title: shRNA RNA-seq from HepG2 (ENCLB839RWB)

description:
https://www.encodeproject.org/experiments/ENCSR389HFU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against FTO. (FTO_BGHLV35)
experiment encode accession: ENCSR389HFU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB839RWB
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/2acc72ad-b164-4c8e-a371-d6ebcd20c926/@@download/attachment/L-FTO_BGHLV35-17.pdf

value: FTO

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FTO. (FTO_BGHLV35-17)

value: child

value: male

value: 15 year

value: ENCBS975IHF at ENCODE; https://www.encodeproject.org/ENCBS975IHF/


title: RAMPAGE from NCI-H460 (ENCLB850LWC)

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/ENCSR824YLV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR824YLV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR586SEE
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB850LWC
size range: >200

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens NCI-H460 immortalized cell line cytosolic fraction

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/9940324a-3493-44b6-be8a-38726fcbc064/@@download/attachment/LID294671.pdf

tag: line

tag: description

value: Epithelial-like large cell lung carcinoma immortalized cells from a 37 year old male.

tag: biosample encode accession

tag: age

value: 37 year

tag: dev stage

value: adult

tag: Sex

tag: lab

value: Thomas Gingeras, CSHL

tag: subcellular fraction term name

value: cytosol

tag: link

value: ENCBS398KLJ at ENCODE; https://www.encodeproject.org/ENCBS398KLJ/

value: Derived from ENCODE donor ENCDO337AAA; https://www.encodeproject.org/ENCDO337AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0459; http://web.expasy.org/cellosaurus/CVCL_0459

value: ATCC sample source; http://www.atcc.org/products/all/HTB-177.aspx


title: RAMPAGE from NCI-H460 (ENCLB278ZKY)

description:
https://www.encodeproject.org/experiments/ENCSR824YLV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR824YLV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR586SEE
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB278ZKY
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/586fbe21-4b5b-45e7-bd5f-2986f8a42b34/@@download/attachment/LID294672.pdf

value: ENCBS814QPR at ENCODE; https://www.encodeproject.org/ENCBS814QPR/


title: shRNA RNA-seq from HepG2 (ENCLB189JVF)

description:
https://www.encodeproject.org/experiments/ENCSR825QXH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PARN in HepG2 cells followed by RNA-seq. (PARN-BGHLV20)
experiment encode accession: ENCSR825QXH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB189JVF
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6eea9f5a-a7d5-45bb-a1f4-84f19c59a860/@@download/attachment/L-PARN-BGHLV20-48_17731.pdf

tag: antibody

value: PARN

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PARN. (PARN-BGHLV20-48_17731)

tag: health state

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS194AMD at ENCODE; https://www.encodeproject.org/ENCBS194AMD/

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 (ENCLB672WPU)

description:
https://www.encodeproject.org/experiments/ENCSR825QXH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PARN in HepG2 cells followed by RNA-seq. (PARN-BGHLV20)
experiment encode accession: ENCSR825QXH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB672WPU
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/8491abd4-4e22-412d-8311-7714d6a9ff94/@@download/attachment/L-PARN-BGHLV20-47_17730.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PARN. (PARN-BGHLV20-47_17730)

value: 15 year

value: child

value: male

value: ENCBS005NKZ at ENCODE; https://www.encodeproject.org/ENCBS005NKZ/


title: shRNA RNA-seq from HepG2 (ENCLB825DOH)

description:
https://www.encodeproject.org/experiments/ENCSR388CNS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX47. (DDX47_BGHLV22)
experiment encode accession: ENCSR388CNS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR968BBQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB825DOH
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX47

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3a0dc89a-d62a-48de-8f71-9e6b8125df74/@@download/attachment/L-DDX47_BGHLV22-10B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX47. (DDX47_BGHLV22-10B)

value: ENCBS300YFU at ENCODE; https://www.encodeproject.org/ENCBS300YFU/


title: shRNA RNA-seq from K562 (ENCLB936SHB)

description:
https://www.encodeproject.org/experiments/ENCSR385UPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBM15. (RBM15_BGKLV32)
experiment encode accession: ENCSR385UPQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB936SHB
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RBM15

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/343e550b-2f87-42b2-8fba-bfabaac06d18/@@download/attachment/L-RBM15_BGKLV32-54.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM15. (RBM15_BGKLV32-54)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS271BPH at ENCODE; https://www.encodeproject.org/ENCBS271BPH/

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 (ENCLB719FFS)

description:
https://www.encodeproject.org/experiments/ENCSR385TMY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM17. (RBM17_BGHLV26)
experiment encode accession: ENCSR385TMY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB719FFS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RBM17

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/31d1badb-50e4-4574-aab8-8350128811f6/@@download/attachment/L-RBM17_BGHLV26_38.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against RBM17 (RBM17_BGHLV26_38)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS775MDU at ENCODE; https://www.encodeproject.org/ENCBS775MDU/

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: microRNA-seq from lower leg skin (ENCLB948WBJ)

description:
https://www.encodeproject.org/experiments/ENCSR819AXA/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human lower leg skin
experiment encode accession: ENCSR819AXA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB948WBJ
size range: <30

source_name: Homo sapiens lower leg skin tissue male adult (37 years)

value: lower leg skin

value: tissue

value: Skin - Sun Exposed (Lower leg)

value: 37 year

value: male

value: Barbara Wold, Caltech

value: ENCBS617UGR at ENCODE; https://www.encodeproject.org/ENCBS617UGR/

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


title: shRNA RNA-seq from HepG2 (ENCLB545YTK)

description:
https://www.encodeproject.org/experiments/ENCSR820ROH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SERBP1 in HepG2 cells followed by RNA-seq. (SERBP1_BGHLV16)
experiment encode accession: ENCSR820ROH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB545YTK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SERBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/636d0344-f2a7-47b0-91a4-2dfa2eb85b5d/@@download/attachment/L-SERBP1_BGHLV16_52.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SERBP1. (SERBP1_BGHLV16_52)

value: 15 year

value: child

value: ENCBS798MOH at ENCODE; https://www.encodeproject.org/ENCBS798MOH/


title: shRNA RNA-seq from HepG2 (ENCLB012PNW)

description:
https://www.encodeproject.org/experiments/ENCSR385TMY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM17. (RBM17_BGHLV26)
experiment encode accession: ENCSR385TMY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB012PNW
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/6df40cff-c864-48b4-b900-25d2a2bdf1a7/@@download/attachment/L-RBM17_BGHLV26_37.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against RBM17 (RBM17_BGHLV26_37)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS226JWQ at ENCODE; https://www.encodeproject.org/ENCBS226JWQ/


title: microRNA-seq from lower leg skin (ENCLB818FSC)

description:
https://www.encodeproject.org/experiments/ENCSR819AXA/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human lower leg skin
experiment encode accession: ENCSR819AXA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB818FSC
size range: <30

value: lower leg skin

value: adult

value: ENCBS926XRV at ENCODE; https://www.encodeproject.org/ENCBS926XRV/


title: shRNA RNA-seq from HepG2 (ENCLB120HPU)

description:
https://www.encodeproject.org/experiments/ENCSR820ROH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SERBP1 in HepG2 cells followed by RNA-seq. (SERBP1_BGHLV16)
experiment encode accession: ENCSR820ROH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB120HPU
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/d6cf4b96-b313-496e-8a5f-924adf104209/@@download/attachment/L-SERBP1_BGHLV16_51.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SERBP1. (SERBP1_BGHLV16_51)

value: ENCBS487KTY at ENCODE; https://www.encodeproject.org/ENCBS487KTY/

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 (ENCLB538HBA)

description:
https://www.encodeproject.org/experiments/ENCSR388CNS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX47. (DDX47_BGHLV22)
experiment encode accession: ENCSR388CNS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR968BBQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB538HBA
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/74998a63-315b-46b8-a21d-6afd77090676/@@download/attachment/L-DDX47_BGHLV22-9B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX47. (DDX47_BGHLV22-9B)

value: male

value: ENCBS740FAU at ENCODE; https://www.encodeproject.org/ENCBS740FAU/


title: shRNA RNA-seq from HepG2 (ENCLB249JKL)

description:
https://www.encodeproject.org/experiments/ENCSR815JDY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against CSTF2 in HepG2 cells followed by RNA-seq. (CSTF2_BGHLV17)
experiment encode accession: ENCSR815JDY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB249JKL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CSTF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b7ff36cc-f971-4611-bb3b-df47d38c17f7/@@download/attachment/L-CSTF2_BGHLV17_9.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CSTF2. (CSTF2_BGHLV17_9)

value: 15 year

value: ENCBS778LCM at ENCODE; https://www.encodeproject.org/ENCBS778LCM/


title: shRNA RNA-seq from K562 (ENCLB486NVV)

description:
https://www.encodeproject.org/experiments/ENCSR384BDV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGKLV36)
experiment encode accession: ENCSR384BDV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB486NVV
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CPSF6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1f891242-4a5a-4579-a448-44d7976f3bcb/@@download/attachment/L-CPSF6_BGKLV36-12.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGKLV36-12)

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS967ZCF at ENCODE; https://www.encodeproject.org/ENCBS967ZCF/

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


title: shRNA RNA-seq from K562 (ENCLB532JLB)

description:
https://www.encodeproject.org/experiments/ENCSR815CVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT BGKLV13)
experiment encode accession: ENCSR815CVQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB532JLB
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/61af5690-bb2c-4a9f-bfcf-463d857f87b8/@@download/attachment/L-NT_BGKLV13_1.pdf

value: Control

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (NT_BGKLV13_1)

value: adult

value: Brenton Graveley, UConn

value: ENCBS393YUA at ENCODE; https://www.encodeproject.org/ENCBS393YUA/

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


title: shRNA RNA-seq from K562 (ENCLB864IZU)

description:
https://www.encodeproject.org/experiments/ENCSR815CVQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT BGKLV13)
experiment encode accession: ENCSR815CVQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB864IZU
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/a401bf12-5729-40d1-bf31-086b1cfbcbcb/@@download/attachment/L-NT_BGKLV13_2.pdf

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (NT_BGKLV13_2)

value: ENCBS170ZQG at ENCODE; https://www.encodeproject.org/ENCBS170ZQG/


title: shRNA RNA-seq from HepG2 (ENCLB209RYC)

description:
https://www.encodeproject.org/experiments/ENCSR815JDY/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against CSTF2 in HepG2 cells followed by RNA-seq. (CSTF2_BGHLV17)
experiment encode accession: ENCSR815JDY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB209RYC
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/d61de5ad-ac76-4bc9-ac9a-dacd738e5da3/@@download/attachment/L-CSTF2_BGHLV17_10.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CSTF2. (CSTF2_BGHLV17_10)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS197XGU at ENCODE; https://www.encodeproject.org/ENCBS197XGU/

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 (ENCLB982ULD)

description:
https://www.encodeproject.org/experiments/ENCSR382QKD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against BUD13. (BUD13_BGHLV30)
experiment encode accession: ENCSR382QKD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB982ULD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/61510654-c065-4f04-9963-1960e1a5b819/@@download/attachment/L-BUD13_BGHLV30-17.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against BUD13. (BUD13_BGHLV30-17)

value: 15 year

value: ENCBS337HXQ at ENCODE; https://www.encodeproject.org/ENCBS337HXQ/


title: shRNA RNA-seq from HepG2 (ENCLB120PRS)

description:
https://www.encodeproject.org/experiments/ENCSR382QKD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against BUD13. (BUD13_BGHLV30)
experiment encode accession: ENCSR382QKD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB120PRS
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/ac457a80-c34e-4072-901c-056aadb1d46c/@@download/attachment/L-BUD13_BGHLV30-18.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against BUD13. (BUD13_BGHLV30-18)

value: ENCBS180QVY at ENCODE; https://www.encodeproject.org/ENCBS180QVY/


title: shRNA RNA-seq from K562 (ENCLB813JOE)

description:
https://www.encodeproject.org/experiments/ENCSR385UPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBM15. (RBM15_BGKLV32)
experiment encode accession: ENCSR385UPQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB813JOE
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/374a0ccf-0af9-4693-89a4-b91a9865aec6/@@download/attachment/L-RBM15_BGKLV32-53.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM15. (RBM15_BGKLV32-53)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS808FZK at ENCODE; https://www.encodeproject.org/ENCBS808FZK/

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


title: shRNA RNA-seq from HepG2 (ENCLB696VIF)

description:
https://www.encodeproject.org/experiments/ENCSR376FGR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF3. (SRSF3_BGHLV35)
experiment encode accession: ENCSR376FGR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB696VIF
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SRSF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/806be62f-506e-4795-86f4-9fada4fe345d/@@download/attachment/L-SRSF3_BGHLV35-50.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF3. (SRSF3_BGHLV35-50)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS943TZA at ENCODE; https://www.encodeproject.org/ENCBS943TZA/


title: shRNA RNA-seq from HepG2 (ENCLB015EAQ)

description:
https://www.encodeproject.org/experiments/ENCSR374NMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGHLV33)
experiment encode accession: ENCSR374NMJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB015EAQ
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SF3A3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3ebf58c9-72e9-4d25-8823-2ac5607e6212/@@download/attachment/L-SF3A3_BGHLV33-29.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGHLV33-29)

value: 15 year

value: ENCBS958SZY at ENCODE; https://www.encodeproject.org/ENCBS958SZY/

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


title: total RNA-seq from HepG2 (ENCLB414HBO)

description:
https://www.encodeproject.org/experiments/ENCSR813BDU/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial insoluble cytoplasmic fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR813BDU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB414HBO
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line insoluble cytoplasmic fraction

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

value: Initial insoluble fractions on HepG2 Long Total from Lecuyer

value: insoluble cytoplasmic fraction

value: Eric Lécuyer, IRCM

value: ENCBS470XDJ at ENCODE; https://www.encodeproject.org/ENCBS470XDJ/

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


title: shRNA RNA-seq from K562 (ENCLB358WZH)

description:
https://www.encodeproject.org/experiments/ENCSR813NZP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGKLV21)
experiment encode accession: ENCSR813NZP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB358WZH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SRFBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c7e4b2b7-aaf9-4335-bd13-177c0e36f01d/@@download/attachment/L-SRFBP1_BGKLV21_59_17586.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGKLV21_59_17586)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS664VDB at ENCODE; https://www.encodeproject.org/ENCBS664VDB/

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


title: shRNA RNA-seq from HepG2 (ENCLB563NSF)

description:
https://www.encodeproject.org/experiments/ENCSR374NMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGHLV33)
experiment encode accession: ENCSR374NMJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR691IVR
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB563NSF
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/8f1d8601-0d41-4680-aafb-de4e490795c0/@@download/attachment/L-SF3A3_BGHLV33-30.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3A3. (SF3A3_BGHLV33-30)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS713WYW at ENCODE; https://www.encodeproject.org/ENCBS713WYW/


title: shRNA RNA-seq from HepG2 (ENCLB826DTD)

description:
https://www.encodeproject.org/experiments/ENCSR376FGR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF3. (SRSF3_BGHLV35)
experiment encode accession: ENCSR376FGR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB826DTD
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/f7571af3-b4cf-4ee4-83e6-199efdbc4f3d/@@download/attachment/L-SRSF3_BGHLV35-49.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF3. (SRSF3_BGHLV35-49)

value: 15 year

value: ENCBS023QER at ENCODE; https://www.encodeproject.org/ENCBS023QER/

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


title: total RNA-seq from HepG2 (ENCLB555LNW)

description:
https://www.encodeproject.org/experiments/ENCSR813BDU/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial insoluble cytoplasmic fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR813BDU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB555LNW
size range: >200
spikeins used: /references/ENCSR422PLF/

value: Initial insoluble fractions on HepG2 Long Total from Lecuyer

value: insoluble cytoplasmic fraction

value: Eric Lécuyer, IRCM

value: ENCBS281JZX at ENCODE; https://www.encodeproject.org/ENCBS281JZX/

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


title: shRNA RNA-seq from HepG2 (ENCLB416FHC)

description:
https://www.encodeproject.org/experiments/ENCSR372UWV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF1. (U2AF1_BGHLV30)
experiment encode accession: ENCSR372UWV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB416FHC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting U2AF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/071b0dbc-ee2d-480e-8c22-0f32ef2f8bf9/@@download/attachment/L-U2AF1_BGHLV30-56.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF1. (U2AF1_BGHLV30-56)

value: Brenton Graveley, UConn

value: ENCBS914FGT at ENCODE; https://www.encodeproject.org/ENCBS914FGT/


title: shRNA RNA-seq from K562 (ENCLB635WXU)

description:
https://www.encodeproject.org/experiments/ENCSR384BDV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGKLV36)
experiment encode accession: ENCSR384BDV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR424QCW
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB635WXU
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/7bc12b95-eb3b-4ba9-8855-9733eaa5499f/@@download/attachment/L-CPSF6_BGKLV36-11.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF6. (CPSF6_BGKLV36-11)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS936QKM at ENCODE; https://www.encodeproject.org/ENCBS936QKM/

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


title: shRNA RNA-seq from HepG2 (ENCLB259TZZ)

description:
https://www.encodeproject.org/experiments/ENCSR372UWV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF1. (U2AF1_BGHLV30)
experiment encode accession: ENCSR372UWV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB259TZZ
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/72ecb78c-d3a7-410d-8a91-f9df0e6cdd95/@@download/attachment/L-U2AF1_BGHLV30-55.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against U2AF1. (U2AF1_BGHLV30-55)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS488UTE at ENCODE; https://www.encodeproject.org/ENCBS488UTE/

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


title: shRNA RNA-seq from K562 (ENCLB185VEX)

description:
https://www.encodeproject.org/experiments/ENCSR812EIA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EXOSC9 in K562 cells followed by RNA-seq. (EXOSC9 BGKLV13)
experiment encode accession: ENCSR812EIA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB185VEX
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EXOSC9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b7b5898e-9ba5-44b0-a045-eeb784ddad9b/@@download/attachment/L-EXOSC9_BGKLV13_7.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EXOSC9.(EXOSC9_BGKLV13_7)

value: Brenton Graveley, UConn

value: ENCBS245AME at ENCODE; https://www.encodeproject.org/ENCBS245AME/

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


title: shRNA RNA-seq from HepG2 (ENCLB954WOR)

description:
https://www.encodeproject.org/experiments/ENCSR364GRM/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV23-B)
experiment encode accession: ENCSR364GRM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB954WOR
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/47257872-3172-4743-8e9f-2514addb0a05/@@download/attachment/L-NT_BGHLV23-2B.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (NT_BGHLV23-2B)

value: ENCBS789ZNN at ENCODE; https://www.encodeproject.org/ENCBS789ZNN/

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


title: shRNA RNA-seq from HepG2 (ENCLB447VDG)

description:
https://www.encodeproject.org/experiments/ENCSR364GRM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV23-B)
experiment encode accession: ENCSR364GRM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB447VDG
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/f63e13d1-00b7-4234-9514-250d833f9ddb/@@download/attachment/L-NT_BGHLV23-1B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (NT_BGHLV23-1B)

value: ENCBS143CPJ at ENCODE; https://www.encodeproject.org/ENCBS143CPJ/


title: shRNA RNA-seq from HepG2 (ENCLB805CJB)

description:
https://www.encodeproject.org/experiments/ENCSR810JYX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGHLV23)
experiment encode accession: ENCSR810JYX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB805CJB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SUCLG1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3abd5f00-b342-4f16-a032-f04edb15fa30/@@download/attachment/L-SUCLG1-BGHLV23-47.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGHLV23-47)

value: 15 year

value: ENCBS905ULQ at ENCODE; https://www.encodeproject.org/ENCBS905ULQ/


title: siRNA RNA-seq from K562 (ENCLB288SXH)

description:
https://www.encodeproject.org/experiments/ENCSR793ISR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting BACH1.
experiment encode accession: ENCSR793ISR
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB288SXH
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting BACH1

value: K562 cells treated with a siRNA knockdown against BACH1, used in RNA-seq experiments.

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS661MDA at ENCODE; https://www.encodeproject.org/ENCBS661MDA/

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


title: RAMPAGE from body of pancreas (ENCLB714OVL)

description:
https://www.encodeproject.org/experiments/ENCSR366BLN/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human female pancreas tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR366BLN
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR586SYA
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB714OVL
size range: >200

source_name: Homo sapiens body of pancreas 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/0c6814a2-488f-4dea-8648-17f04d2d94b0/@@download/attachment/296819.pdf

value: body of pancreas

value: tissue

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

value: Thomas Gingeras, CSHL

value: ENCBS273XDV at ENCODE; https://www.encodeproject.org/ENCBS273XDV/

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


title: shRNA RNA-seq from K562 (ENCLB985HAO)

description:
https://www.encodeproject.org/experiments/ENCSR813NZP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGKLV21)
experiment encode accession: ENCSR813NZP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB985HAO
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/dea37362-2646-4327-89ed-a0f278daf2f0/@@download/attachment/L-SRFBP1_BGKLV21_60_17587.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRFBP1. (SRFBP1_BGKLV21_60_17587)

value: Brenton Graveley, UConn

value: ENCBS274WIM at ENCODE; https://www.encodeproject.org/ENCBS274WIM/

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


title: shRNA RNA-seq from HepG2 (ENCLB981AHJ)

description:
https://www.encodeproject.org/experiments/ENCSR810JYX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGHLV23)
experiment encode accession: ENCSR810JYX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB981AHJ
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/6acaf752-6cc3-4e0b-8553-428657bc6cc0/@@download/attachment/L-SUCLG1-BGHLV23-48.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGHLV23-48)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS402VZL at ENCODE; https://www.encodeproject.org/ENCBS402VZL/

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 (ENCLB640CHN)

description:
https://www.encodeproject.org/experiments/ENCSR362XMY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGKLV25)
experiment encode accession: ENCSR362XMY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB640CHN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting UBE2L3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5a7e25b8-fb4a-4e22-8213-3312dee92b74/@@download/attachment/L-UBE2L3-BGKLV25-62.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGKLV25-62)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS721OCY at ENCODE; https://www.encodeproject.org/ENCBS721OCY/

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


title: shRNA RNA-seq from K562 (ENCLB308MFG)

description:
https://www.encodeproject.org/experiments/ENCSR362XMY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGKLV25)
experiment encode accession: ENCSR362XMY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB308MFG
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/e3b7d0bd-6ac9-43ae-b7df-17d0ad8f6b3a/@@download/attachment/L-UBE2L3-BGKLV25-61.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGKLV25-61)

value: Brenton Graveley, UConn

value: ENCBS548BNW at ENCODE; https://www.encodeproject.org/ENCBS548BNW/


title: total RNA-seq from esophagus squamous epithelium (ENCLB726HDC)

description:
https://www.encodeproject.org/experiments/ENCSR354QPN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the mucosa of the esophagus obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR354QPN
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB726HDC
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a20b21b6-3655-436f-8171-659bc20bd74d/@@download/attachment/296185.pdf

value: esophagus squamous epithelium

value: tissue

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

value: 37 year

value: Thomas Gingeras, CSHL

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

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


title: total RNA-seq from esophagus squamous epithelium (ENCLB275LRT)

description:
https://www.encodeproject.org/experiments/ENCSR351OTL/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the mucosa of the esophagus obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR351OTL
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB275LRT
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens esophagus squamous epithelium tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/da197771-3c06-40d1-b439-84f958615f6b/@@download/attachment/296190.pdf

value: 53 year

value: ENCBS504VDB at ENCODE; https://www.encodeproject.org/ENCBS504VDB/

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


title: shRNA RNA-seq from K562 (ENCLB248POP)

description:
https://www.encodeproject.org/experiments/ENCSR788YGG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RPS3A. (RPS3A_BGKLV24_B)
experiment encode accession: ENCSR788YGG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB248POP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RPS3A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4aee1ad5-a49a-4d38-a8c5-4cb610aa3ae0/@@download/attachment/L-RPS3A_BGKLV24_49B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS3A. (RPS3A_BGKLV24_49B)

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS392QEL at ENCODE; https://www.encodeproject.org/ENCBS392QEL/

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


title: shRNA RNA-seq from HepG2 (ENCLB058TGD)

description:
https://www.encodeproject.org/experiments/ENCSR355OQC/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NAA15. (NAA15_BGHLV30)
experiment encode accession: ENCSR355OQC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB058TGD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NAA15

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/11bdf96b-fb85-4a57-a368-0ab9faab6285/@@download/attachment/L-NAA15_BGHLV30-46.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NAA15. (NAA15_BGHLV30-46)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS702PRB at ENCODE; https://www.encodeproject.org/ENCBS702PRB/

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 (ENCLB615FGN)

description:
https://www.encodeproject.org/experiments/ENCSR355OQC/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NAA15. (NAA15_BGHLV30)
experiment encode accession: ENCSR355OQC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB615FGN
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/0600f36f-78e4-4e27-b50f-82c8c4917106/@@download/attachment/L-NAA15_BGHLV30-45.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NAA15. (NAA15_BGHLV30-45)

value: ENCBS339SIT at ENCODE; https://www.encodeproject.org/ENCBS339SIT/


title: shRNA RNA-seq from K562 (ENCLB723XKF)

description:
https://www.encodeproject.org/experiments/ENCSR788YGG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RPS3A. (RPS3A_BGKLV24_B)
experiment encode accession: ENCSR788YGG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB723XKF
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/947bac9a-323e-4dbf-8778-a42f673cdbaf/@@download/attachment/L-RPS3A_BGKLV24_50B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS3A. (RPS3A_BGKLV24_50B)

value: 53 year

value: adult

value: ENCBS748FCA at ENCODE; https://www.encodeproject.org/ENCBS748FCA/

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


title: total RNA-seq from testis (ENCLB270TKT)

description:
https://www.encodeproject.org/experiments/ENCSR344MQK/
***************
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 testis tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR344MQK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB270TKT
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0dd40e30-4b71-4ef4-9678-4c41c0716813/@@download/attachment/296607.pdf

value: testis

value: tissue

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

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS255MJZ at ENCODE; https://www.encodeproject.org/ENCBS255MJZ/

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


title: RAMPAGE from SK-N-DZ (ENCLB046VFF)

description:
https://www.encodeproject.org/experiments/ENCSR786DTS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SK-N-DZ, a metastatic neuroblastoma from a 2 year old female. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR786DTS
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR136WGP
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB046VFF
size range: >200

source_name: Homo sapiens SK-N-DZ immortalized cell line treated with dimethyl sulfoxide for 72 hours

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/06b94773-f97e-4ebb-a4e3-b54e0782d0a2/@@download/attachment/289912.pdf

value: SK-N-DZ

value: immortalized cell line

value: 2 year

value: child

value: female

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:72; duration_units:hour;

value: John Stamatoyannopoulos, UW

value: ENCBS521AAA at ENCODE; https://www.encodeproject.org/ENCBS521AAA/

value: Derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701


title: siRNA RNA-seq from K562 (ENCLB451ZCI)

description:
https://www.encodeproject.org/experiments/ENCSR793ISR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting BACH1.
experiment encode accession: ENCSR793ISR
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB451ZCI
size range: >200
spikeins used: /references/ENCSR866KGS/

value: K562 cells treated with a siRNA knockdown against BACH1, used in RNA-seq experiments.

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS896UGP at ENCODE; https://www.encodeproject.org/ENCBS896UGP/

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


title: shRNA RNA-seq from HepG2 (ENCLB729EVF)

description:
https://www.encodeproject.org/experiments/ENCSR788HVK/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF3D in HepG2 cells followed by RNA-seq. (EIF3D_BGHLV16)
experiment encode accession: ENCSR788HVK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB729EVF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EIF3D

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a1d06ebb-6001-489e-93a9-fdd845169be6/@@download/attachment/L-EIF3D_BGHLV16_24.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF3D. (EIF3D_BGHLV16_24)

value: 15 year

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS295BTT at ENCODE; https://www.encodeproject.org/ENCBS295BTT/

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 (ENCLB863ZLS)

description:
https://www.encodeproject.org/experiments/ENCSR788HVK/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF3D in HepG2 cells followed by RNA-seq. (EIF3D_BGHLV16)
experiment encode accession: ENCSR788HVK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB863ZLS
size range: >200
spikeins used: /references/ENCSR449DXG/
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9a527ac3-36a0-4eef-ba6a-1b609faf5fe6/@@download/attachment/L-EIF3D_BGHLV16_23.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF3D. (EIF3D_BGHLV16_23)

value: child

value: ENCBS230TCM at ENCODE; https://www.encodeproject.org/ENCBS230TCM/


title: shRNA RNA-seq from K562 (ENCLB264ZZY)

description:
https://www.encodeproject.org/experiments/ENCSR812EIA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EXOSC9 in K562 cells followed by RNA-seq. (EXOSC9 BGKLV13)
experiment encode accession: ENCSR812EIA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB264ZZY
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/7a1b7ebf-8996-4eee-8878-9867028f0b4b/@@download/attachment/L-EXOSC9_BGKLV13_8.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EXOSC9.(EXOSC9_BGKLV13_8)

value: 53 year

value: adult

value: female

value: ENCBS821KLW at ENCODE; https://www.encodeproject.org/ENCBS821KLW/

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


title: shRNA RNA-seq from K562 (ENCLB920UKY)

description:
https://www.encodeproject.org/experiments/ENCSR346DZQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NPM1. (NPM1_BGKLV28)
experiment encode accession: ENCSR346DZQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB920UKY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting NPM1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b7d8647a-0be9-4978-b4cd-3cfba5dea190/@@download/attachment/L-NPM1_BGKLV28-32.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NPM1. (NPM1_BGKLV28-32)

value: chronic myelogenous leukemia (CML)

value: ENCBS313HKT at ENCODE; https://www.encodeproject.org/ENCBS313HKT/

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


title: shRNA RNA-seq from K562 (ENCLB002ISL)

description:
https://www.encodeproject.org/experiments/ENCSR346DZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NPM1. (NPM1_BGKLV28)
experiment encode accession: ENCSR346DZQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB002ISL
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/cf17e827-c346-4631-9251-f4b774aae4e1/@@download/attachment/L-NPM1_BGKLV28-31.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NPM1. (NPM1_BGKLV28-31)

value: Brenton Graveley, UConn

value: ENCBS409HCD at ENCODE; https://www.encodeproject.org/ENCBS409HCD/


title: shRNA RNA-seq from HepG2 (ENCLB143ISX)

description:
https://www.encodeproject.org/experiments/ENCSR784FTX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1-BGHLV22)
experiment encode accession: ENCSR784FTX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB143ISX
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting KHDRBS1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1f8319ba-8e66-499d-8201-1ca794de02d0/@@download/attachment/L-KHDRBS1-BGHLV22-32.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1-BGHLV22-32)

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS650CRD at ENCODE; https://www.encodeproject.org/ENCBS650CRD/

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 (ENCLB076UFN)

description:
https://www.encodeproject.org/experiments/ENCSR341PZW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against WDR43. (WDR43_BGKLV34)
experiment encode accession: ENCSR341PZW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB076UFN
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting WDR43

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/33876834-7b50-4cab-a38f-b5b35fc7960b/@@download/attachment/L-WDR43_BGKLV34-52.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against WDR43. (WDR43_BGKLV34-52)

value: 53 year

value: adult

value: female

value: ENCBS624IMT at ENCODE; https://www.encodeproject.org/ENCBS624IMT/


title: microRNA-seq from ovary (ENCLB351PNL)

description:
https://www.encodeproject.org/experiments/ENCSR782FPG/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human female gonad
experiment encode accession: ENCSR782FPG
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB351PNL
size range: <30

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

value: ovary

value: tissue

value: Ovary 4-1

value: 51 year

value: Barbara Wold, Caltech

value: ENCBS988BTE at ENCODE; https://www.encodeproject.org/ENCBS988BTE/

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


title: shRNA RNA-seq from K562 (ENCLB573IPZ)

description:
https://www.encodeproject.org/experiments/ENCSR783YSQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RTF1 in K562 cells followed by RNA-seq. (RTF1 BGKLV13)
experiment encode accession: ENCSR783YSQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB573IPZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RTF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/89b10d07-9ce9-423c-9617-1f03c93485ce/@@download/attachment/L-RTF1_BGKLV13_20.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RTF1.(RTF1_BGKLV13_20)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS615ZVR at ENCODE; https://www.encodeproject.org/ENCBS615ZVR/

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 (ENCLB599SLA)

description:
https://www.encodeproject.org/experiments/ENCSR783YSQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RTF1 in K562 cells followed by RNA-seq. (RTF1 BGKLV13)
experiment encode accession: ENCSR783YSQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB599SLA
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/41d724fc-74b3-4fe6-bd7a-2f24dcaf9edf/@@download/attachment/L-RTF1_BGKLV13_19.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RTF1.(RTF1_BGKLV13_19)

value: 53 year

value: adult

value: ENCBS388NGV at ENCODE; https://www.encodeproject.org/ENCBS388NGV/


title: total RNA-seq from spleen (ENCLB546WAK)

description:
https://www.encodeproject.org/experiments/ENCSR330UMQ/
***************
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 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: ENCSR330UMQ
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB546WAK
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/55513db6-1a97-4536-843a-360f416c5f6b/@@download/attachment/296573.pdf

value: spleen

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS297IUS at ENCODE; https://www.encodeproject.org/ENCBS297IUS/

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


title: shRNA RNA-seq from K562 (ENCLB368QAO)

description:
https://www.encodeproject.org/experiments/ENCSR783LUA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PRPF6 in K562 cells followed by RNA-seq. (PRPF6 BGKLV13)
experiment encode accession: ENCSR783LUA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB368QAO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PRPF6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b227c568-54c0-4d71-b43c-ccf824eb34fb/@@download/attachment/L-PRPF6_BGKLV13_9.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PRPF6.(PRPF6_BGKLV13_9)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS638QCL at ENCODE; https://www.encodeproject.org/ENCBS638QCL/


title: RAMPAGE from SK-N-DZ (ENCLB265IDJ)

description:
https://www.encodeproject.org/experiments/ENCSR786DTS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SK-N-DZ, a metastatic neuroblastoma from a 2 year old female. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR786DTS
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR136WGP
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB265IDJ
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/fb4eedd4-1215-46a7-b950-919db992aaee/@@download/attachment/289911.pdf

value: SK-N-DZ

value: 2 year

value: child

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:72; duration_units:hour;

value: John Stamatoyannopoulos, UW

value: ENCBS520AAA at ENCODE; https://www.encodeproject.org/ENCBS520AAA/

value: Derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701


title: shRNA RNA-seq from HepG2 (ENCLB351GOR)

description:
https://www.encodeproject.org/experiments/ENCSR784FTX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1-BGHLV22)
experiment encode accession: ENCSR784FTX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB351GOR
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/79997dfd-2c5a-4003-a986-893555c60dd6/@@download/attachment/L-KHDRBS1-BGHLV22-31.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1-BGHLV22-31)

value: 15 year

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS502APU at ENCODE; https://www.encodeproject.org/ENCBS502APU/

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 spleen (ENCLB684QDH)

description:
https://www.encodeproject.org/experiments/ENCSR329YVA/
***************
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: ENCSR329YVA
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR330UMQ
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB684QDH
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/9965bd56-71f8-44b3-8a47-dd7dad26cd1e/@@download/attachment/296773.pdf

value: spleen

value: tissue

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

value: 37 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS297IUS at ENCODE; https://www.encodeproject.org/ENCBS297IUS/

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


title: shRNA RNA-seq from K562 (ENCLB762FUT)

description:
https://www.encodeproject.org/experiments/ENCSR334BTA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against WDR3. (WDR3_BGKLV34)
experiment encode accession: ENCSR334BTA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB762FUT
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting WDR3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ca28da3c-d987-4fea-802e-361f77cdb4a9/@@download/attachment/L-WDR3_BGKLV34-50.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against WDR3. (WDR3_BGKLV34-50)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS554MTP at ENCODE; https://www.encodeproject.org/ENCBS554MTP/

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


title: shRNA RNA-seq from K562 (ENCLB251LHH)

description:
https://www.encodeproject.org/experiments/ENCSR783LUA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PRPF6 in K562 cells followed by RNA-seq. (PRPF6 BGKLV13)
experiment encode accession: ENCSR783LUA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB251LHH
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/357b5a02-aae6-482c-b7ac-10a6758f0988/@@download/attachment/L-PRPF6_BGKLV13_10.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PRPF6.(PRPF6_BGKLV13_10)

value: Brenton Graveley, UConn

value: ENCBS990XUV at ENCODE; https://www.encodeproject.org/ENCBS990XUV/

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


title: shRNA RNA-seq from K562 (ENCLB243BBM)

description:
https://www.encodeproject.org/experiments/ENCSR341PZW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against WDR43. (WDR43_BGKLV34)
experiment encode accession: ENCSR341PZW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB243BBM
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/c3e579ea-19dd-4468-b921-b3509151be39/@@download/attachment/L-WDR43_BGKLV34-51.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against WDR43. (WDR43_BGKLV34-51)

value: ENCBS148RQY at ENCODE; https://www.encodeproject.org/ENCBS148RQY/


title: shRNA RNA-seq from K562 (ENCLB073YYB)

description:
https://www.encodeproject.org/experiments/ENCSR334BTA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against WDR3. (WDR3_BGKLV34)
experiment encode accession: ENCSR334BTA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB073YYB
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/8e8428e7-ce1a-4eda-8aab-5a19339fc06d/@@download/attachment/L-WDR3_BGKLV34-49.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against WDR3. (WDR3_BGKLV34-49)

value: adult

value: ENCBS395JCN at ENCODE; https://www.encodeproject.org/ENCBS395JCN/


title: microRNA-seq from ovary (ENCLB893YNM)

description:
https://www.encodeproject.org/experiments/ENCSR782FPG/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human female gonad
experiment encode accession: ENCSR782FPG
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB893YNM
size range: <30

value: ovary

value: tissue

value: Ovary 4-2

value: 51 year

value: Barbara Wold, Caltech

value: ENCBS430YCW at ENCODE; https://www.encodeproject.org/ENCBS430YCW/

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


title: shRNA RNA-seq from HepG2 (ENCLB469BYQ)

description:
https://www.encodeproject.org/experiments/ENCSR781YNI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF5. (SRSF5-BGHLV23)
experiment encode accession: ENCSR781YNI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB469BYQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SRSF5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c728a228-cdb4-488d-98f8-6d341c897a89/@@download/attachment/L-SRSF5-BGHLV23-45.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF5. (SRSF5-BGHLV23-45)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS311FWL at ENCODE; https://www.encodeproject.org/ENCBS311FWL/

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 sigmoid colon (ENCLB125ISW)

description:
https://www.encodeproject.org/experiments/ENCSR321NPB/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human sigmoid colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR321NPB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR094GVZ
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB125ISW
size range: >200

source_name: Homo sapiens sigmoid colon 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/099e4037-1a73-4ab2-9301-826023dc9ddb/@@download/attachment/296784.pdf

value: sigmoid colon

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

value: 53 year

value: adult

value: female

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from HepG2 (ENCLB245COP)

description:
https://www.encodeproject.org/experiments/ENCSR781YNI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF5. (SRSF5-BGHLV23)
experiment encode accession: ENCSR781YNI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB245COP
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/d16b86a1-2e95-435d-a88d-21cb45bcbef3/@@download/attachment/L-SRSF5-BGHLV23-46.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF5. (SRSF5-BGHLV23-46)

value: Brenton Graveley, UConn

value: ENCBS762HAX at ENCODE; https://www.encodeproject.org/ENCBS762HAX/


title: shRNA RNA-seq from K562 (ENCLB598EOS)

description:
https://www.encodeproject.org/experiments/ENCSR778WPL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB_BGKLV24_B)
experiment encode accession: ENCSR778WPL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB598EOS
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3244fec1-aaae-41dc-8a0f-670b09a8f1c5/@@download/attachment/L-HNRNPAB_BGKLV24_31B.pdf

value: HNRNPAB

value: RNA-seq on k562 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB_BGKLV24_31B)

value: chronic myelogenous leukemia (CML)

value: ENCBS591LWJ at ENCODE; https://www.encodeproject.org/ENCBS591LWJ/

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 (ENCLB858FWZ)

description:
https://www.encodeproject.org/experiments/ENCSR778WPL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB_BGKLV24_B)
experiment encode accession: ENCSR778WPL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB858FWZ
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/cae5a0e4-b38f-4bfd-8c0e-3c4766e40fb2/@@download/attachment/L-HNRNPAB_BGKLV24_32B.pdf

value: RNA-seq on k562 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB_BGKLV24_32B)

value: ENCBS964YGP at ENCODE; https://www.encodeproject.org/ENCBS964YGP/


title: shRNA RNA-seq from K562 (ENCLB467TUI)

description:
https://www.encodeproject.org/experiments/ENCSR778SIU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SUPV3L1 in K562 cells followed by RNA-seq. (SUPV3L1_BGKLV19)
experiment encode accession: ENCSR778SIU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB467TUI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SUPV3L1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a4c8ecd6-dacf-434b-87fb-7c79915572ed/@@download/attachment/L-SUPV3L1_BGKLV19_53B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUPV3L1. (SUPV3L1_BGKLV19_53B)

value: 53 year

value: adult

value: ENCBS534VZR at ENCODE; https://www.encodeproject.org/ENCBS534VZR/


title: shRNA RNA-seq from HepG2 (ENCLB426FZR)

description:
https://www.encodeproject.org/experiments/ENCSR778RWJ/
***************
biological replicate number: 2
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: ENCLB426FZR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting XPO5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d0cb412d-ddd5-4a52-882b-7dfa641e8e6a/@@download/attachment/L-XPO5-BGHLV22-58.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XPO5. (XPO5-BGHLV22-58)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS669DWT at ENCODE; https://www.encodeproject.org/ENCBS669DWT/

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 (ENCLB910EIB)

description:
https://www.encodeproject.org/experiments/ENCSR778SIU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SUPV3L1 in K562 cells followed by RNA-seq. (SUPV3L1_BGKLV19)
experiment encode accession: ENCSR778SIU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB910EIB
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/c829021c-e16e-4b3e-a54e-d7b96e183fc3/@@download/attachment/L-SUPV3L1_BGKLV19_54B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUPV3L1. (SUPV3L1_BGKLV19_54B)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS022LAM at ENCODE; https://www.encodeproject.org/ENCBS022LAM/


title: total RNA-seq from upper lobe of left lung (ENCLB381WRT)

description:
https://www.encodeproject.org/experiments/ENCSR313COD/
***************
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 lung 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: ENCSR313COD
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB381WRT
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens upper lobe of left lung tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9c1a84e1-25c9-42ad-8c2b-7c34f9efd886/@@download/attachment/296289.pdf

value: upper lobe of left lung

value: tissue

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

value: 37 year

value: Thomas Gingeras, CSHL

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

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


title: RAMPAGE from gastroesophageal sphincter (ENCLB502VVM)

description:
https://www.encodeproject.org/experiments/ENCSR315BZA/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human esophagogastric junction tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR315BZA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR485WBR
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB502VVM
size range: >200

source_name: Homo sapiens gastroesophageal sphincter tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/321d5486-08ae-4727-853d-ff206c7b015b/@@download/attachment/296777.pdf

value: gastroesophageal sphincter

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

value: 54 year

value: adult

value: male

value: ENCBS812ZNH at ENCODE; https://www.encodeproject.org/ENCBS812ZNH/

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


title: shRNA RNA-seq from K562 (ENCLB794VDV)

description:
https://www.encodeproject.org/experiments/ENCSR771ZZL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-25B)
experiment encode accession: ENCSR771ZZL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB794VDV
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/ae340b06-dc13-492a-8283-d5bbc02ff4c9/@@download/attachment/L-K-NT-25B-1.pdf

value: Control

value: immortalized cell line

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (K-NT-25B-1)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS396WFI at ENCODE; https://www.encodeproject.org/ENCBS396WFI/

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 (ENCLB015YKQ)

description:
https://www.encodeproject.org/experiments/ENCSR771ZZL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-25B)
experiment encode accession: ENCSR771ZZL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB015YKQ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/5337b99f-f92c-4beb-92f8-882e318b2ff6/@@download/attachment/L-K-NT-25B-2.pdf

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (K-NT-25B-2)

value: Brenton Graveley, UConn

value: ENCBS430DZA at ENCODE; https://www.encodeproject.org/ENCBS430DZA/


title: shRNA RNA-seq from HepG2 (ENCLB513LII)

description:
https://www.encodeproject.org/experiments/ENCSR312SFA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGHLV31)
experiment encode accession: ENCSR312SFA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB513LII
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/c038476d-754c-4eb9-a699-372d8a7511dd/@@download/attachment/L-DDX19B_BGHLV31-25.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGHLV31-25)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS068DNA at ENCODE; https://www.encodeproject.org/ENCBS068DNA/

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 (ENCLB735BPE)

description:
https://www.encodeproject.org/experiments/ENCSR771QMJ/
***************
biological replicate number: 2
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: ENCLB735BPE
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/29548646-454c-4964-9b3e-9426338541dd/@@download/attachment/L-GEMIN5_BGHLV16_30.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GEMIN5. (GEMIN5_BGHLV16_30)

value: male

value: ENCBS976OQX at ENCODE; https://www.encodeproject.org/ENCBS976OQX/


title: shRNA RNA-seq from HepG2 (ENCLB566PIS)

description:
https://www.encodeproject.org/experiments/ENCSR312SFA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGHLV31)
experiment encode accession: ENCSR312SFA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR538QOG
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB566PIS
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/96cae0f8-793c-43c8-9b3e-8592a85fad8e/@@download/attachment/L-DDX19B_BGHLV31-26.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX19B. (DDX19B_BGHLV31-26)

value: ENCBS233NIP at ENCODE; https://www.encodeproject.org/ENCBS233NIP/