécuyer, IRCM

value: ENCBS024ZBK at ENCODE; https://www.encodeproject.org/ENCBS024ZBK/

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

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


title: RAMPAGE from esophagus squamous epithelium (ENCLB936FXA)

description:
https://www.encodeproject.org/experiments/ENCSR161GPD/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human esophagus mucosa tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR161GPD
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR354QPN
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB936FXA
size range: >200

source_name: Homo sapiens esophagus squamous epithelium 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/c2a370d4-bb8b-4054-88d1-993779bdcee2/@@download/attachment/296743.pdf

value: esophagus squamous epithelium

value: tissue

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

value: male

value: 37 year

value: Thomas Gingeras, CSHL

value: ENCBS903FMK at ENCODE; https://www.encodeproject.org/ENCBS903FMK/

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


title: shRNA RNA-seq from K562 (ENCLB962XBU)

description:
https://www.encodeproject.org/experiments/ENCSR164MUK/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV28)
experiment encode accession: ENCSR164MUK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB962XBU
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/31d77641-a1f7-49c5-b192-665f9c262460/@@download/attachment/L-non-target_BGKLV28-2.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (non-target_BGKLV28-2)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS221YFO at ENCODE; https://www.encodeproject.org/ENCBS221YFO/


title: shRNA RNA-seq from HepG2 (ENCLB524NQG)

description:
https://www.encodeproject.org/experiments/ENCSR693MZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against HNRNPF in HepG2 cells followed by RNA-seq. (HNRNPF-BGHLV20)
experiment encode accession: ENCSR693MZJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB524NQG
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/158dc736-ba4c-4317-8425-5e2fa4bede26/@@download/attachment/L-HNRNPF-BGHLV20-35_17724.pdf

value: HNRNPF

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPF. (HNRNPF-BGHLV20-35_17724)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS399GAF at ENCODE; https://www.encodeproject.org/ENCBS399GAF/

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 (ENCLB626NCX)

description:
https://www.encodeproject.org/experiments/ENCSR689PHN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV16)
experiment encode accession: ENCSR689PHN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB626NCX
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/9434866f-d245-498f-9e95-bda7222a211b/@@download/attachment/L-NT_BGHLV16_2.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target. (NT_BGHLV16_2)

value: male

value: ENCBS634THO at ENCODE; https://www.encodeproject.org/ENCBS634THO/


title: shRNA RNA-seq from HepG2 (ENCLB588ZNH)

description:
https://www.encodeproject.org/experiments/ENCSR689PHN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV16)
experiment encode accession: ENCSR689PHN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB588ZNH
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/c174f593-70dc-4adf-8c7e-d411cac257be/@@download/attachment/L-NT_BGHLV16_1.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target. (NT_BGHLV16_1)

value: ENCBS415VLW at ENCODE; https://www.encodeproject.org/ENCBS415VLW/


title: microRNA-seq from heart left ventricle (ENCLB582GRG)

description:
https://www.encodeproject.org/experiments/ENCSR688RNO/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human heart left ventricle
experiment encode accession: ENCSR688RNO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB582GRG
size range: <30

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

value: heart left ventricle

value: tissue

value: Heart - Left Ventricle

value: 53 year

value: adult

value: female

value: Barbara Wold, Caltech

value: ENCBS156VIV at ENCODE; https://www.encodeproject.org/ENCBS156VIV/

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


title: microRNA-seq from heart left ventricle (ENCLB545AQM)

description:
https://www.encodeproject.org/experiments/ENCSR688RNO/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human heart left ventricle
experiment encode accession: ENCSR688RNO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB545AQM
size range: <30

value: ENCBS504IQD at ENCODE; https://www.encodeproject.org/ENCBS504IQD/


title: shRNA RNA-seq from K562 (ENCLB591CGS)

description:
https://www.encodeproject.org/experiments/ENCSR155EZL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX47. (DDX47_BGKLV25)
experiment encode accession: ENCSR155EZL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR031RRO
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB591CGS
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX47

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d5a4451d-fdb3-4135-89f5-c529b29a9133/@@download/attachment/L-DDX47_BGKLV25-13B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX47. (DDX47_BGKLV25-13B)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS089OTW at ENCODE; https://www.encodeproject.org/ENCBS089OTW/

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 (ENCLB506NGI)

description:
https://www.encodeproject.org/experiments/ENCSR164MUK/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV28)
experiment encode accession: ENCSR164MUK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB506NGI
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/2ff9fe61-0750-4f75-8dcc-c9a4eb9c6fd0/@@download/attachment/L-non-target_BGKLV28-1.pdf

value: Control

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (non-target_BGKLV28-1)

value: ENCBS136ZNW at ENCODE; https://www.encodeproject.org/ENCBS136ZNW/


title: shRNA RNA-seq from HepG2 (ENCLB297YZH)

description:
https://www.encodeproject.org/experiments/ENCSR685JXU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RCC2 in HepG2 cells followed by RNA-seq. (RCC2_BGHLV18)
experiment encode accession: ENCSR685JXU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB297YZH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/8985733f-835e-492f-97aa-760c5d54f1c5/@@download/attachment/L-RCC2_BGHLV18_50.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RCC2. (RCC2_BGHLV18_50)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS075HYT at ENCODE; https://www.encodeproject.org/ENCBS075HYT/

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 (ENCLB684FAA)

description:
https://www.encodeproject.org/experiments/ENCSR155EZL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX47. (DDX47_BGKLV25)
experiment encode accession: ENCSR155EZL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR031RRO
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB684FAA
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/6485c4ab-c038-45d2-805e-3522e71ccb96/@@download/attachment/L-DDX47_BGKLV25-14B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX47. (DDX47_BGKLV25-14B)

value: adult

value: female

value: 53 year

value: ENCBS857RNB at ENCODE; https://www.encodeproject.org/ENCBS857RNB/


title: shRNA RNA-seq from HepG2 (ENCLB553JQC)

description:
https://www.encodeproject.org/experiments/ENCSR695XOD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1-BGHLV23)
experiment encode accession: ENCSR695XOD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB553JQC
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/fd21b54e-334a-42e7-87d8-e627d862963c/@@download/attachment/L-CUGBP1-BGHLV23-10.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CUGBP1. (CUGBP1-BGHLV23-10)

value: Brenton Graveley, UConn

value: ENCBS257WFM at ENCODE; https://www.encodeproject.org/ENCBS257WFM/


title: shRNA RNA-seq from K562 (ENCLB455QLY)

description:
https://www.encodeproject.org/experiments/ENCSR154OBA/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV24C)
experiment encode accession: ENCSR154OBA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB455QLY
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/650eb73c-0d13-423f-b8f1-6cb6f167152e/@@download/attachment/L-NT_BGKLV24-2C.pdf

value: Control

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV24-2C)

value: chronic myelogenous leukemia (CML)

value: ENCBS044WJW at ENCODE; https://www.encodeproject.org/ENCBS044WJW/

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 (ENCLB425MPV)

description:
https://www.encodeproject.org/experiments/ENCSR150QJY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's adipose tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR150QJY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB425MPV
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens subcutaneous adipose tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/eb67bb4f-0ae7-40be-9c44-70df49ef009a/@@download/attachment/296166.pdf

value: subcutaneous adipose tissue

value: tissue

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

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS606FXX at ENCODE; https://www.encodeproject.org/ENCBS606FXX/

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


title: total RNA-seq from vagina (ENCLB757UWS)

description:
https://www.encodeproject.org/experiments/ENCSR146LBD/
***************
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 vaginal 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: ENCSR146LBD
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB757UWS
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7df88a9e-86d3-4424-9bee-07744ab7211e/@@download/attachment/296668.pdf

value: vagina

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

value: 53 year

value: adult

value: female

value: ENCBS158OEU at ENCODE; https://www.encodeproject.org/ENCBS158OEU/

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


title: shRNA RNA-seq from HepG2 (ENCLB661QFY)

description:
https://www.encodeproject.org/experiments/ENCSR685JXU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RCC2 in HepG2 cells followed by RNA-seq. (RCC2_BGHLV18)
experiment encode accession: ENCSR685JXU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB661QFY
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/54310f1e-9401-4f54-bf5a-0cc64ce92b5f/@@download/attachment/L-RCC2_BGHLV18_49.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RCC2. (RCC2_BGHLV18_49)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS637UJM at ENCODE; https://www.encodeproject.org/ENCBS637UJM/

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 (ENCLB758NTZ)

description:
https://www.encodeproject.org/experiments/ENCSR684HTV/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against UCHL5 in HepG2 cells followed by RNA-seq. (UCHL5_BGHLV17)
experiment encode accession: ENCSR684HTV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB758NTZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting UCHL5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5a2467e8-cbe9-4fb8-aa92-868c9537337a/@@download/attachment/L-UCHL5_BGHLV17_38.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UCHL5. (UCHL5_BGHLV17_38)

value: ENCBS021UTC at ENCODE; https://www.encodeproject.org/ENCBS021UTC/


title: shRNA RNA-seq from K562 (ENCLB038TTF)

description:
https://www.encodeproject.org/experiments/ENCSR152IWT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TRIP6. (TRIP6_BGKLV29)
experiment encode accession: ENCSR152IWT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB038TTF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TRIP6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6d0b5a38-d390-4ef9-a41b-446d267f872c/@@download/attachment/L-TRIP6_BGKLV29-64.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TRIP6. (TRIP6_BGKLV29-64)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS019QZZ at ENCODE; https://www.encodeproject.org/ENCBS019QZZ/

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 (ENCLB890VXO)

description:
https://www.encodeproject.org/experiments/ENCSR152IWT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TRIP6. (TRIP6_BGKLV29)
experiment encode accession: ENCSR152IWT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB890VXO
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/5fb35717-b311-4d59-b87d-3f7c796f7d13/@@download/attachment/L-TRIP6_BGKLV29-63.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against TRIP6. (TRIP6_BGKLV29-63)

value: adult

value: female

value: ENCBS863CBS at ENCODE; https://www.encodeproject.org/ENCBS863CBS/


title: shRNA RNA-seq from HepG2 (ENCLB486RXW)

description:
https://www.encodeproject.org/experiments/ENCSR681SMT/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PHF6 in HepG2 cells followed by RNA-seq. (PHF6_BGHLV18)
experiment encode accession: ENCSR681SMT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB486RXW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PHF6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/39034f3c-b16d-42db-b49d-cf1ff32c301e/@@download/attachment/L-PHF6_BGHLV18_39.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PHF6. (PHF6_BGHLV18_39)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS301IGN at ENCODE; https://www.encodeproject.org/ENCBS301IGN/


title: siRNA RNA-seq from K562 (ENCLB593ZTJ)

description:
https://www.encodeproject.org/experiments/ENCSR675SDG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAX.
experiment encode accession: ENCSR675SDG
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB593ZTJ
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: MAX

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

value: 53 year

value: Sherman Weissman, Yale

value: ENCBS047FHC at ENCODE; https://www.encodeproject.org/ENCBS047FHC/


title: siRNA RNA-seq from K562 (ENCLB254TTW)

description:
https://www.encodeproject.org/experiments/ENCSR675SDG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAX.
experiment encode accession: ENCSR675SDG
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB254TTW
size range: >200
spikeins used: /references/ENCSR866KGS/

value: immortalized cell line

value: chronic myelogenous leukemia (CML)

value: ENCBS142DVU at ENCODE; https://www.encodeproject.org/ENCBS142DVU/

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


title: shRNA RNA-seq from HepG2 (ENCLB144RMP)

description:
https://www.encodeproject.org/experiments/ENCSR681SMT/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PHF6 in HepG2 cells followed by RNA-seq. (PHF6_BGHLV18)
experiment encode accession: ENCSR681SMT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB144RMP
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/1726271c-1782-4266-9946-6cf6b516d1e4/@@download/attachment/L-PHF6_BGHLV18_40.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PHF6. (PHF6_BGHLV18_40)

value: ENCBS740NNE at ENCODE; https://www.encodeproject.org/ENCBS740NNE/

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 (ENCLB023BAH)

description:
https://www.encodeproject.org/experiments/ENCSR143COQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV32B)
experiment encode accession: ENCSR143COQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB023BAH
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7609d01b-7830-49e4-95d1-d816612f1e18/@@download/attachment/L-NT_BGKLV32-1.pdf

value: Control

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV32-1)

value: adult

value: female

value: ENCBS061XBB at ENCODE; https://www.encodeproject.org/ENCBS061XBB/

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


title: shRNA RNA-seq from K562 (ENCLB042UYK)

description:
https://www.encodeproject.org/experiments/ENCSR143COQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV32B)
experiment encode accession: ENCSR143COQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB042UYK
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/719a4411-555d-4053-8c95-b68598aad4ed/@@download/attachment/L-NT_BGKLV32-2.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV32-2)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS619KUS at ENCODE; https://www.encodeproject.org/ENCBS619KUS/


title: shRNA RNA-seq from K562 (ENCLB567ZRW)

description:
https://www.encodeproject.org/experiments/ENCSR154OBA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV24C)
experiment encode accession: ENCSR154OBA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB567ZRW
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/c91beff1-5985-4d39-96b5-06275fc17d64/@@download/attachment/L-NT_BGKLV24-1C.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against non-target. (NT_BGKLV24-1C)

value: chronic myelogenous leukemia (CML)

value: ENCBS815LSY at ENCODE; https://www.encodeproject.org/ENCBS815LSY/


title: shRNA RNA-seq from K562 (ENCLB710MVZ)

description:
https://www.encodeproject.org/experiments/ENCSR678MVE/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against UCHL5 in K562 cells followed by RNA-seq. (UCHL5_BGKLV19)
experiment encode accession: ENCSR678MVE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB710MVZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting UCHL5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fa8ac8f8-86b1-4e9f-83b7-5f3fc129d0dd/@@download/attachment/L-UCHL5_BGKLV19_59B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UCHL5. (UCHL5_BGKLV19_59B)

value: ENCBS123DAX at ENCODE; https://www.encodeproject.org/ENCBS123DAX/

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


title: shRNA RNA-seq from K562 (ENCLB790BTM)

description:
https://www.encodeproject.org/experiments/ENCSR678MVE/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against UCHL5 in K562 cells followed by RNA-seq. (UCHL5_BGKLV19)
experiment encode accession: ENCSR678MVE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB790BTM
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/67d53896-5619-49f1-9efd-c8b02724c558/@@download/attachment/L-UCHL5_BGKLV19_60B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UCHL5. (UCHL5_BGKLV19_60B)

value: ENCBS632QPM at ENCODE; https://www.encodeproject.org/ENCBS632QPM/


title: shRNA RNA-seq from HepG2 (ENCLB596CYC)

description:
https://www.encodeproject.org/experiments/ENCSR135LXL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV20B)
experiment encode accession: ENCSR135LXL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB596CYC
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/0f70b5e2-fb6f-4284-a5ab-b0b62a21d175/@@download/attachment/L-NT_BGHLV20-1B.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV20-1B)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS705HMQ at ENCODE; https://www.encodeproject.org/ENCBS705HMQ/

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 (ENCLB568KRT)

description:
https://www.encodeproject.org/experiments/ENCSR675KPR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBM3. (K562-RBM3)
experiment encode accession: ENCSR675KPR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR936VPP
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB568KRT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RBM3

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/3e8b553f-9e6f-4b37-a1ae-151526787e1d/@@download/attachment/L-K562-RBM3-1.pdf

value: immortalized cell line

value: K562 cells treated with an shRNA knockdown against RBM3, used in RNA-seq experiments. (K562-RBM3-1)

value: 53 year

value: adult

value: female

value: Brenton Graveley, UConn

value: ENCBS397GXE at ENCODE; https://www.encodeproject.org/ENCBS397GXE/

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


title: shRNA RNA-seq from HepG2 (ENCLB383DKR)

description:
https://www.encodeproject.org/experiments/ENCSR684HTV/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against UCHL5 in HepG2 cells followed by RNA-seq. (UCHL5_BGHLV17)
experiment encode accession: ENCSR684HTV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB383DKR
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/42bed6c6-2336-4847-aa2b-f503331fa28d/@@download/attachment/L-UCHL5_BGHLV17_37.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UCHL5. (UCHL5_BGHLV17_37)

value: ENCBS085IZZ at ENCODE; https://www.encodeproject.org/ENCBS085IZZ/


title: shRNA RNA-seq from HepG2 (ENCLB384BJR)

description:
https://www.encodeproject.org/experiments/ENCSR135LXL/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV20B)
experiment encode accession: ENCSR135LXL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB384BJR
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/4625e63b-5547-4b9f-8576-7dd0df9ef2a7/@@download/attachment/L-NT_BGHLV20-2B.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV20-2B)

value: 15 year

value: ENCBS117BTL at ENCODE; https://www.encodeproject.org/ENCBS117BTL/


title: shRNA RNA-seq from HepG2 (ENCLB868FHV)

description:
https://www.encodeproject.org/experiments/ENCSR124KCF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against STAU1. (STAU1_BGHLV30)
experiment encode accession: ENCSR124KCF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB868FHV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting STAU1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2edf2e96-fe5a-495d-9405-d727e2507a36/@@download/attachment/L-STAU1_BGHLV30-51.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against STAU1. (STAU1_BGHLV30-51)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS296SQC at ENCODE; https://www.encodeproject.org/ENCBS296SQC/


title: shRNA RNA-seq from HepG2 (ENCLB557GCT)

description:
https://www.encodeproject.org/experiments/ENCSR674KEK/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV18)
experiment encode accession: ENCSR674KEK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB557GCT
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/95ddcf82-159d-48cc-87aa-2287d9d0f4ba/@@download/attachment/L-NT_BGHLV18_1.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target. (NT_BGHLV18_1)

value: ENCBS665LZL at ENCODE; https://www.encodeproject.org/ENCBS665LZL/

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 (ENCLB498RQT)

description:
https://www.encodeproject.org/experiments/ENCSR118KUN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DKC1. (DKC1_BGHLV31)
experiment encode accession: ENCSR118KUN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB498RQT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/cd3aa1ca-1497-451e-b57a-b0319aeb2347/@@download/attachment/L-DKC1_BGHLV31-33.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DKC1. (DKC1_BGHLV31-33)

value: Brenton Graveley, UConn

value: ENCBS152RQC at ENCODE; https://www.encodeproject.org/ENCBS152RQC/


title: shRNA RNA-seq from HepG2 (ENCLB918JLJ)

description:
https://www.encodeproject.org/experiments/ENCSR124KCF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against STAU1. (STAU1_BGHLV30)
experiment encode accession: ENCSR124KCF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB918JLJ
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/dec08336-e2d7-49c3-b8e2-c534a4a4fb13/@@download/attachment/L-STAU1_BGHLV30-52.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against STAU1. (STAU1_BGHLV30-52)

value: ENCBS106DQT at ENCODE; https://www.encodeproject.org/ENCBS106DQT/


title: shRNA RNA-seq from HepG2 (ENCLB826EYR)

description:
https://www.encodeproject.org/experiments/ENCSR118KUN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DKC1. (DKC1_BGHLV31)
experiment encode accession: ENCSR118KUN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB826EYR
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/f35d60e9-1db7-48e0-842c-a497f661ca0d/@@download/attachment/L-DKC1_BGHLV31-34.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DKC1. (DKC1_BGHLV31-34)

value: 15 year

value: ENCBS813FSC at ENCODE; https://www.encodeproject.org/ENCBS813FSC/


title: shRNA RNA-seq from K562 (ENCLB779XQN)

description:
https://www.encodeproject.org/experiments/ENCSR118EFE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NTB_BGKLV29)
experiment encode accession: ENCSR118EFE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB779XQN
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/a2c34d7e-b06e-47bc-b446-5d891b0fc47e/@@download/attachment/L-NTB_BGKLV29-1.pdf

value: Control

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

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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 (ENCLB029ZMR)

description:
https://www.encodeproject.org/experiments/ENCSR674KDQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against GRSF1. (GRSF1-BGHLV22)
experiment encode accession: ENCSR674KDQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB029ZMR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting GRSF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/baaee4dc-0597-4cd4-a271-bb5e7a49a7bf/@@download/attachment/L-GRSF1-BGHLV22-17_17754.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GRSF1. (GRSF1-BGHLV22-17_17754)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS013LLU at ENCODE; https://www.encodeproject.org/ENCBS013LLU/

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 (ENCLB045CPU)

description:
https://www.encodeproject.org/experiments/ENCSR674KDQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against GRSF1. (GRSF1-BGHLV22)
experiment encode accession: ENCSR674KDQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB045CPU
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/697c14ef-06cb-4428-847a-a274d57f7272/@@download/attachment/L-GRSF1-BGHLV22-18_17755.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GRSF1. (GRSF1-BGHLV22-18_17755)

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS501AJE at ENCODE; https://www.encodeproject.org/ENCBS501AJE/


title: shRNA RNA-seq from HepG2 (ENCLB399ZQW)

description:
https://www.encodeproject.org/experiments/ENCSR674KEK/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV18)
experiment encode accession: ENCSR674KEK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB399ZQW
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/dceb3c16-25cd-4e52-8976-de744fdaaf77/@@download/attachment/L-NT_BGHLV18_2.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target. (NT_BGHLV18_2)

value: ENCBS192GTP at ENCODE; https://www.encodeproject.org/ENCBS192GTP/


title: shRNA RNA-seq from HepG2 (ENCLB943WFS)

description:
https://www.encodeproject.org/experiments/ENCSR667RIA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPS2 in HepG2 cells followed by RNA-seq. (RPS2_BGHLV18)
experiment encode accession: ENCSR667RIA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB943WFS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RPS2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/14ce839b-7180-4edc-bd44-6b9a18c40c91/@@download/attachment/L-RPS2_BGHLV18_55.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS2. (RPS2_BGHLV18_55)

value: ENCBS575HTN at ENCODE; https://www.encodeproject.org/ENCBS575HTN/


title: shRNA RNA-seq from K562 (ENCLB200LRK)

description:
https://www.encodeproject.org/experiments/ENCSR118EFE/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NTB_BGKLV29)
experiment encode accession: ENCSR118EFE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB200LRK
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/a16d66ac-fa40-4fe6-a48d-2058333572d0/@@download/attachment/L-NTB_BGKLV29-2.pdf

value: immortalized cell line

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

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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 (ENCLB555IWO)

description:
https://www.encodeproject.org/experiments/ENCSR675KPR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBM3. (K562-RBM3)
experiment encode accession: ENCSR675KPR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR936VPP
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB555IWO
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/542b5009-5b81-42e0-ac17-0b16e8a304b3/@@download/attachment/L-K562-RBM3-2.pdf

value: K562 cells treated with an shRNA knockdown against RBM3, used in RNA-seq experiments. (K562-RBM3-2)

value: ENCBS718GJU at ENCODE; https://www.encodeproject.org/ENCBS718GJU/


title: shRNA RNA-seq from K562 (ENCLB420RAA)

description:
https://www.encodeproject.org/experiments/ENCSR667PLJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV24)
experiment encode accession: ENCSR667PLJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB420RAA
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/3e08673e-4d48-4fd9-a0ad-e4a8b3c7daba/@@download/attachment/L-non-target_BGKLV24_2_17595.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (non-target_BGKLV24_2_17595)

value: Brenton Graveley, UConn

value: ENCBS537KCG at ENCODE; https://www.encodeproject.org/ENCBS537KCG/


title: RAMPAGE from mammary microvascular endothelial cell (ENCLB533BRK)

description:
https://www.encodeproject.org/experiments/ENCSR663WYF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of mammary microvascular endothelial cell primary cell line (HMMEC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR663WYF
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR815UVL
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB533BRK
size range: >200

source_name: Homo sapiens mammary microvascular endothelial primary cell female adult (26 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/192771f1-798d-4218-b410-f031f3e54f20/@@download/attachment/295489.pdf

value: mammary microvascular endothelial cell

value: primary cell

value: Human Mammary Microvascular Endothelial Cells (HMMEC) from the breast tissue of a 26 year old female.

value: 26 year

value: Thomas Gingeras, CSHL

value: ENCBS291IGF at ENCODE; https://www.encodeproject.org/ENCBS291IGF/

value: Derived from ENCODE donor ENCDO779FJA; https://www.encodeproject.org/ENCDO779FJA/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=7605


title: shRNA RNA-seq from HepG2 (ENCLB627VRC)

description:
https://www.encodeproject.org/experiments/ENCSR110HAA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGHLV30)
experiment encode accession: ENCSR110HAA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB627VRC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EIF2S2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/46fe188b-9d75-4217-b86e-be727b4b7c9e/@@download/attachment/L-EIF2S2_BGHLV30-32.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGHLV30-32)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS768ZGL at ENCODE; https://www.encodeproject.org/ENCBS768ZGL/

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 (ENCLB622CAA)

description:
https://www.encodeproject.org/experiments/ENCSR667PLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV24)
experiment encode accession: ENCSR667PLJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB622CAA
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/211303e5-3319-4dce-8662-ec73cc6e9ea2/@@download/attachment/L-non-target_BGKLV24_1_17594.pdf

value: Control

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (non-target_BGKLV24_1_17594)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS895KNQ at ENCODE; https://www.encodeproject.org/ENCBS895KNQ/

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 (ENCLB676KLE)

description:
https://www.encodeproject.org/experiments/ENCSR116QBU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGHLV30)
experiment encode accession: ENCSR116QBU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB676KLE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/d2dbedc5-2bd8-49b3-a38c-d4b5c2c4c829/@@download/attachment/L-FIP1L1_BGHLV30-40.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGHLV30-40)

value: 15 year

value: ENCBS713BFI at ENCODE; https://www.encodeproject.org/ENCBS713BFI/


title: total RNA-seq from suprapubic skin (ENCLB397AMI)

description:
https://www.encodeproject.org/experiments/ENCSR108MAU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a54 year old male's suprapubic skin tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR108MAU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB397AMI
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens suprapubic skin tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/04d387c0-e116-448d-b992-0544d3943f59/@@download/attachment/296376.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: 54 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS368KLM at ENCODE; https://www.encodeproject.org/ENCBS368KLM/

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


title: RAMPAGE from mammary microvascular endothelial cell (ENCLB138LSO)

description:
https://www.encodeproject.org/experiments/ENCSR663WYF/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of mammary microvascular endothelial cell primary cell line (HMMEC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR663WYF
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR815UVL
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB138LSO
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7763b5f2-7461-4e3d-ac9c-cec52ee389e0/@@download/attachment/295490.pdf

value: mammary microvascular endothelial cell

value: primary cell

value: Human Mammary Microvascular Endothelial Cells (HMMEC).

value: 26 year

value: adult

tag: passage number

value: female

value: ENCBS118XHF at ENCODE; https://www.encodeproject.org/ENCBS118XHF/

value: Derived from ENCODE donor ENCDO779FJA; https://www.encodeproject.org/ENCDO779FJA/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=7605


title: shRNA RNA-seq from HepG2 (ENCLB916LOW)

description:
https://www.encodeproject.org/experiments/ENCSR667RIA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RPS2 in HepG2 cells followed by RNA-seq. (RPS2_BGHLV18)
experiment encode accession: ENCSR667RIA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB916LOW
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/69410250-9181-4373-9da5-22af7a56a497/@@download/attachment/L-RPS2_BGHLV18_56.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS2. (RPS2_BGHLV18_56)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS542YDW at ENCODE; https://www.encodeproject.org/ENCBS542YDW/

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 (ENCLB094CGB)

description:
https://www.encodeproject.org/experiments/ENCSR110HAA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGHLV30)
experiment encode accession: ENCSR110HAA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB094CGB
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/1c905d0e-a34b-420b-8479-13c3bddeb2bc/@@download/attachment/L-EIF2S2_BGHLV30-31.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2S2. (EIF2S2_BGHLV30-31)

value: male

value: ENCBS897HQV at ENCODE; https://www.encodeproject.org/ENCBS897HQV/


title: total RNA-seq from spleen (ENCLB196DEE)

description:
https://www.encodeproject.org/experiments/ENCSR106SZN/
***************
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 spleen tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR106SZN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB196DEE
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens spleen tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/21958f15-1ba8-487f-bbd2-116987cf87c1/@@download/attachment/296574.pdf

value: spleen

value: tissue

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

value: 54 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS379XNT at ENCODE; https://www.encodeproject.org/ENCBS379XNT/

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


title: shRNA RNA-seq from K562 (ENCLB662KSO)

description:
https://www.encodeproject.org/experiments/ENCSR661HEL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-B)
experiment encode accession: ENCSR661HEL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB662KSO
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/b0144bdb-6df2-4dd0-b4c2-e15b1d021091/@@download/attachment/L-NT_BGKLV19_1B.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (NT_BGKLV19_1)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS661YYO at ENCODE; https://www.encodeproject.org/ENCBS661YYO/

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 uterus (ENCLB030AMW)

description:
https://www.encodeproject.org/experiments/ENCSR113HQM/
***************
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 uterus tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR113HQM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB030AMW
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/21cd63a2-f236-4612-9098-7ee5de943d72/@@download/attachment/296671.pdf

value: uterus

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

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

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


title: shRNA RNA-seq from HepG2 (ENCLB369FSS)

description:
https://www.encodeproject.org/experiments/ENCSR104ABF/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV26)
experiment encode accession: ENCSR104ABF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB369FSS
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/e1758c53-16c4-40e3-94c9-3d0de3daaac4/@@download/attachment/L-non-target_BGHLV26-2.pdf

value: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV26-2)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS967UNG at ENCODE; https://www.encodeproject.org/ENCBS967UNG/

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 (ENCLB015ZMU)

description:
https://www.encodeproject.org/experiments/ENCSR116QBU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGHLV30)
experiment encode accession: ENCSR116QBU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB015ZMU
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/37960c23-3598-42b9-9b63-c18fd28ff0a3/@@download/attachment/L-FIP1L1_BGHLV30-39.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FIP1L1. (FIP1L1_BGHLV30-39)

value: ENCBS671WOF at ENCODE; https://www.encodeproject.org/ENCBS671WOF/


title: shRNA RNA-seq from HepG2 (ENCLB222MXG)

description:
https://www.encodeproject.org/experiments/ENCSR104ABF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV26)
experiment encode accession: ENCSR104ABF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB222MXG
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/b116ea17-6c86-4ec0-bd28-3f622d38a88c/@@download/attachment/L-non-target_BGHLV26-1.pdf

value: Control

value: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV26-1)

value: ENCBS356MOV at ENCODE; https://www.encodeproject.org/ENCBS356MOV/


title: RAMPAGE from esophagus squamous epithelium (ENCLB329MXH)

description:
https://www.encodeproject.org/experiments/ENCSR102OEK/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human esophagus mucosa tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR102OEK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR474TRG
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB329MXH
size range: >200

source_name: Homo sapiens esophagus squamous epithelium 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/ef2b1d82-4ed8-42d2-ad62-9724bc49bade/@@download/attachment/296745.pdf

value: esophagus squamous epithelium

value: tissue

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

value: 54 year

value: adult

value: Thomas Gingeras, CSHL

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

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


title: total RNA-seq from sigmoid colon (ENCLB554PCH)

description:
https://www.encodeproject.org/experiments/ENCSR094GVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the sigmoid colon obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR094GVZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB554PCH
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/db80fa10-3ce2-4f06-a1b7-4e8f39f5c85b/@@download/attachment/296141.pdf

value: sigmoid colon

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

value: 53 year

value: female

value: ENCBS581JIS at ENCODE; https://www.encodeproject.org/ENCBS581JIS/

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


title: total RNA-seq from esophagus muscularis mucosa (ENCLB159BNG)

description:
https://www.encodeproject.org/experiments/ENCSR098BUF/
***************
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 esophagal muscle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR098BUF
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB159BNG
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/848294b3-dfc2-4a64-a853-0acfac3cd07d/@@download/attachment/296294.pdf

value: esophagus muscularis mucosa

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

value: ENCBS571LWZ at ENCODE; https://www.encodeproject.org/ENCBS571LWZ/


title: shRNA RNA-seq from HepG2 (ENCLB793HBU)

description:
https://www.encodeproject.org/experiments/ENCSR660MZN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPD. (HNRNPD-BGHLV22)
experiment encode accession: ENCSR660MZN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB793HBU
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b715defc-503a-47d1-a4c6-9dc24b87702b/@@download/attachment/L-HNRNPD-BGHLV22-26_17761.pdf

value: HNRNPD

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPD. (HNRNPD-BGHLV22-26_17761)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS248XEV at ENCODE; https://www.encodeproject.org/ENCBS248XEV/

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 (ENCLB174DNP)

description:
https://www.encodeproject.org/experiments/ENCSR660MZN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPD. (HNRNPD-BGHLV22)
experiment encode accession: ENCSR660MZN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB174DNP
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/31a93297-ff67-4d64-a432-648b1bdc3fb7/@@download/attachment/L-HNRNPD-BGHLV22-25_17760.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPD. (HNRNPD-BGHLV22-25_17760)

value: ENCBS205JEO at ENCODE; https://www.encodeproject.org/ENCBS205JEO/


title: total RNA-seq from breast epithelium (ENCLB226IQQ)

description:
https://www.encodeproject.org/experiments/ENCSR094VRQ/
***************
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 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: ENCSR094VRQ
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB226IQQ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens breast epithelium tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0ad6288d-0a82-4ec5-bce6-1f8cbb645959/@@download/attachment/296313.pdf

value: breast epithelium

value: tissue

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

value: 37 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS453ISE at ENCODE; https://www.encodeproject.org/ENCBS453ISE/

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


title: siRNA RNA-seq from K562 (ENCLB804BSZ)

description:
https://www.encodeproject.org/experiments/ENCSR656ZOI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting LMNB1.
experiment encode accession: ENCSR656ZOI
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB804BSZ
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: immortalized cell line

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

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS944NZR at ENCODE; https://www.encodeproject.org/ENCBS944NZR/

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


title: shRNA RNA-seq from K562 (ENCLB892HBQ)

description:
https://www.encodeproject.org/experiments/ENCSR661HEL/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-B)
experiment encode accession: ENCSR661HEL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB892HBQ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7b9a6e95-ce00-4246-9347-584e17e3c579/@@download/attachment/L-NT_BGKLV19_2B.pdf

value: Control

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (NT_BGKLV19_2)

value: Brenton Graveley, UConn

value: ENCBS250HLF at ENCODE; https://www.encodeproject.org/ENCBS250HLF/

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