title: shRNA RNA-seq from HepG2 (ENCLB135EUE)

description:
https://www.encodeproject.org/experiments/ENCSR778RWJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against XPO5. (XPO5-BGHLV22)
experiment encode accession: ENCSR778RWJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB135EUE
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/233eb5f1-8c7e-4ed8-bcff-65fd6a6cd0a7/@@download/attachment/L-XPO5-BGHLV22-57.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XPO5. (XPO5-BGHLV22-57)

value: ENCBS716VBH at ENCODE; https://www.encodeproject.org/ENCBS716VBH/


title: shRNA RNA-seq from K562 (ENCLB889LLU)

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/ENCSR770OWW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against LARP7. (LARP7_BGKLV21)
experiment encode accession: ENCSR770OWW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB889LLU
size range: >200
spikeins used: /references/ENCSR449DXG/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting LARP7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0cf2cd46-a65a-459b-b8ee-2c337d395ee8/@@download/attachment/L-LARP7_BGKLV21_25_17571.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against LARP7. (LARP7_BGKLV21_25_17571)

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

value: Brenton Graveley, UConn

tag: link

value: ENCBS790YFX at ENCODE; https://www.encodeproject.org/ENCBS790YFX/

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 (ENCLB056CGJ)

description:
https://www.encodeproject.org/experiments/ENCSR770OWW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against LARP7. (LARP7_BGKLV21)
experiment encode accession: ENCSR770OWW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB056CGJ
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/d30e456b-8673-4dd0-8bf8-21116076028a/@@download/attachment/L-LARP7_BGKLV21_26_17572.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against LARP7. (LARP7_BGKLV21_26_17572)

value: ENCBS058MBJ at ENCODE; https://www.encodeproject.org/ENCBS058MBJ/


title: total RNA-seq from cardiac muscle cell (ENCLB431LEI)

description:
https://www.encodeproject.org/experiments/ENCSR294NDO/
***************
biological replicate number: 1
technical replicate number: 1
description: cardiac myocyte
experiment encode accession: ENCSR294NDO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB431LEI
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.350
nucleic acid starting quantity units: ng

source_name: Homo sapiens cardiac muscle in vitro differentiated cells fetal

value: cardiac muscle cell

value: in vitro differentiated cells

value: unknown

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS343AKO at ENCODE; https://www.encodeproject.org/ENCBS343AKO/

value: Derived from ENCODE donor ENCDO924HBJ; https://www.encodeproject.org/ENCDO924HBJ/


title: total RNA-seq from stomach (ENCLB916YCI)

description:
https://www.encodeproject.org/experiments/ENCSR296PMS/
***************
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 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: ENCSR296PMS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB916YCI
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/80c4fbce-9b50-4837-8a5a-21fec76aa74f/@@download/attachment/296674.pdf

value: stomach

value: tissue

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

value: 54 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS141UOA at ENCODE; https://www.encodeproject.org/ENCBS141UOA/

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


title: total RNA-seq from tibial nerve (ENCLB966RBB)

description:
https://www.encodeproject.org/experiments/ENCSR272UNO/
***************
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 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: ENCSR272UNO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB966RBB
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens tibial nerve tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3937c8dd-b94a-4ffe-a1f0-3dd63096ab7e/@@download/attachment/296344.pdf

value: tibial nerve

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

value: 51 year

value: female

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

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


title: shRNA RNA-seq from HepG2 (ENCLB926FPG)

description:
https://www.encodeproject.org/experiments/ENCSR269SJB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CKAP4. (CKAP4_BGHLV31)
experiment encode accession: ENCSR269SJB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB926FPG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CKAP4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7443c335-46c0-49d6-9ad2-7d1851dd9005/@@download/attachment/L-CKAP4_BGHLV31-23.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CKAP4. (CKAP4_BGHLV31-23)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS610IGG at ENCODE; https://www.encodeproject.org/ENCBS610IGG/

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 (ENCLB066OOM)

description:
https://www.encodeproject.org/experiments/ENCSR269ZAO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP18. (UTP18_BGHLV33)
experiment encode accession: ENCSR269ZAO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB066OOM
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting UTP18

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d7eda759-32c2-4d60-8d79-cefcddaf8277/@@download/attachment/L-UTP18_BGHLV33-36.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP18. (UTP18_BGHLV33-36)

value: male

value: ENCBS666KXY at ENCODE; https://www.encodeproject.org/ENCBS666KXY/


title: shRNA RNA-seq from HepG2 (ENCLB723BFT)

description:
https://www.encodeproject.org/experiments/ENCSR269ZAO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP18. (UTP18_BGHLV33)
experiment encode accession: ENCSR269ZAO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB723BFT
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/b7804b96-af0d-4df8-b9ca-251b9c214162/@@download/attachment/L-UTP18_BGHLV33-35.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP18. (UTP18_BGHLV33-35)

value: ENCBS934AFY at ENCODE; https://www.encodeproject.org/ENCBS934AFY/


title: shRNA RNA-seq from HepG2 (ENCLB499RIN)

description:
https://www.encodeproject.org/experiments/ENCSR769GES/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1-BGHLV23)
experiment encode accession: ENCSR769GES
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB499RIN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting HNRNPA2B1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/46c4fe77-5161-4798-9d0d-db05abee2808/@@download/attachment/L-HNRNPA2B1-BGHLV23-19.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1-BGHLV23-19)

value: ENCBS034ENA at ENCODE; https://www.encodeproject.org/ENCBS034ENA/


title: shRNA RNA-seq from HepG2 (ENCLB539MDT)

description:
https://www.encodeproject.org/experiments/ENCSR769GES/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1-BGHLV23)
experiment encode accession: ENCSR769GES
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB539MDT
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/62477945-0da3-4e4c-9f6c-5a2344ae0f03/@@download/attachment/L-HNRNPA2B1-BGHLV23-20.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA2B1. (HNRNPA2B1-BGHLV23-20)

value: ENCBS287RQP at ENCODE; https://www.encodeproject.org/ENCBS287RQP/


title: total RNA-seq from cardiac muscle cell (ENCLB330LPJ)

description:
https://www.encodeproject.org/experiments/ENCSR294NDO/
***************
biological replicate number: 2
technical replicate number: 1
description: cardiac myocyte
experiment encode accession: ENCSR294NDO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB330LPJ
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.350
nucleic acid starting quantity units: ng

value: cardiac muscle cell

value: in vitro differentiated cells

value: unknown

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS806KLM at ENCODE; https://www.encodeproject.org/ENCBS806KLM/

value: Derived from ENCODE donor ENCDO924HBJ; https://www.encodeproject.org/ENCDO924HBJ/


title: shRNA RNA-seq from HepG2 (ENCLB009YLS)

description:
https://www.encodeproject.org/experiments/ENCSR296ERI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUS1. (PUS1_BGHLV31)
experiment encode accession: ENCSR296ERI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB009YLS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PUS1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6a7a4998-9219-4290-90df-9ca560a26d72/@@download/attachment/L-PUS1_BGHLV31-52.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUS1. (PUS1_BGHLV31-52)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS053QGR at ENCODE; https://www.encodeproject.org/ENCBS053QGR/

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 (ENCLB173SSA)

description:
https://www.encodeproject.org/experiments/ENCSR296ERI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUS1. (PUS1_BGHLV31)
experiment encode accession: ENCSR296ERI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB173SSA
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/9b9472d1-9558-425d-aafd-4687853b9896/@@download/attachment/L-PUS1_BGHLV31-51.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUS1. (PUS1_BGHLV31-51)

value: male

value: ENCBS918RGX at ENCODE; https://www.encodeproject.org/ENCBS918RGX/


title: shRNA RNA-seq from K562 (ENCLB252WPQ)

description:
https://www.encodeproject.org/experiments/ENCSR281IUF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGKLV32)
experiment encode accession: ENCSR281IUF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB252WPQ
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX19B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5d697b7a-875d-4311-ad30-8ce5514e19e1/@@download/attachment/L-DDX19B_BGKLV32-18.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGKLV32-18)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS949FLF at ENCODE; https://www.encodeproject.org/ENCBS949FLF/

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 skeletal muscle myoblast (ENCLB107VGB)

description:
https://www.encodeproject.org/experiments/ENCSR765LMM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skeletal myoblasts. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR765LMM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR444WHQ
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB107VGB
size range: >200

source_name: Homo sapiens skeletal muscle myoblast primary cell

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/2b5d8dc4-ffa5-434c-9d06-7a7dfaeda776/@@download/attachment/293013.pdf

value: skeletal muscle myoblast

value: primary cell

value: skeletal muscle myoblasts

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS328AAA at ENCODE; https://www.encodeproject.org/ENCBS328AAA/

value: Derived from ENCODE donor ENCDO094AAA; https://www.encodeproject.org/ENCDO094AAA/

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

value: Lonza  sample source; http://www.lonza.com/


title: shRNA RNA-seq from HepG2 (ENCLB735CLH)

description:
https://www.encodeproject.org/experiments/ENCSR269SJB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CKAP4. (CKAP4_BGHLV31)
experiment encode accession: ENCSR269SJB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB735CLH
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/5a8c88c0-10cd-4bf8-b7b9-7e14b12d0fa0/@@download/attachment/L-CKAP4_BGHLV31-24.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CKAP4. (CKAP4_BGHLV31-24)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS200OKV at ENCODE; https://www.encodeproject.org/ENCBS200OKV/

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

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


title: RAMPAGE from skeletal muscle myoblast (ENCLB938YFZ)

description:
https://www.encodeproject.org/experiments/ENCSR765LMM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skeletal myoblasts. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR765LMM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR444WHQ
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB938YFZ
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c7c48882-c43f-4892-b411-b12258309ab1/@@download/attachment/293014.pdf

value: skeletal muscle myoblast

value: primary cell

value: unknown

value: ENCBS665DRD at ENCODE; https://www.encodeproject.org/ENCBS665DRD/


title: shRNA RNA-seq from HepG2 (ENCLB054NQP)

description:
https://www.encodeproject.org/experiments/ENCSR771QMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against GEMIN5 in HepG2 cells followed by RNA-seq. (GEMIN5_BGHLV16)
experiment encode accession: ENCSR771QMJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB054NQP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting GEMIN5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/157a6b38-1047-4cc2-91e5-af6fb4a888ac/@@download/attachment/L-GEMIN5_BGHLV16_29.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GEMIN5. (GEMIN5_BGHLV16_29)

value: ENCBS363GXU at ENCODE; https://www.encodeproject.org/ENCBS363GXU/


title: siRNA RNA-seq from K562 (ENCLB514YBK)

description:
https://www.encodeproject.org/experiments/ENCSR756JGE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR756JGE
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB514YBK
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: Control

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

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS731TUE at ENCODE; https://www.encodeproject.org/ENCBS731TUE/

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


title: shRNA RNA-seq from K562 (ENCLB528WKB)

description:
https://www.encodeproject.org/experiments/ENCSR267RHP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against BUD13. (BUD13_BGKLV29)
experiment encode accession: ENCSR267RHP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB528WKB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting BUD13

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7ca00def-a66a-40f7-84e5-3e886c208d95/@@download/attachment/L-BUD13_BGKLV29-15.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against BUD13. (BUD13_BGKLV29-15)

value: Brenton Graveley, UConn

value: ENCBS199SKB at ENCODE; https://www.encodeproject.org/ENCBS199SKB/

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


title: shRNA RNA-seq from K562 (ENCLB568GQD)

description:
https://www.encodeproject.org/experiments/ENCSR267RHP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against BUD13. (BUD13_BGKLV29)
experiment encode accession: ENCSR267RHP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB568GQD
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/55156e94-0a65-4753-8b99-c74188a81886/@@download/attachment/L-BUD13_BGKLV29-16.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against BUD13. (BUD13_BGKLV29-16)

value: ENCBS695KRB at ENCODE; https://www.encodeproject.org/ENCBS695KRB/


title: shRNA RNA-seq from K562 (ENCLB299PMK)

description:
https://www.encodeproject.org/experiments/ENCSR281IUF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGKLV32)
experiment encode accession: ENCSR281IUF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB299PMK
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/a2a8acc6-6016-4cba-8ee6-c625e7c3b1e7/@@download/attachment/L-DDX19B_BGKLV32-17.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGKLV32-17)

value: ENCBS413TJM at ENCODE; https://www.encodeproject.org/ENCBS413TJM/


title: shRNA RNA-seq from HepG2 (ENCLB128RUQ)

description:
https://www.encodeproject.org/experiments/ENCSR281KCL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGHLV30)
experiment encode accession: ENCSR281KCL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB128RUQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SUPT6H

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/020c24b4-10e4-4398-b4c6-2343611865fd/@@download/attachment/L-SUPT6H_BGHLV30-53.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGHLV30-53)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS689DEE at ENCODE; https://www.encodeproject.org/ENCBS689DEE/

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 (ENCLB465RMG)

description:
https://www.encodeproject.org/experiments/ENCSR281KCL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGHLV30)
experiment encode accession: ENCSR281KCL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB465RMG
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/ffeb6d7f-18fd-4503-93e8-dbfea679471c/@@download/attachment/L-SUPT6H_BGHLV30-54.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUPT6H. (SUPT6H_BGHLV30-54)

value: ENCBS600ITX at ENCODE; https://www.encodeproject.org/ENCBS600ITX/


title: shRNA RNA-seq from HepG2 (ENCLB351LSE)

description:
https://www.encodeproject.org/experiments/ENCSR264TUE/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV35)
experiment encode accession: ENCSR264TUE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB351LSE
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/49a3a218-8801-49a1-b2f1-647587d935ed/@@download/attachment/L-NT_BGHLV35-2.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV35-2)

value: Brenton Graveley, UConn

value: ENCBS542QTQ at ENCODE; https://www.encodeproject.org/ENCBS542QTQ/


title: shRNA RNA-seq from K562 (ENCLB691DUI)

description:
https://www.encodeproject.org/experiments/ENCSR762FEO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against LSM11. (LSM11_BGKLV21)
experiment encode accession: ENCSR762FEO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB691DUI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting LSM11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2dd04297-f650-4992-a2d5-2d768ebc243b/@@download/attachment/L-LSM11_BGKLV21_29_17576.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against LSM11. (LSM11_BGKLV21_29_17576)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS595QXS at ENCODE; https://www.encodeproject.org/ENCBS595QXS/

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 (ENCLB747JPW)

description:
https://www.encodeproject.org/experiments/ENCSR762FEO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against LSM11. (LSM11_BGKLV21)
experiment encode accession: ENCSR762FEO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB747JPW
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/46034711-2bcd-4c83-8843-debec6d60738/@@download/attachment/L-LSM11_BGKLV21_30_17577.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against LSM11. (LSM11_BGKLV21_30_17577)

value: ENCBS656VZE at ENCODE; https://www.encodeproject.org/ENCBS656VZE/


title: shRNA RNA-seq from HepG2 (ENCLB953AVQ)

description:
https://www.encodeproject.org/experiments/ENCSR755KOM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP3. (FUBP3-BGHLV12)
experiment encode accession: ENCSR755KOM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR376RJN
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB953AVQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting FUBP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a260f850-0bea-49e7-994d-f49d0a4726fb/@@download/attachment/L-FUBP3-BGHLV12-28_17745.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP3. (FUBP3-BGHLV12-28_17745)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS598VSF at ENCODE; https://www.encodeproject.org/ENCBS598VSF/

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

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


title: RAMPAGE from thyroid gland (ENCLB483WZW)

description:
https://www.encodeproject.org/experiments/ENCSR260RBO/
***************
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 thyroid 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: ENCSR260RBO
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR532LJV
encode release date: 2016-03-16
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB483WZW
size range: >200

source_name: Homo sapiens thyroid 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/a55470d0-793c-49d4-b718-31d21f1c5fc8/@@download/attachment/295970.pdf

value: thyroid gland

value: tissue

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

value: 37 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS376ASB at ENCODE; https://www.encodeproject.org/ENCBS376ASB/

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


title: total RNA-seq from Peyer's patch (ENCLB833ZLW)

description:
https://www.encodeproject.org/experiments/ENCSR257NIR/
***************
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 small intestine tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR257NIR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB833ZLW
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens Peyer's patch tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a38fbbe0-bef7-4b7c-aff3-e6691eacdb06/@@download/attachment/296377.pdf

value: Peyer's patch

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

value: 54 year

value: ENCBS943XLR at ENCODE; https://www.encodeproject.org/ENCBS943XLR/

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


title: shRNA RNA-seq from HepG2 (ENCLB718NAR)

description:
https://www.encodeproject.org/experiments/ENCSR264TUE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV35)
experiment encode accession: ENCSR264TUE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB718NAR
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/9266a5b2-4a0e-4cf6-8ac4-c089a24f061b/@@download/attachment/L-NT_BGHLV35-1.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV35-1)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS599TQI at ENCODE; https://www.encodeproject.org/ENCBS599TQI/


title: shRNA RNA-seq from HepG2 (ENCLB583OBB)

description:
https://www.encodeproject.org/experiments/ENCSR755KOM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP3. (FUBP3-BGHLV12)
experiment encode accession: ENCSR755KOM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR376RJN
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB583OBB
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/48902f48-4b92-4110-adb8-a62af590b9f3/@@download/attachment/L-FUBP3-BGHLV12-27_17744.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUBP3. (FUBP3-BGHLV12-27_17744)

value: ENCBS745AQT at ENCODE; https://www.encodeproject.org/ENCBS745AQT/

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 (ENCLB623ENB)

description:
https://www.encodeproject.org/experiments/ENCSR745WVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PUM1. (PUM1-BGKLV25)
experiment encode accession: ENCSR745WVZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB623ENB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PUM1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ddf803e6-586c-4b8c-8900-eb5d4354706a/@@download/attachment/L-PUM1-BGKLV25-46.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PUM1. (PUM1-BGKLV25-46)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS492BQN at ENCODE; https://www.encodeproject.org/ENCBS492BQN/

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 thyroid gland (ENCLB147HEL)

description:
https://www.encodeproject.org/experiments/ENCSR260RBO/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's thyroid 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: ENCSR260RBO
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR532LJV
encode release date: 2016-03-16
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB147HEL
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5e4092fc-b677-4461-a60f-f296e20d31f1/@@download/attachment/295971.pdf

value: thyroid gland

value: tissue

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

value: 37 year

value: Thomas Gingeras, CSHL

value: ENCBS376ASB at ENCODE; https://www.encodeproject.org/ENCBS376ASB/

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


title: shRNA RNA-seq from K562 (ENCLB404RRN)

description:
https://www.encodeproject.org/experiments/ENCSR745WVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PUM1. (PUM1-BGKLV25)
experiment encode accession: ENCSR745WVZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB404RRN
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/2028908d-f117-4285-b158-0c5310156849/@@download/attachment/L-PUM1-BGKLV25-45.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PUM1. (PUM1-BGKLV25-45)

value: Brenton Graveley, UConn

value: ENCBS425EWY at ENCODE; https://www.encodeproject.org/ENCBS425EWY/


title: RAMPAGE from lower leg skin (ENCLB896HBZ)

description:
https://www.encodeproject.org/experiments/ENCSR251EJL/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human lower leg skin tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR251EJL
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR991HIR
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB896HBZ
size range: >200

source_name: Homo sapiens lower leg skin 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/bd2216db-9602-4f53-8769-830b2e27a343/@@download/attachment/296813.pdf

value: lower leg skin

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

value: 53 year

value: adult

value: ENCBS432ZSQ at ENCODE; https://www.encodeproject.org/ENCBS432ZSQ/

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


title: shRNA RNA-seq from HepG2 (ENCLB336EFN)

description:
https://www.encodeproject.org/experiments/ENCSR744YVR/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PSIP1 in HepG2 cells followed by RNA-seq. (PSIP1_BGHLV18)
experiment encode accession: ENCSR744YVR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB336EFN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PSIP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/083a117a-35d3-42b9-9b7c-07d1a1b70d80/@@download/attachment/L-PSIP1_BGHLV18_44.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PSIP1. (PSIP1_BGHLV18_44)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS827QKB at ENCODE; https://www.encodeproject.org/ENCBS827QKB/

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 (ENCLB523HCE)

description:
https://www.encodeproject.org/experiments/ENCSR728BOL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FASTKD1. (FASTKD1-BGHLV22)
experiment encode accession: ENCSR728BOL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB523HCE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting FASTKD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/13b5b7f3-8c31-41d7-9828-6feda111af45/@@download/attachment/L-FASTKD1-BGHLV22-16_17753.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FASTKD1. (FASTKD1-BGHLV22-16_17753)

value: ENCBS381BBR at ENCODE; https://www.encodeproject.org/ENCBS381BBR/


title: shRNA RNA-seq from HepG2 (ENCLB717PRE)

description:
https://www.encodeproject.org/experiments/ENCSR744YVR/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PSIP1 in HepG2 cells followed by RNA-seq. (PSIP1_BGHLV18)
experiment encode accession: ENCSR744YVR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB717PRE
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/5b889ada-a1ee-4a01-abdd-2b0a1c7d0d68/@@download/attachment/L-PSIP1_BGHLV18_43.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PSIP1. (PSIP1_BGHLV18_43)

value: Brenton Graveley, UConn

value: ENCBS171TJQ at ENCODE; https://www.encodeproject.org/ENCBS171TJQ/


title: shRNA RNA-seq from HepG2 (ENCLB167EXT)

description:
https://www.encodeproject.org/experiments/ENCSR246RRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV27)
experiment encode accession: ENCSR246RRQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB167EXT
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/58e3bfbc-c079-47f7-b3f2-204ac7e743c8/@@download/attachment/L-non-target_BGHLV27-1.pdf

value: Control

value: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV27-1)

value: ENCBS811GQK at ENCODE; https://www.encodeproject.org/ENCBS811GQK/


title: shRNA RNA-seq from K562 (ENCLB146LYT)

description:
https://www.encodeproject.org/experiments/ENCSR251ABP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UPF1. (UPF1_BGKLV34)
experiment encode accession: ENCSR251ABP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB146LYT
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 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/8f9aeab1-9202-4fe3-8f5e-ba733e957784/@@download/attachment/L-UPF1_BGKLV34-43.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UPF1. (UPF1_BGKLV34-43)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS389HVA at ENCODE; https://www.encodeproject.org/ENCBS389HVA/

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


title: shRNA RNA-seq from HepG2 (ENCLB946ZUF)

description:
https://www.encodeproject.org/experiments/ENCSR246RRQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV27)
experiment encode accession: ENCSR246RRQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB946ZUF
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/956c1535-ba98-4714-8e52-2fa1d20b414c/@@download/attachment/L-non-target_BGHLV27-2.pdf

value: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target_BGHLV27-2)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS129BNW at ENCODE; https://www.encodeproject.org/ENCBS129BNW/

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 (ENCLB849GYD)

description:
https://www.encodeproject.org/experiments/ENCSR243IGA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HSPD1. (HSPD1_BGHLV27)
experiment encode accession: ENCSR243IGA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB849GYD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting HSPD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8e6c5c4d-d46f-41e0-bef6-f2e3287baf50/@@download/attachment/L-HSPD1_BGHLV27-26.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against HSPD1 (HSPD1_BGHLV27-26)

value: Brenton Graveley, UConn

value: ENCBS706BWK at ENCODE; https://www.encodeproject.org/ENCBS706BWK/


title: shRNA RNA-seq from K562 (ENCLB357ECB)

description:
https://www.encodeproject.org/experiments/ENCSR251ABP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UPF1. (UPF1_BGKLV34)
experiment encode accession: ENCSR251ABP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB357ECB
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/2eda1017-9966-4bd5-8b2e-7e7f038aefc1/@@download/attachment/L-UPF1_BGKLV34-44.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UPF1. (UPF1_BGKLV34-44)

value: 53 year

value: adult

value: ENCBS162ZFM at ENCODE; https://www.encodeproject.org/ENCBS162ZFM/


title: shRNA RNA-seq from HepG2 (ENCLB500FZE)

description:
https://www.encodeproject.org/experiments/ENCSR728BOL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FASTKD1. (FASTKD1-BGHLV22)
experiment encode accession: ENCSR728BOL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB500FZE
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/7c80b496-e712-45d7-9717-5df3b30b1f80/@@download/attachment/L-FASTKD1-BGHLV22-15_17752.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FASTKD1. (FASTKD1-BGHLV22-15_17752)

value: ENCBS175ALJ at ENCODE; https://www.encodeproject.org/ENCBS175ALJ/


title: microRNA-seq from body of pancreas (ENCLB434NPL)

description:
https://www.encodeproject.org/experiments/ENCSR723WQE/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human pancreas
experiment encode accession: ENCSR723WQE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB434NPL
size range: <30

source_name: Homo sapiens body of pancreas tissue male adult (54 years)

value: body of pancreas

value: tissue

value: Pancreas

value: 54 year

value: Barbara Wold, Caltech

value: ENCBS213PZE at ENCODE; https://www.encodeproject.org/ENCBS213PZE/

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


title: total RNA-seq from thyroid gland (ENCLB463XDK)

description:
https://www.encodeproject.org/experiments/ENCSR238ZZD/
***************
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 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: ENCSR238ZZD
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB463XDK
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/86b99959-7242-4851-ba3f-cca5b0faa1af/@@download/attachment/296608.pdf

value: thyroid gland

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

value: female

value: Thomas Gingeras, CSHL

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

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


title: RAMPAGE from heart (ENCLB498ZDL)

description:
https://www.encodeproject.org/experiments/ENCSR724SZY/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from heart tissue from a 34 year old adult. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR724SZY
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AHH
encode release date: 2014-09-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB498ZDL
size range: >200

source_name: Homo sapiens heart tissue male adult (34 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/2311df2a-683a-4c03-b3d3-1b4fe2669215/@@download/attachment/SID30047.pdf

value: heart

value: Human heart Tissue obtained from a healthy, 34 year old Caucasian male donor

value: 34 year

value: adult

value: male

value: healthy with polysubstance abuse

value: ENCBS044RNA at ENCODE; https://www.encodeproject.org/ENCBS044RNA/

value: Derived from ENCODE donor ENCDO058AAA; https://www.encodeproject.org/ENCDO058AAA/

value: ENCODE dbxrefs Heart_STL003; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Heart_STL003


title: microRNA-seq from body of pancreas (ENCLB912ZDT)

description:
https://www.encodeproject.org/experiments/ENCSR723WQE/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human pancreas
experiment encode accession: ENCSR723WQE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB912ZDT
size range: <30

value: body of pancreas

value: tissue

value: Pancreas

value: 54 year

value: Barbara Wold, Caltech

value: ENCBS126RDV at ENCODE; https://www.encodeproject.org/ENCBS126RDV/


title: shRNA RNA-seq from HepG2 (ENCLB838UKB)

description:
https://www.encodeproject.org/experiments/ENCSR720BPO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0-BGHLV22)
experiment encode accession: ENCSR720BPO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB838UKB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting HNRNPA0

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7971a877-a0cd-43cc-8721-242e89d3ec26/@@download/attachment/L-HNRNPA0-BGHLV22-19_17756.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0-BGHLV22-19_17756)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS121IFK at ENCODE; https://www.encodeproject.org/ENCBS121IFK/

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 (ENCLB757XBN)

description:
https://www.encodeproject.org/experiments/ENCSR732ICL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPU. (K-HNRNPU)
experiment encode accession: ENCSR732ICL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB757XBN
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/9da3e07a-c46a-4ad6-a678-3733b94009c1/@@download/attachment/L-K-HNRNPU-1.pdf

value: HNRNPU

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

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS771NTZ at ENCODE; https://www.encodeproject.org/ENCBS771NTZ/

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 (ENCLB829PAU)

description:
https://www.encodeproject.org/experiments/ENCSR720BPO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0-BGHLV22)
experiment encode accession: ENCSR720BPO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB829PAU
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/f83e58d7-0b04-4bbd-8287-2ff86c2c83d7/@@download/attachment/L-HNRNPA0-BGHLV22-20_17757.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0-BGHLV22-20_17757)

value: male

value: ENCBS868JIC at ENCODE; https://www.encodeproject.org/ENCBS868JIC/


title: shRNA RNA-seq from K562 (ENCLB029RCY)

description:
https://www.encodeproject.org/experiments/ENCSR732ICL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPU. (K-HNRNPU)
experiment encode accession: ENCSR732ICL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB029RCY
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/402b7e37-9104-46f6-9c52-b1add23dd3ed/@@download/attachment/L-K-HNRNPU-2.pdf

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

value: Brenton Graveley, UConn

value: ENCBS936VOR at ENCODE; https://www.encodeproject.org/ENCBS936VOR/


title: total RNA-seq from smooth muscle cell (ENCLB894YYX)

description:
https://www.encodeproject.org/experiments/ENCSR236URT/
***************
biological replicate number: 2
technical replicate number: 1
description: smooth muscle cell
experiment encode accession: ENCSR236URT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB894YYX
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.350
nucleic acid starting quantity units: ng

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

value: smooth muscle cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS899TTJ at ENCODE; https://www.encodeproject.org/ENCBS899TTJ/

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


title: shRNA RNA-seq from K562 (ENCLB117TBD)

description:
https://www.encodeproject.org/experiments/ENCSR717SJA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against XRN2 in K562 cells followed by RNA-seq. (XRN2_BGKLV19)
experiment encode accession: ENCSR717SJA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB117TBD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting XRN2

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

value: RNA-seq on K562 cells treated with an shRNA knockdown against XRN2. (XRN2_BGKLV19_63B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS394LTC at ENCODE; https://www.encodeproject.org/ENCBS394LTC/

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 spleen (ENCLB195QJB)

description:
https://www.encodeproject.org/experiments/ENCSR236PTD/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human spleen tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR236PTD
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR900SGE
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB195QJB
size range: >200

source_name: Homo sapiens spleen 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/e102c3df-831b-4b42-806a-e73d7228860a/@@download/attachment/296812.pdf

value: spleen

value: tissue

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

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from K562 (ENCLB805XLG)

description:
https://www.encodeproject.org/experiments/ENCSR717SJA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against XRN2 in K562 cells followed by RNA-seq. (XRN2_BGKLV19)
experiment encode accession: ENCSR717SJA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB805XLG
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/ccfe4786-ae1b-4b4f-9bf7-35ef1dab0702/@@download/attachment/L-XRN2_BGKLV19_64B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against XRN2. (XRN2_BGKLV19_64B)

value: Brenton Graveley, UConn

value: ENCBS729IGE at ENCODE; https://www.encodeproject.org/ENCBS729IGE/


title: shRNA RNA-seq from HepG2 (ENCLB811CHG)

description:
https://www.encodeproject.org/experiments/ENCSR243IGA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HSPD1. (HSPD1_BGHLV27)
experiment encode accession: ENCSR243IGA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB811CHG
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/d7af79c5-6575-4e18-b3b6-b6b5ac5a67ec/@@download/attachment/L-HSPD1_BGHLV27-25.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against HSPD1 (HSPD1_BGHLV27-25)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS440GZN at ENCODE; https://www.encodeproject.org/ENCBS440GZN/

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

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


title: total RNA-seq from right lobe of liver (ENCLB139JXN)

description:
https://www.encodeproject.org/experiments/ENCSR226KML/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's liver tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR226KML
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB139JXN
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f9078786-5d2b-4cec-ab1a-bc82768aacf5/@@download/attachment/296324.pdf

value: right lobe of liver

value: tissue

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

value: 53 year

value: adult

value: female

value: ENCBS773RMK at ENCODE; https://www.encodeproject.org/ENCBS773RMK/


title: total RNA-seq from smooth muscle cell (ENCLB889PET)

description:
https://www.encodeproject.org/experiments/ENCSR236URT/
***************
biological replicate number: 1
technical replicate number: 1
description: smooth muscle cell
experiment encode accession: ENCSR236URT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB889PET
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 0.350
nucleic acid starting quantity units: ng

value: smooth muscle cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS780PCJ at ENCODE; https://www.encodeproject.org/ENCBS780PCJ/

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


title: shRNA RNA-seq from K562 (ENCLB777BDA)

description:
https://www.encodeproject.org/experiments/ENCSR231DXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGKLV32)
experiment encode accession: ENCSR231DXJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB777BDA
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 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/acdccb5f-3276-494d-b912-67b084358b77/@@download/attachment/L-ATP5C1_BGKLV32-11.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGKLV32-11)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS560YCY at ENCODE; https://www.encodeproject.org/ENCBS560YCY/

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 (ENCLB197DFT)

description:
https://www.encodeproject.org/experiments/ENCSR231DXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGKLV32)
experiment encode accession: ENCSR231DXJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB197DFT
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/60e55ce6-9924-4a89-bb5a-9d99f502506a/@@download/attachment/L-ATP5C1_BGKLV32-12.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ATP5C1. (ATP5C1_BGKLV32-12)

value: 53 year

value: adult

value: female

value: ENCBS452HCE at ENCODE; https://www.encodeproject.org/ENCBS452HCE/


title: RAMPAGE from heart left ventricle (ENCLB813FAE)

description:
https://www.encodeproject.org/experiments/ENCSR226BLJ/
***************
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 heart left ventricle 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: ENCSR226BLJ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR436QDU
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB813FAE
size range: >200

source_name: Homo sapiens heart left ventricle 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/78371c69-365d-47ac-8d79-4bf82a94022c/@@download/attachment/296703.pdf

value: heart left ventricle

value: tissue

value: Heart (left ventricle) tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS038PFI at ENCODE; https://www.encodeproject.org/ENCBS038PFI/

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


title: shRNA RNA-seq from K562 (ENCLB377OOS)

description:
https://www.encodeproject.org/experiments/ENCSR715XZS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against XRCC5 in K562 cells followed by RNA-seq. (XRCC5 BGKLV13)
experiment encode accession: ENCSR715XZS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB377OOS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting XRCC5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8189bc80-601b-467d-9c88-34fbb3d8eff0/@@download/attachment/L-XRCC5_BGKLV13_36.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against XRCC5.(XRCC5_BGKLV13_36)

value: chronic myelogenous leukemia (CML)

value: ENCBS278ISQ at ENCODE; https://www.encodeproject.org/ENCBS278ISQ/


title: shRNA RNA-seq from K562 (ENCLB806GNS)

description:
https://www.encodeproject.org/experiments/ENCSR712CSN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1_BGKLV24)
experiment encode accession: ENCSR712CSN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB806GNS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF4G1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b33616d1-ea87-41b4-94ad-23c6cda2932a/@@download/attachment/L-EIF4G1_BGKLV24_25_17615.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1_BGKLV24_25_17615)

value: Brenton Graveley, UConn

value: ENCBS809UHL at ENCODE; https://www.encodeproject.org/ENCBS809UHL/

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 (ENCLB177DRL)

description:
https://www.encodeproject.org/experiments/ENCSR712CSN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1_BGKLV24)
experiment encode accession: ENCSR712CSN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB177DRL
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/3e1b6f58-39ce-424e-8491-48ea35763e63/@@download/attachment/L-EIF4G1_BGKLV24_26_17616.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1_BGKLV24_26_17616)

value: 53 year

value: adult

value: female

value: ENCBS433HMF at ENCODE; https://www.encodeproject.org/ENCBS433HMF/


title: RAMPAGE from esophagus squamous epithelium (ENCLB727FOS)

description:
https://www.encodeproject.org/experiments/ENCSR201ARN/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human esophagus mucosa tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR201ARN
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR510MIA
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB727FOS
size range: >200

source_name: Homo sapiens esophagus squamous epithelium 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/94f60a18-1ca6-43b1-8d97-6272dc52de2b/@@download/attachment/296750.pdf

value: esophagus squamous epithelium

value: tissue

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

value: 51 year

value: Thomas Gingeras, CSHL

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


title: shRNA RNA-seq from K562 (ENCLB023TDY)

description:
https://www.encodeproject.org/experiments/ENCSR222COT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MBNL1. (MBNL1_BGKLV32)
experiment encode accession: ENCSR222COT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB023TDY
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting MBNL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/274051e3-3e2c-4a38-a469-71e9f9e8cf59/@@download/attachment/L-MBNL1_BGKLV32-40.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against MBNL1. (MBNL1_BGKLV32-40)

value: chronic myelogenous leukemia (CML)

value: ENCBS803KFY at ENCODE; https://www.encodeproject.org/ENCBS803KFY/


title: shRNA RNA-seq from HepG2 (ENCLB207TKT)

description:
https://www.encodeproject.org/experiments/ENCSR711ZJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM47. (RBM47-BGHLV22)
experiment encode accession: ENCSR711ZJQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB207TKT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RBM47

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/152c3a80-1d5a-4bae-a1e5-4ad7efc438ed/@@download/attachment/L-RBM47-BGHLV22-40.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM47. (RBM47-BGHLV22-40)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS456NEZ at ENCODE; https://www.encodeproject.org/ENCBS456NEZ/

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 (ENCLB694RUR)

description:
https://www.encodeproject.org/experiments/ENCSR711ZJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM47. (RBM47-BGHLV22)
experiment encode accession: ENCSR711ZJQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB694RUR
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/add51ace-0cac-4c7f-a260-b86981909546/@@download/attachment/L-RBM47-BGHLV22-39.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM47. (RBM47-BGHLV22-39)

value: ENCBS011NDE at ENCODE; https://www.encodeproject.org/ENCBS011NDE/


title: RAMPAGE from vagina (ENCLB467LCJ)

description:
https://www.encodeproject.org/experiments/ENCSR219EAT/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human vagina tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR219EAT
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR146LBD
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB467LCJ
size range: >200

source_name: Homo sapiens vagina 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/eddfdfd1-60ca-4cf1-acd9-85b12cdffdda/@@download/attachment/296846.pdf

value: vagina

value: tissue

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

value: 53 year

value: adult

value: female

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from K562 (ENCLB712XUC)

description:
https://www.encodeproject.org/experiments/ENCSR222ABK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HSPD1. (HSPD1_BGKLV29)
experiment encode accession: ENCSR222ABK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB712XUC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting HSPD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c0b89e88-f006-4c75-8ee3-f0ab3743af4a/@@download/attachment/L-HSPD1_BGKLV29-42.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HSPD1. (HSPD1_BGKLV29-42)

value: chronic myelogenous leukemia (CML)

value: ENCBS254JMT at ENCODE; https://www.encodeproject.org/ENCBS254JMT/

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 (ENCLB517LZB)

description:
https://www.encodeproject.org/experiments/ENCSR222ABK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HSPD1. (HSPD1_BGKLV29)
experiment encode accession: ENCSR222ABK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR032YMP
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB517LZB
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/57740eaa-064d-44af-946e-e3b220e40150/@@download/attachment/L-HSPD1_BGKLV29-41.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against HSPD1. (HSPD1_BGKLV29-41)

value: Brenton Graveley, UConn

value: ENCBS850BRB at ENCODE; https://www.encodeproject.org/ENCBS850BRB/


title: shRNA RNA-seq from HepG2 (ENCLB069LNY)

description:
https://www.encodeproject.org/experiments/ENCSR710NWE/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against IGF2BP3 in HepG2 cells followed by RNA-seq. (IGF2BP3-BGHLV12)
experiment encode accession: ENCSR710NWE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB069LNY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting IGF2BP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/22e7a834-bfce-433e-bac8-557bd18f07f9/@@download/attachment/L-IGF2BP3-BGHLV12-44.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against IGF2BP3. (IGF2BP3-BGHLV12-44)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS040DES at ENCODE; https://www.encodeproject.org/ENCBS040DES/

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 (ENCLB364DPW)

description:
https://www.encodeproject.org/experiments/ENCSR710NWE/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against IGF2BP3 in HepG2 cells followed by RNA-seq. (IGF2BP3-BGHLV12)
experiment encode accession: ENCSR710NWE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB364DPW
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/469663c6-1ec8-44bc-87db-3f1e301c7696/@@download/attachment/L-IGF2BP3-BGHLV12-43.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against IGF2BP3. (IGF2BP3-BGHLV12-43)

value: ENCBS641AVI at ENCODE; https://www.encodeproject.org/ENCBS641AVI/


title: shRNA RNA-seq from K562 (ENCLB346IYZ)

description:
https://www.encodeproject.org/experiments/ENCSR715XZS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against XRCC5 in K562 cells followed by RNA-seq. (XRCC5 BGKLV13)
experiment encode accession: ENCSR715XZS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB346IYZ
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/6e9ade4f-8c0b-437a-8fcd-ae28e4c8f273/@@download/attachment/L-XRCC5_BGKLV13_35.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against XRCC5.(XRCC5_BGKLV13_35)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS664AUV at ENCODE; https://www.encodeproject.org/ENCBS664AUV/


title: shRNA RNA-seq from K562 (ENCLB547AMZ)

description:
https://www.encodeproject.org/experiments/ENCSR222COT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MBNL1. (MBNL1_BGKLV32)
experiment encode accession: ENCSR222COT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB547AMZ
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/cf7703d3-dd6d-441f-9836-c65a84685c65/@@download/attachment/L-MBNL1_BGKLV32-39.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against MBNL1. (MBNL1_BGKLV32-39)

value: Brenton Graveley, UConn

value: ENCBS209TDT at ENCODE; https://www.encodeproject.org/ENCBS209TDT/

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

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


title: total RNA-seq from spleen (ENCLB990KQA)

description:
https://www.encodeproject.org/experiments/ENCSR194HVU/
***************
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 spleen tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR194HVU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB990KQA
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/17461be7-f98e-4956-afd8-3cc906d4ab69/@@download/attachment/296576.pdf

value: spleen

value: tissue

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

value: 51 year

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from HepG2 (ENCLB847UFY)

description:
https://www.encodeproject.org/experiments/ENCSR706SXN/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPL23A in HepG2 cells followed by RNA-seq. (RPL23A_BGHLV18)
experiment encode accession: ENCSR706SXN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB847UFY
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5f6b7314-ab5f-4e98-80fa-297e3e98bc52/@@download/attachment/L-RPL23A_BGHLV18_51.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPL23A. (RPL23A_BGHLV18_51)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS218PEV at ENCODE; https://www.encodeproject.org/ENCBS218PEV/

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

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


title: RAMPAGE from Daoy (ENCLB675KUG)

description:
https://www.encodeproject.org/experiments/ENCSR700NMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line Daoy isolated from the cerebellar region of a 4 year old caucasian male with desmoplastic cerebellar medulloblastoma. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR700NMZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR254JJM
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB675KUG
size range: >200

source_name: Homo sapiens Daoy immortalized cell line

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/18ddb82d-bc3d-41f7-95c7-4cf6f0f1b3c1/@@download/attachment/292966.pdf

value: Daoy

value: 4 year

value: John Stamatoyannopoulos, UW

value: ENCBS055ILX at ENCODE; https://www.encodeproject.org/ENCBS055ILX/

value: Derived from ENCODE donor ENCDO735HIP; https://www.encodeproject.org/ENCDO735HIP/

value: ENCODE dbxrefs Cellosaurus CVCL_1167; http://web.expasy.org/cellosaurus/CVCL_1167


title: RAMPAGE from Daoy (ENCLB878RPT)

description:
https://www.encodeproject.org/experiments/ENCSR700NMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line Daoy isolated from the cerebellar region of a 4 year old caucasian male with desmoplastic cerebellar medulloblastoma. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR700NMZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR254JJM
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB878RPT
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/76e82b14-46fb-48f8-9afa-93cb09b19441/@@download/attachment/292967.pdf

value: ENCBS812KQP at ENCODE; https://www.encodeproject.org/ENCBS812KQP/


title: shRNA RNA-seq from K562 (ENCLB456SMQ)

description:
https://www.encodeproject.org/experiments/ENCSR192BPV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGKLV28)
experiment encode accession: ENCSR192BPV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB456SMQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SUGP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3b0db4ec-58ec-40f6-8391-70e3234a18bf/@@download/attachment/L-SUGP2_BGKLV28-55.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGKLV28-55)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS243YPN at ENCODE; https://www.encodeproject.org/ENCBS243YPN/

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 Peyer's patch (ENCLB424NXB)

description:
https://www.encodeproject.org/experiments/ENCSR199XGY/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human ileum tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR199XGY
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR544SAU
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB424NXB
size range: >200

source_name: Homo sapiens Peyer's patch 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/5711713b-1fae-4fb8-ab53-24e567e51c0a/@@download/attachment/296785.pdf

value: Peyer's patch

value: tissue

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

value: Thomas Gingeras, CSHL

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

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