title: shRNA RNA-seq from HepG2 (ENCLB102XBC)

description:
https://www.encodeproject.org/experiments/ENCSR782MXN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SFPQ. (SFPQ_BGHLV26)
experiment encode accession: ENCSR782MXN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB102XBC
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dfc06c3d-b9bc-43ae-b0e1-0d4765686e87/@@download/attachment/L-SFPQ_BGHLV26_56.pdf

value: SFPQ

value: RNA-seq on HepG2 cells treated with an Control shRNA against SFPQ (SFPQ_BGHLV26_56)

value: male

value: Brenton Graveley, UConn

value: ENCBS292XKE at ENCODE; https://www.encodeproject.org/ENCBS292XKE/


title: RAMPAGE from gastroesophageal sphincter (ENCLB047JUH)

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/ENCSR779OWH/
***************
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 esophagogastric junction tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR779OWH
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR035SKV
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB047JUH
size range: >200

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/574e37e7-fc85-4c7c-8e3b-c6e44c3568c9/@@download/attachment/296730.pdf

value: gastroesophageal sphincter

value: tissue

tag: description

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

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

tag: age

value: 51 year

tag: lab

value: Thomas Gingeras, CSHL

tag: link

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

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


title: shRNA RNA-seq from HepG2 (ENCLB638SDF)

description:
https://www.encodeproject.org/experiments/ENCSR782MXN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SFPQ. (SFPQ_BGHLV26)
experiment encode accession: ENCSR782MXN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB638SDF
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/6d6271ef-46f0-420f-870c-b8d1046bf710/@@download/attachment/L-SFPQ_BGHLV26_55.pdf

tag: antibody

tag: line

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against SFPQ (SFPQ_BGHLV26_55)

value: child

value: 15 year

tag: health state

value: hepatocellular carcinoma

value: ENCBS887RIJ at ENCODE; https://www.encodeproject.org/ENCBS887RIJ/

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 (ENCLB288FLH)

description:
https://www.encodeproject.org/experiments/ENCSR777EDL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against STAU1. (STAU1_BGKLV29)
experiment encode accession: ENCSR777EDL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB288FLH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 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/3554e355-1c88-45bf-b92e-dbe02cb7496c/@@download/attachment/L-STAU1_BGKLV29-58.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against STAU1. (STAU1_BGKLV29-58)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS871MOK at ENCODE; https://www.encodeproject.org/ENCBS871MOK/

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 (ENCLB864WSF)

description:
https://www.encodeproject.org/experiments/ENCSR776SXA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV30B)
experiment encode accession: ENCSR776SXA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB864WSF
size range: >200
spikeins used: /references/ENCSR358OMW/

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/95846c0a-8a89-4b1b-9b17-fdba2d1bc717/@@download/attachment/L-NT_BGHLV30-1B.pdf

value: Control

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

value: male

value: ENCBS443JPP at ENCODE; https://www.encodeproject.org/ENCBS443JPP/


title: shRNA RNA-seq from K562 (ENCLB384LKA)

description:
https://www.encodeproject.org/experiments/ENCSR777EDL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against STAU1. (STAU1_BGKLV29)
experiment encode accession: ENCSR777EDL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB384LKA
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/12ab0aca-fae7-40f5-b581-fc11ae5f1808/@@download/attachment/L-STAU1_BGKLV29-57.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against STAU1. (STAU1_BGKLV29-57)

value: adult

value: female

value: ENCBS534WDC at ENCODE; https://www.encodeproject.org/ENCBS534WDC/


title: shRNA RNA-seq from HepG2 (ENCLB945BXD)

description:
https://www.encodeproject.org/experiments/ENCSR776SXA/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV30B)
experiment encode accession: ENCSR776SXA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB945BXD
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/a64aac74-03b9-44a4-8522-cd26ba8fbc09/@@download/attachment/L-NT_BGHLV30-2B.pdf

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

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS066SAB at ENCODE; https://www.encodeproject.org/ENCBS066SAB/

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 (ENCLB676MEB)

description:
https://www.encodeproject.org/experiments/ENCSR775TMW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against BOP1. (BOP1_BGKLV36)
experiment encode accession: ENCSR775TMW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB676MEB
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting BOP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2a5ea2cb-7a66-49cd-8a4d-6013de65ad3c/@@download/attachment/L-BOP1_BGKLV36-8.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against BOP1. (BOP1_BGKLV36-8)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS759JIC at ENCODE; https://www.encodeproject.org/ENCBS759JIC/

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


title: RAMPAGE from stomach (ENCLB979AMJ)

description:
https://www.encodeproject.org/experiments/ENCSR792XFE/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human stomach tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR792XFE
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR471RUK
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB979AMJ
size range: >200

source_name: Homo sapiens stomach 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/fe61a02b-10c9-428b-af4a-7c010792c8a0/@@download/attachment/296841.pdf

value: stomach

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from K562 (ENCLB456PVK)

description:
https://www.encodeproject.org/experiments/ENCSR775TMW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against BOP1. (BOP1_BGKLV36)
experiment encode accession: ENCSR775TMW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB456PVK
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/cc0fae66-5a7e-4d4f-90d0-9ad92a9a33dd/@@download/attachment/L-BOP1_BGKLV36-7.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against BOP1. (BOP1_BGKLV36-7)

value: adult

value: female

value: ENCBS964ERX at ENCODE; https://www.encodeproject.org/ENCBS964ERX/


title: total RNA-seq from adrenal gland (ENCLB864EZB)

description:
https://www.encodeproject.org/experiments/ENCSR801MKV/
***************
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 adrenal gland 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: ENCSR801MKV
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB864EZB
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5e210ac5-57a6-4688-855a-ddfb0a5caa48/@@download/attachment/296666.pdf

value: adrenal gland

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

value: 51 year

value: ENCBS423TBO at ENCODE; https://www.encodeproject.org/ENCBS423TBO/

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


title: shRNA RNA-seq from HepG2 (ENCLB613MMW)

description:
https://www.encodeproject.org/experiments/ENCSR767LLP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBFOX2. (RBFOX2_BGHLV26)
experiment encode accession: ENCSR767LLP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB613MMW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RBFOX2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/882cc69d-89b6-4107-976c-a6a30a76dfef/@@download/attachment/L-RBFOX2_BGHLV26_35.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against RBFOX2 (RBFOX2_BGHLV26_35)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS722TNF at ENCODE; https://www.encodeproject.org/ENCBS722TNF/

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 (ENCLB310BIT)

description:
https://www.encodeproject.org/experiments/ENCSR770LYW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SAFB2. (SAFB2_BGKLV24)
experiment encode accession: ENCSR770LYW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR154OBA
encode release date: 2016-08-01
lab: Brenton Graveley, UConn
library encode accession: ENCLB310BIT
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SAFB2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7f151fcd-a234-48bd-9498-c60a9f7f4319/@@download/attachment/L-SAFB2_BGKLV24-52C.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SAFB2. (SAFB2_BGKLV24-52C)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS789DTV at ENCODE; https://www.encodeproject.org/ENCBS789DTV/

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 adrenal gland (ENCLB890GOC)

description:
https://www.encodeproject.org/experiments/ENCSR754WLW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR754WLW
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB890GOC
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens adrenal gland tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f6a69697-b8b9-46a8-a4d9-ed86a7048744/@@download/attachment/296665.pdf

value: adrenal gland

value: tissue

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

value: adult

value: female

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from K562 (ENCLB578JHZ)

description:
https://www.encodeproject.org/experiments/ENCSR770LYW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SAFB2. (SAFB2_BGKLV24)
experiment encode accession: ENCSR770LYW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR154OBA
encode release date: 2016-08-01
lab: Brenton Graveley, UConn
library encode accession: ENCLB578JHZ
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/d741c760-e7c3-4023-a790-bad2e65abfde/@@download/attachment/L-SAFB2_BGKLV24-51C.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SAFB2. (SAFB2_BGKLV24-51C)

value: Brenton Graveley, UConn

value: ENCBS998FPD at ENCODE; https://www.encodeproject.org/ENCBS998FPD/


title: shRNA RNA-seq from HepG2 (ENCLB998XFU)

description:
https://www.encodeproject.org/experiments/ENCSR760EGM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM39. (RBM39_BGHLV26)
experiment encode accession: ENCSR760EGM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB998XFU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RBM39

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e8fa0dcc-2717-472a-9c17-f48c2063b9eb/@@download/attachment/L-RBM39_BGHLV26_40.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against RBM39 (RBM39_BGHLV26_40)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS144MRF at ENCODE; https://www.encodeproject.org/ENCBS144MRF/

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 (ENCLB361RKD)

description:
https://www.encodeproject.org/experiments/ENCSR760EGM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM39. (RBM39_BGHLV26)
experiment encode accession: ENCSR760EGM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB361RKD
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/e90ef727-826d-4518-aea6-71bccfefbd61/@@download/attachment/L-RBM39_BGHLV26_39.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against RBM39 (RBM39_BGHLV26_39)

value: ENCBS285EHM at ENCODE; https://www.encodeproject.org/ENCBS285EHM/


title: shRNA RNA-seq from HepG2 (ENCLB593UGL)

description:
https://www.encodeproject.org/experiments/ENCSR767LLP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBFOX2. (RBFOX2_BGHLV26)
experiment encode accession: ENCSR767LLP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB593UGL
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/691659d3-bde5-4d3e-92b7-6c7ea5461348/@@download/attachment/L-RBFOX2_BGHLV26_36.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against RBFOX2 (RBFOX2_BGHLV26_36)

value: ENCBS967WNR at ENCODE; https://www.encodeproject.org/ENCBS967WNR/


title: shRNA RNA-seq from K562 (ENCLB113DDS)

description:
https://www.encodeproject.org/experiments/ENCSR754RJA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NUFIP2. (NUFIP2_BGKLV34)
experiment encode accession: ENCSR754RJA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB113DDS
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting NUFIP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/93ccb798-b484-4e1d-8bb4-d4f227c421fb/@@download/attachment/L-NUFIP2_BGKLV34-27.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NUFIP2. (NUFIP2_BGKLV34-27)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS107JKY at ENCODE; https://www.encodeproject.org/ENCBS107JKY/

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


title: shRNA RNA-seq from K562 (ENCLB195IAC)

description:
https://www.encodeproject.org/experiments/ENCSR754RJA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NUFIP2. (NUFIP2_BGKLV34)
experiment encode accession: ENCSR754RJA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB195IAC
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/5d30f780-3844-4c92-96a4-98115cec26f5/@@download/attachment/L-NUFIP2_BGKLV34-28.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against NUFIP2. (NUFIP2_BGKLV34-28)

value: Brenton Graveley, UConn

value: ENCBS395MVC at ENCODE; https://www.encodeproject.org/ENCBS395MVC/


title: total RNA-seq from induced pluripotent stem cell (ENCLB874KAP)

description:
https://www.encodeproject.org/experiments/ENCSR748GVH/
***************
biological replicate number: 2
technical replicate number: 1
description: induced pluripotent stem cell
experiment encode accession: ENCSR748GVH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB874KAP
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: male

value: Thomas Gingeras, CSHL

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: total RNA-seq from esophagus muscularis mucosa (ENCLB581IKK)

description:
https://www.encodeproject.org/experiments/ENCSR750ETS/
***************
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 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: ENCSR750ETS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB581IKK
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/09d44fd8-0655-4ca2-a0ce-ae6a6c401eac/@@download/attachment/296292.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: 54 year

value: adult

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

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


title: total RNA-seq from induced pluripotent stem cell (ENCLB983UAV)

description:
https://www.encodeproject.org/experiments/ENCSR748GVH/
***************
biological replicate number: 1
technical replicate number: 1
description: induced pluripotent stem cell
experiment encode accession: ENCSR748GVH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB983UAV
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng

value: 53 year

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/


title: shRNA RNA-seq from K562 (ENCLB865AWD)

description:
https://www.encodeproject.org/experiments/ENCSR795VAK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CPEB4. (CPEB4_BGKLV25)
experiment encode accession: ENCSR795VAK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR031RRO
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB865AWD
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2f94f6eb-5349-4c71-ae3a-8451b15c6028/@@download/attachment/L-CPEB4_BGKLV25-7B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against CPEB4. (CPEB4_BGKLV25-7B)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS797SGL at ENCODE; https://www.encodeproject.org/ENCBS797SGL/

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 stomach (ENCLB580LKL)

description:
https://www.encodeproject.org/experiments/ENCSR752UNJ/
***************
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 stomach tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR752UNJ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB580LKL
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/32d0862e-8585-4810-8324-e380e2e91e9c/@@download/attachment/296675.pdf

value: stomach

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

value: Thomas Gingeras, CSHL

value: ENCBS607DWD at ENCODE; https://www.encodeproject.org/ENCBS607DWD/

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


title: shRNA RNA-seq from K562 (ENCLB315GOO)

description:
https://www.encodeproject.org/experiments/ENCSR746NIM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGKLV29)
experiment encode accession: ENCSR746NIM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB315GOO
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cd0da041-95a2-4dd5-9a75-33010776f450/@@download/attachment/L-HNRNPM_BGKLV29-39.pdf

value: HNRNPM

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGKLV29-39)

value: adult

value: ENCBS701VZK at ENCODE; https://www.encodeproject.org/ENCBS701VZK/


title: shRNA RNA-seq from HepG2 (ENCLB509YWW)

description:
https://www.encodeproject.org/experiments/ENCSR744PAQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against LARP4. (LARP4_BGHLV20)
experiment encode accession: ENCSR744PAQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR135LXL
encode release date: 2016-08-01
lab: Brenton Graveley, UConn
library encode accession: ENCLB509YWW
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting LARP4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4afe1ddc-eeff-4068-b7ed-0b06e8935e57/@@download/attachment/L-LARP4_BGHLV20-42B.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against LARP4. (LARP4_BGHLV20-42B)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS665IBY at ENCODE; https://www.encodeproject.org/ENCBS665IBY/

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 (ENCLB522HIE)

description:
https://www.encodeproject.org/experiments/ENCSR741YCA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against TBRG4. (TBRG4_BGHLV27)
experiment encode accession: ENCSR741YCA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB522HIE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting TBRG4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/03905e29-b666-41be-a692-68600ff48a64/@@download/attachment/L-TBRG4_BGHLV27-55.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against TBRG4 (TBRG4_BGHLV27-55)

value: Brenton Graveley, UConn

value: ENCBS049RJI at ENCODE; https://www.encodeproject.org/ENCBS049RJI/


title: RAMPAGE from upper lobe of left lung (ENCLB009ENC)

description:
https://www.encodeproject.org/experiments/ENCSR738HKC/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human upper lobe of left lung tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR738HKC
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR313COD
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB009ENC
size range: >200

source_name: Homo sapiens upper lobe of left lung 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/1af8b0a8-aee7-49ac-82d0-ae8486f26633/@@download/attachment/296774.pdf

value: upper lobe of left lung

value: tissue

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

value: 37 year

value: Thomas Gingeras, CSHL

value: ENCBS320PNF at ENCODE; https://www.encodeproject.org/ENCBS320PNF/

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


title: total RNA-seq from omental fat pad (ENCLB919SXV)

description:
https://www.encodeproject.org/experiments/ENCSR729CAZ/
***************
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: ENCSR729CAZ
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB919SXV
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens omental fat pad tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1074ce07-56a9-4334-b7fb-9d0f1d9c9977/@@download/attachment/296314.pdf

value: omental fat pad

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

value: adult

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


title: total RNA-seq from ascending aorta (ENCLB313RZG)

description:
https://www.encodeproject.org/experiments/ENCSR719PXC/
***************
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 aorta tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR719PXC
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB313RZG
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens ascending aorta tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6d603d9c-922a-40e3-b930-3099aa766a0b/@@download/attachment/296667.pdf

value: ascending aorta

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

value: 53 year

value: female

value: ENCBS482ANH at ENCODE; https://www.encodeproject.org/ENCBS482ANH/

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


title: shRNA RNA-seq from HepG2 (ENCLB078QKF)

description:
https://www.encodeproject.org/experiments/ENCSR741YCA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against TBRG4. (TBRG4_BGHLV27)
experiment encode accession: ENCSR741YCA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB078QKF
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/85c4e013-5d81-4275-9818-0ac8f865723a/@@download/attachment/L-TBRG4_BGHLV27-56.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against TBRG4 (TBRG4_BGHLV27-56)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS501FGJ at ENCODE; https://www.encodeproject.org/ENCBS501FGJ/

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 (ENCLB620HPE)

description:
https://www.encodeproject.org/experiments/ENCSR713OLV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGHLV30)
experiment encode accession: ENCSR713OLV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB620HPE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ATP5C1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7eff5d04-8d15-4cce-b841-5fd05f90487b/@@download/attachment/L-ATP5C1_BGHLV30-13.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGHLV30-13)

value: ENCBS624DUS at ENCODE; https://www.encodeproject.org/ENCBS624DUS/


title: total RNA-seq from subcutaneous adipose tissue (ENCLB627TOE)

description:
https://www.encodeproject.org/experiments/ENCSR708VVE/
***************
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: ENCSR708VVE
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB627TOE
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens subcutaneous adipose tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b001a111-a741-4494-8b9a-286f6682275c/@@download/attachment/296161.pdf

value: subcutaneous adipose tissue

value: tissue

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

value: 37 year

value: adult

value: Thomas Gingeras, CSHL

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

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


title: RAMPAGE from gastrocnemius medialis (ENCLB211UVA)

description:
https://www.encodeproject.org/experiments/ENCSR710LGT/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human skeletal muscle tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR710LGT
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR678TMV
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB211UVA
size range: >200

source_name: Homo sapiens gastrocnemius medialis tissue female adult (53 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/85a0f74f-1cd7-47fd-bec4-4162fb1dce05/@@download/attachment/296747.pdf

value: gastrocnemius medialis

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

value: female

value: 53 year

value: ENCBS868XRL at ENCODE; https://www.encodeproject.org/ENCBS868XRL/

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


title: shRNA RNA-seq from HepG2 (ENCLB374KMG)

description:
https://www.encodeproject.org/experiments/ENCSR713OLV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGHLV30)
experiment encode accession: ENCSR713OLV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB374KMG
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/eeb99794-d8a6-4f11-a7a6-57d0a1a4df65/@@download/attachment/L-ATP5C1_BGHLV30-14.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGHLV30-14)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS697FZF at ENCODE; https://www.encodeproject.org/ENCBS697FZF/

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 (ENCLB259DIT)

description:
https://www.encodeproject.org/experiments/ENCSR721MXZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGKLV29)
experiment encode accession: ENCSR721MXZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB259DIT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting ABCF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a33ca885-6265-427f-9fb5-dde086670853/@@download/attachment/L-ABCF1_BGKLV29-4.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGKLV29-4)

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS465RFQ at ENCODE; https://www.encodeproject.org/ENCBS465RFQ/

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 (ENCLB015ARF)

description:
https://www.encodeproject.org/experiments/ENCSR721MXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGKLV29)
experiment encode accession: ENCSR721MXZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB015ARF
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/206474ca-ee3f-4d31-acc6-a2488f660c1b/@@download/attachment/L-ABCF1_BGKLV29-3.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGKLV29-3)

value: 53 year

value: female

value: ENCBS078OYF at ENCODE; https://www.encodeproject.org/ENCBS078OYF/


title: RAMPAGE from tibial nerve (ENCLB816ICI)

description:
https://www.encodeproject.org/experiments/ENCSR706VZW/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human tibial nerve tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR706VZW
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR858QEL
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB816ICI
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6e366fb3-c89d-4952-9f80-4ef4ab619978/@@download/attachment/296844.pdf

value: tibial nerve

value: tissue

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

value: Thomas Gingeras, CSHL

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

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


title: total RNA-seq from prostate gland (ENCLB643EVS)

description:
https://www.encodeproject.org/experiments/ENCSR701TST/
***************
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 prostate tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR701TST
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB643EVS
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/76457077-910c-46d1-b677-637246e4577f/@@download/attachment/296601.pdf

value: prostate gland

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

value: 54 year

value: male

value: ENCBS291PVP at ENCODE; https://www.encodeproject.org/ENCBS291PVP/

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


title: shRNA RNA-seq from K562 (ENCLB051LRI)

description:
https://www.encodeproject.org/experiments/ENCSR746NIM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGKLV29)
experiment encode accession: ENCSR746NIM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB051LRI
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/146decfc-50b0-4293-a296-684a7cd25c8b/@@download/attachment/L-HNRNPM_BGKLV29-40.pdf

value: HNRNPM

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGKLV29-40)

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS948QXW at ENCODE; https://www.encodeproject.org/ENCBS948QXW/

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

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


title: RAMPAGE from adrenal gland (ENCLB747CKH)

description:
https://www.encodeproject.org/experiments/ENCSR743LXD/
***************
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 adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR743LXD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR801MKV
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB747CKH
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/689ad60f-0410-436e-86c1-0081ae8bc428/@@download/attachment/296729.pdf

value: adrenal gland

value: tissue

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

value: 51 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS423TBO at ENCODE; https://www.encodeproject.org/ENCBS423TBO/

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


title: RAMPAGE from thyroid gland (ENCLB507IDL)

description:
https://www.encodeproject.org/experiments/ENCSR700YLA/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human thyroid gland tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR700YLA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR238ZZD
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB507IDL
size range: >200

source_name: Homo sapiens thyroid gland tissue female adult (53 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2458b46c-cbd9-4c35-b875-5c15ff9f513b/@@download/attachment/296748.pdf

value: thyroid gland

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

value: 53 year

value: ENCBS207DLU at ENCODE; https://www.encodeproject.org/ENCBS207DLU/

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


title: RAMPAGE from sigmoid colon (ENCLB536CBO)

description:
https://www.encodeproject.org/experiments/ENCSR698NAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human sigmoid colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR698NAQ
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR857WJK
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB536CBO
size range: >200

source_name: Homo sapiens sigmoid colon 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/f28668a7-6295-4347-a2a9-31c033aa6df3/@@download/attachment/296775.pdf

value: sigmoid colon

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

value: 37 year

value: adult

value: male

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

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


title: shRNA RNA-seq from HepG2 (ENCLB492FVO)

description:
https://www.encodeproject.org/experiments/ENCSR701GSV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGHLV35)
experiment encode accession: ENCSR701GSV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB492FVO
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e8d4bc65-1c31-4414-b180-1fd10e2bf534/@@download/attachment/L-MTPAP_BGHLV35-27.pdf

value: MTPAP

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGHLV35-27)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS050AND at ENCODE; https://www.encodeproject.org/ENCBS050AND/

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


title: total RNA-seq from gastroesophageal sphincter (ENCLB414WBQ)

description:
https://www.encodeproject.org/experiments/ENCSR740YMS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the esophagogastric junction obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR740YMS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB414WBQ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens gastroesophageal sphincter tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a2dface5-1cb1-4d04-83ea-8b72997ec14f/@@download/attachment/296189.pdf

value: gastroesophageal sphincter

value: tissue

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

value: 53 year

value: female

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from HepG2 (ENCLB920EAF)

description:
https://www.encodeproject.org/experiments/ENCSR689ZJC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGHLV26)
experiment encode accession: ENCSR689ZJC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB920EAF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting HNRNPUL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/123df807-609b-4d8f-845c-f85b4d37604a/@@download/attachment/L-HNRNPUL1_BGHLV26-19.pdf

value: RNA-seq on HEPG2 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGHLV26-19)

value: male

value: ENCBS870TBE at ENCODE; https://www.encodeproject.org/ENCBS870TBE/

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


title: shRNA RNA-seq from HepG2 (ENCLB857GFG)

description:
https://www.encodeproject.org/experiments/ENCSR689ZJC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGHLV26)
experiment encode accession: ENCSR689ZJC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB857GFG
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/8421d32b-8141-4ff4-a9bc-c3a1f2761d1a/@@download/attachment/L-HNRNPUL1_BGHLV26-20.pdf

value: immortalized cell line

value: RNA-seq on HEPG2 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGHLV26-20)

value: 15 year

value: child

value: ENCBS103LSZ at ENCODE; https://www.encodeproject.org/ENCBS103LSZ/


title: shRNA RNA-seq from HepG2 (ENCLB207TJI)

description:
https://www.encodeproject.org/experiments/ENCSR689MIY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against UPF1. (UPF1_BGHLV33)
experiment encode accession: ENCSR689MIY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB207TJI
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting UPF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/12362be8-a4fd-4d0d-917f-ce6f6e84efd2/@@download/attachment/L-UPF1_BGHLV33-34.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UPF1. (UPF1_BGHLV33-34)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS344ZTY at ENCODE; https://www.encodeproject.org/ENCBS344ZTY/

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


title: shRNA RNA-seq from HepG2 (ENCLB694GHZ)

description:
https://www.encodeproject.org/experiments/ENCSR689MIY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against UPF1. (UPF1_BGHLV33)
experiment encode accession: ENCSR689MIY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB694GHZ
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/ee6f5477-9ad9-4a6a-a222-d1cd2e290334/@@download/attachment/L-UPF1_BGHLV33-33.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UPF1. (UPF1_BGHLV33-33)

value: ENCBS018RXG at ENCODE; https://www.encodeproject.org/ENCBS018RXG/


title: shRNA RNA-seq from HepG2 (ENCLB713OMK)

description:
https://www.encodeproject.org/experiments/ENCSR691IVR/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV33)
experiment encode accession: ENCSR691IVR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB713OMK
size range: >200
spikeins used: /references/ENCSR358OMW/

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/095383ff-a366-414d-9980-f1a6e7d36c55/@@download/attachment/L-NT_BGHLV33-2.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV33-2)

value: ENCBS849PSG at ENCODE; https://www.encodeproject.org/ENCBS849PSG/


title: shRNA RNA-seq from HepG2 (ENCLB269COP)

description:
https://www.encodeproject.org/experiments/ENCSR744PAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against LARP4. (LARP4_BGHLV20)
experiment encode accession: ENCSR744PAQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR135LXL
encode release date: 2016-08-01
lab: Brenton Graveley, UConn
library encode accession: ENCLB269COP
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting LARP4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bbd37b9e-7758-4584-8176-b196e5cba4eb/@@download/attachment/L-LARP4_BGHLV20-41B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against LARP4. (LARP4_BGHLV20-41B)

value: male

value: ENCBS992ZRR at ENCODE; https://www.encodeproject.org/ENCBS992ZRR/


title: shRNA RNA-seq from HepG2 (ENCLB760DYW)

description:
https://www.encodeproject.org/experiments/ENCSR701GSV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGHLV35)
experiment encode accession: ENCSR701GSV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB760DYW
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/8210c534-88d1-4c4b-ac4f-9f1cec0cb5a7/@@download/attachment/L-MTPAP_BGHLV35-28.pdf

value: MTPAP

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGHLV35-28)

value: ENCBS493QBO at ENCODE; https://www.encodeproject.org/ENCBS493QBO/


title: shRNA RNA-seq from HepG2 (ENCLB925VQD)

description:
https://www.encodeproject.org/experiments/ENCSR691IVR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV33)
experiment encode accession: ENCSR691IVR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB925VQD
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/a2d08a04-9386-41bd-93e2-885f836a6f26/@@download/attachment/L-NT_BGHLV33-1.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV33-1)

value: 15 year

value: child

value: ENCBS133MBP at ENCODE; https://www.encodeproject.org/ENCBS133MBP/


title: total RNA-seq from thyroid gland (ENCLB892JFI)

description:
https://www.encodeproject.org/experiments/ENCSR687HJY/
***************
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 thyroid gland 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: ENCSR687HJY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB892JFI
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d51d3197-6732-4925-9ded-35f9b11ecf6f/@@download/attachment/296609.pdf

value: thyroid gland

value: tissue

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

value: 51 year

value: adult

value: female

value: Thomas Gingeras, CSHL

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

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


title: total RNA-seq from gastrocnemius medialis (ENCLB468MFC)

description:
https://www.encodeproject.org/experiments/ENCSR678TMV/
***************
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 skeletal muscle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR678TMV
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB468MFC
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e296adeb-4af5-4b85-ad29-71f6fbeb991f/@@download/attachment/296326.pdf

value: gastrocnemius medialis

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

value: 53 year

value: ENCBS868XRL at ENCODE; https://www.encodeproject.org/ENCBS868XRL/

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


title: RAMPAGE from esophagus muscularis mucosa (ENCLB413ZVG)

description:
https://www.encodeproject.org/experiments/ENCSR679TCM/
***************
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 muscle layer of esophagus tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR679TCM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR620LQN
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB413ZVG
size range: >200

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/428e0506-694c-4f9a-a2eb-472852ecdaa8/@@download/attachment/296727.pdf

value: esophagus muscularis mucosa

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

value: ENCBS072KNR at ENCODE; https://www.encodeproject.org/ENCBS072KNR/


title: total RNA-seq from subcutaneous adipose tissue (ENCLB026NLN)

description:
https://www.encodeproject.org/experiments/ENCSR671WMH/
***************
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 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: ENCSR671WMH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB026NLN
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens subcutaneous adipose tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/99193761-848a-41a0-a279-a261aa6df3df/@@download/attachment/296162.pdf

value: subcutaneous adipose tissue

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

value: 54 year

value: male

value: ENCBS183IBX at ENCODE; https://www.encodeproject.org/ENCBS183IBX/

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


title: shRNA RNA-seq from K562 (ENCLB291LZT)

description:
https://www.encodeproject.org/experiments/ENCSR678WOA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBM39. (RBM39_BGKLV28)
experiment encode accession: ENCSR678WOA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB291LZT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RBM39

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e43f799a-6596-4a75-ad38-708dea9c055a/@@download/attachment/L-RBM39_BGKLV28-44.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM39. (RBM39_BGKLV28-44)

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS192SEZ at ENCODE; https://www.encodeproject.org/ENCBS192SEZ/

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 (ENCLB168FRX)

description:
https://www.encodeproject.org/experiments/ENCSR678WOA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBM39. (RBM39_BGKLV28)
experiment encode accession: ENCSR678WOA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB168FRX
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/47b5980c-2f28-4351-9527-438ce324a363/@@download/attachment/L-RBM39_BGKLV28-43.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM39. (RBM39_BGKLV28-43)

value: 53 year

value: ENCBS023ECI at ENCODE; https://www.encodeproject.org/ENCBS023ECI/


title: total RNA-seq from transverse colon (ENCLB373HEH)

description:
https://www.encodeproject.org/experiments/ENCSR653ZJF/
***************
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 transverse colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR653ZJF
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB373HEH
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/67cd2e9d-6ba1-40eb-aee0-d7bfcd3c3180/@@download/attachment/296669.pdf

value: transverse colon

value: tissue

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

value: 37 year

value: Thomas Gingeras, CSHL

value: ENCBS767MGS at ENCODE; https://www.encodeproject.org/ENCBS767MGS/

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


title: shRNA RNA-seq from HepG2 (ENCLB873KJY)

description:
https://www.encodeproject.org/experiments/ENCSR676EKU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGHLV35)
experiment encode accession: ENCSR676EKU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB873KJY
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CPSF6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1d5249fd-7525-40fb-af16-084eda4b1787/@@download/attachment/L-CPSF6_BGHLV35-13.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGHLV35-13)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS344NUB at ENCODE; https://www.encodeproject.org/ENCBS344NUB/

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


title: total RNA-seq from tibial nerve (ENCLB575RKD)

description:
https://www.encodeproject.org/experiments/ENCSR648OSR/
***************
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 tibial nerve tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR648OSR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB575RKD
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens tibial nerve tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3f08526c-2b3c-4287-9aa8-3255fd85dcf0/@@download/attachment/296338.pdf

value: tibial nerve

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

value: 54 year

value: adult

value: ENCBS649YYM at ENCODE; https://www.encodeproject.org/ENCBS649YYM/

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


title: RAMPAGE from prostate gland (ENCLB903BKO)

description:
https://www.encodeproject.org/experiments/ENCSR671RMD/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human prostate tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR671RMD
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR701TST
encode release date: 2016-08-22
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB903BKO
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f38fb181-de70-42f2-9f8e-1f682d6c8c34/@@download/attachment/296746.pdf

value: prostate gland

value: tissue

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

value: Thomas Gingeras, CSHL

value: ENCBS291PVP at ENCODE; https://www.encodeproject.org/ENCBS291PVP/


title: total RNA-seq from body of pancreas (ENCLB538OCX)

description:
https://www.encodeproject.org/experiments/ENCSR671IYC/
***************
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 pancreas 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: ENCSR671IYC
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB538OCX
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens body of pancreas tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a228e668-ebc0-4654-b35c-7c1a20f997fc/@@download/attachment/296342.pdf

value: body of pancreas

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

value: 51 year

value: female

value: ENCBS389HVX at ENCODE; https://www.encodeproject.org/ENCBS389HVX/

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


title: RAMPAGE from prostate gland (ENCLB089GWY)

description:
https://www.encodeproject.org/experiments/ENCSR655HUL/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human prostate tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR655HUL
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR495HDM
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB089GWY
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5e047cd2-cd23-437a-81d4-4b02b567b61e/@@download/attachment/296772.pdf

value: 37 year

value: male

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

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


title: pNanogP8+Dox+NgIP

city: Smithville

first: Collene

last: Jeter

state: TX

address: 1808 Park Rd 1C, Box 389

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

library_source: genomic

data_processing:
Sequenced DNA reads were mapped to human genome hg18 using Illumina analysis pipeline (Eland) and only the reads that were mapped to unique position were retained.To avoid PCR bias, for multiple reads that were mapped to the same genomic position, only one copy was retained for further analysis.
The peaks were called by MACS (version 1.3.7.1). The window size was 300bp and the pvalue cutoff was 1e-5.
pNanog1 peaks were initially called by comparing pNanog1+Dox+NgIP to pNanog1-Dox+NgIP (control). pNanogP8 peaks were initially called by comparing pNanogP8+Dox+NgIP to pNanogP8-Dox+NgIP (control). Then for both pNanog1 and pNanogP8, the peaks that were not significant when using pLvx+Dox+IgG and pLvx+Dox+NgIP as control were removed.
Genome_build: hg18
Supplementary_files_format_and_content: _peaks.txt: Chr (chromosome of the peak); Start (start position of the peak); End (end position of the peak)

molecule: genomic DNA

source_name: cultured LNCaP prostate cancer cells

extract_protocol:
After formaldehyde fixation, lysed cell DNA was sheared by sonication and immunoprecipitated with an anti-NANOG antibody (Santa Cruz, H-155) vs IgG control and protein-A beads overnight.
ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer cells

tag: genotype/variation

value: NANOGP8 overexpression

tag: cultured with

value: doxycycline for 4 days

tag: chip antibody

value: NANOG IgG


title: shRNA RNA-seq from HepG2 (ENCLB994VFC)

description:
https://www.encodeproject.org/experiments/ENCSR676EKU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGHLV35)
experiment encode accession: ENCSR676EKU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB994VFC
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/64a52001-b3b3-4986-b3df-a8cd9563de8a/@@download/attachment/L-CPSF6_BGHLV35-14.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGHLV35-14)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS592KVD at ENCODE; https://www.encodeproject.org/ENCBS592KVD/

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


title: pNanogP8-Dox+NgIP

value: without doxycycline for 4 days


title: RAMPAGE from transverse colon (ENCLB439DZV)

description:
https://www.encodeproject.org/experiments/ENCSR649WDK/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human transverse colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR649WDK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR630VJN
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB439DZV
size range: >200

source_name: Homo sapiens transverse colon tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ed256006-459a-4c72-b08d-edcf13360d1b/@@download/attachment/296778.pdf

value: transverse colon

value: tissue

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

value: 54 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS668MJW at ENCODE; https://www.encodeproject.org/ENCBS668MJW/

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


title: RAMPAGE from esophagus muscularis mucosa (ENCLB998GPY)

description:
https://www.encodeproject.org/experiments/ENCSR669JBL/
***************
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 muscle layer of esophagus tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR669JBL
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR098BUF
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB998GPY
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be72b3af-e22b-4799-8926-f62498c4cb12/@@download/attachment/296724.pdf

value: esophagus muscularis mucosa

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

value: 53 year

value: female

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

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


title: pLvx+Dox+NgIP

value: LNCaP

value: prostate cancer cells

value: expressing pLVX (empty vector)

value: doxycycline for 4 days

value: NANOG IgG


title: pLvx+Dox+IgG

value: IgG


title: shRNA RNA-seq from HepG2 (ENCLB402JMJ)

description:
https://www.encodeproject.org/experiments/ENCSR808FBR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX5. (DDX5_BGHLV30)
experiment encode accession: ENCSR808FBR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR776SXA
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB402JMJ
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/84f4079a-4c75-4f47-b1ce-b07c1cde2ddf/@@download/attachment/L-DDX5_BGHLV30-25B.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX5. (DDX5_BGHLV30-25B)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS269MQH at ENCODE; https://www.encodeproject.org/ENCBS269MQH/

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 (ENCLB435CQK)

description:
https://www.encodeproject.org/experiments/ENCSR644AIM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF1. (SF1_BGHLV26)
experiment encode accession: ENCSR644AIM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB435CQK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e497fd8f-79b3-4993-9951-62212a901d0a/@@download/attachment/L-SF1_BGHLV26_51.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against SF1 (SF1_BGHLV26_51)

value: male

value: ENCBS239AGG at ENCODE; https://www.encodeproject.org/ENCBS239AGG/


title: total RNA-seq from omental fat pad (ENCLB811ZXD)

description:
https://www.encodeproject.org/experiments/ENCSR645TCG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's adipose tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR645TCG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB811ZXD
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a8db8bae-c91a-42a6-a99a-b06698ac31c8/@@download/attachment/296316.pdf

value: omental fat pad

value: tissue

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

value: 53 year

value: adult

value: female

value: Thomas Gingeras, CSHL

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

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


title: pNanog1-Dox+NgIP

value: LNCaP

value: prostate cancer cells

value: NANOG1 overexpression

value: without doxycycline for 4 days

value: NANOG IgG


title: shRNA RNA-seq from HepG2 (ENCLB903ADY)

description:
https://www.encodeproject.org/experiments/ENCSR644AIM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF1. (SF1_BGHLV26)
experiment encode accession: ENCSR644AIM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB903ADY
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/dfe416eb-c04f-44cd-94eb-b3e59c3a2d07/@@download/attachment/L-SF1_BGHLV26_52.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against SF1 (SF1_BGHLV26_52)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS435MPV at ENCODE; https://www.encodeproject.org/ENCBS435MPV/

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 (ENCLB807XCC)

description:
https://www.encodeproject.org/experiments/ENCSR635BOO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SNRNP70. (SNRNP70_BGHLV35)
experiment encode accession: ENCSR635BOO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB807XCC
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SNRNP70

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7614ae88-06d1-4f14-97bb-f2ffb2cfa6a9/@@download/attachment/L-SNRNP70_BGHLV35-46.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SNRNP70. (SNRNP70_BGHLV35-46)

value: male

value: ENCBS794FIB at ENCODE; https://www.encodeproject.org/ENCBS794FIB/


title: shRNA RNA-seq from HepG2 (ENCLB567EML)

description:
https://www.encodeproject.org/experiments/ENCSR635BOO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SNRNP70. (SNRNP70_BGHLV35)
experiment encode accession: ENCSR635BOO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB567EML
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/1641bd5d-40aa-4c5e-bb20-038b0fb26567/@@download/attachment/L-SNRNP70_BGHLV35-45.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SNRNP70. (SNRNP70_BGHLV35-45)

value: ENCBS018QKX at ENCODE; https://www.encodeproject.org/ENCBS018QKX/


title: shRNA RNA-seq from HepG2 (ENCLB772VOI)

description:
https://www.encodeproject.org/experiments/ENCSR634KHL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HDGF. (HDGF_BGHLV31)
experiment encode accession: ENCSR634KHL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB772VOI
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/de7f04b2-29b7-443b-a350-1025a20a5fd4/@@download/attachment/L-HDGF_BGHLV31-39.pdf

value: HDGF

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HDGF. (HDGF_BGHLV31-39)

value: ENCBS540JSU at ENCODE; https://www.encodeproject.org/ENCBS540JSU/


title: shRNA RNA-seq from HepG2 (ENCLB614RNR)

description:
https://www.encodeproject.org/experiments/ENCSR634KHL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HDGF. (HDGF_BGHLV31)
experiment encode accession: ENCSR634KHL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB614RNR
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/139fb59a-f980-4152-b7ce-6f845e652edf/@@download/attachment/L-HDGF_BGHLV31-40.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HDGF. (HDGF_BGHLV31-40)

value: ENCBS978CGB at ENCODE; https://www.encodeproject.org/ENCBS978CGB/


title: shRNA RNA-seq from K562 (ENCLB988URW)

description:
https://www.encodeproject.org/experiments/ENCSR631RFX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGKLV34)
experiment encode accession: ENCSR631RFX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB988URW
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8003516c-53af-4202-80de-b638801d8fa0/@@download/attachment/L-MTPAP_BGKLV34-23.pdf

value: MTPAP

value: RNA-seq on K562 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGKLV34-23)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS579ZTI at ENCODE; https://www.encodeproject.org/ENCBS579ZTI/

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


title: shRNA RNA-seq from HepG2 (ENCLB637ZUM)

description:
https://www.encodeproject.org/experiments/ENCSR998MZP/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PRPF8 in HepG2 cells followed by RNA-seq. (PRPF8_BGHLV17)
experiment encode accession: ENCSR998MZP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB637ZUM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PRPF8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/dddd770d-39a0-4274-8525-ca73df0f0238/@@download/attachment/L-PRPF8_BGHLV17_24.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF8. (PRPF8_BGHLV17_24)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS045OVM at ENCODE; https://www.encodeproject.org/ENCBS045OVM/

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: pNanog1+Dox+NgIP

value: LNCaP

value: prostate cancer cells

value: NANOG1 overexpression

value: doxycycline for 4 days

value: NANOG IgG