title: shRNA RNA-seq from HepG2 (ENCLB080ZNB)

description:
https://www.encodeproject.org/experiments/ENCSR957EEG/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF4A3 in HepG2 cells followed by RNA-seq. (EIF4A3-BGHLV12)
experiment encode accession: ENCSR957EEG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB080ZNB
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/2feb677a-20a3-4473-b46b-753d63a6bf97/@@download/attachment/L-EIF4A3-BGHLV12-21.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4A3. (EIF4A3-BGHLV12-21)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS902IAH at ENCODE; https://www.encodeproject.org/ENCBS902IAH/


title: shRNA RNA-seq from K562 (ENCLB602UYI)

status: Public on May 26 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/ENCSR952RRH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against IGF2BP2 in K562 cells followed by RNA-seq. (IGF2BP2-LV11)
experiment encode accession: ENCSR952RRH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB602UYI
size range: >200
spikeins used: /references/ENCSR449DXG/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting IGF2BP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/05d2642a-61fa-45d1-8a0a-d291f966e3d9/@@download/attachment/L-IGF2BP2-LV11-22.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP2. (IGF2BP2-LV11-22)

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

tag: link

value: ENCBS846HWI at ENCODE; https://www.encodeproject.org/ENCBS846HWI/

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 (ENCLB130NSO)

description:
https://www.encodeproject.org/experiments/ENCSR945UYL/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against G3BP2 in HepG2 cells followed by RNA-seq. (G3BP2-BGHLV12)
experiment encode accession: ENCSR945UYL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB130NSO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting G3BP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/18b38c10-d80a-4eb0-bf27-a9619255cbe4/@@download/attachment/L-G3BP2-BGHLV12-35.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against G3BP2. (G3BP2-BGHLV12-35)

value: ENCBS088KUZ at ENCODE; https://www.encodeproject.org/ENCBS088KUZ/

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 (ENCLB573TLZ)

description:
https://www.encodeproject.org/experiments/ENCSR947OIM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RBM22 in K562 cells followed by RNA-seq. (RBM22-LV11)
experiment encode accession: ENCSR947OIM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB573TLZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RBM22

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/29366a86-3b70-4edc-9e42-157b8aa2ef70/@@download/attachment/L-RBM22-LV11-42.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM22. (RBM22-LV11-42)

value: ENCBS474XLY at ENCODE; https://www.encodeproject.org/ENCBS474XLY/


title: shRNA RNA-seq from K562 (ENCLB205CPB)

description:
https://www.encodeproject.org/experiments/ENCSR952RRH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against IGF2BP2 in K562 cells followed by RNA-seq. (IGF2BP2-LV11)
experiment encode accession: ENCSR952RRH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB205CPB
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/8e455b80-0c0f-441e-9b37-6b028e7d3797/@@download/attachment/L-IGF2BP2-LV11-21.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP2. (IGF2BP2-LV11-21)

value: Brenton Graveley, UConn

value: ENCBS501VGA at ENCODE; https://www.encodeproject.org/ENCBS501VGA/


title: shRNA RNA-seq from HepG2 (ENCLB090GAB)

description:
https://www.encodeproject.org/experiments/ENCSR945UYL/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against G3BP2 in HepG2 cells followed by RNA-seq. (G3BP2-BGHLV12)
experiment encode accession: ENCSR945UYL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB090GAB
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/5d6e6c32-c060-4848-8ec1-4fad2f01f1b9/@@download/attachment/L-G3BP2-BGHLV12-36.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against G3BP2. (G3BP2-BGHLV12-36)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS607IVB at ENCODE; https://www.encodeproject.org/ENCBS607IVB/


title: shRNA RNA-seq from HepG2 (ENCLB451JCP)

description:
https://www.encodeproject.org/experiments/ENCSR939ZRA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RDBP in HepG2 cells followed by RNA-seq. (RDBP-BGHLV12)
experiment encode accession: ENCSR939ZRA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB451JCP
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ee29272e-8782-4594-95b7-d0b2c2142894/@@download/attachment/L-RDBP-BGHLV12-70.pdf

value: NELFE

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RDBP. (RDBP-BGHLV12-70)

value: ENCBS715MWV at ENCODE; https://www.encodeproject.org/ENCBS715MWV/


title: shRNA RNA-seq from K562 (ENCLB358DIG)

description:
https://www.encodeproject.org/experiments/ENCSR947OIM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RBM22 in K562 cells followed by RNA-seq. (RBM22-LV11)
experiment encode accession: ENCSR947OIM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB358DIG
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/3ffa6c9a-9587-4a40-a27d-2c13fed04d6d/@@download/attachment/L-RBM22-LV11-41.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM22. (RBM22-LV11-41)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS649VHZ at ENCODE; https://www.encodeproject.org/ENCBS649VHZ/

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 (ENCLB097NXC)

description:
https://www.encodeproject.org/experiments/ENCSR927JXU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FUS in HepG2 cells followed by RNA-seq. (FUS BGHLV14)
experiment encode accession: ENCSR927JXU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB097NXC
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8ed463e5-edb0-4412-a03c-a2311c238cd2/@@download/attachment/L-FUS_BGHLV14-22.pdf

value: FUS

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUS. (FUS_BGHLV14-22)

value: Brenton Graveley, UConn

value: ENCBS877WFF at ENCODE; https://www.encodeproject.org/ENCBS877WFF/

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 (ENCLB210OQD)

description:
https://www.encodeproject.org/experiments/ENCSR995ZGJ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SMNDC1 in HepG2 cells followed by RNA-seq. (SMNDC1 BGHLV14)
experiment encode accession: ENCSR995ZGJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB210OQD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SMNDC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5cc0ade4-f915-4eb3-af3c-423f27980272/@@download/attachment/L-SMNDC1_BGHLV14-50.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SMNDC1. (SMNDC1_BGHLV14-50)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS307OQZ at ENCODE; https://www.encodeproject.org/ENCBS307OQZ/


title: shRNA RNA-seq from K562 (ENCLB135NOB)

description:
https://www.encodeproject.org/experiments/ENCSR916WOI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TRA2A in K562 cells followed by RNA-seq. (TRA2A-LV11)
experiment encode accession: ENCSR916WOI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB135NOB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TRA2A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5d08b459-754c-4649-9414-da4a313c4fc2/@@download/attachment/L-TRA2A-LV11-63.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TRA2A. (TRA2A-LV11-63)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS305KEA at ENCODE; https://www.encodeproject.org/ENCBS305KEA/


title: shRNA RNA-seq from HepG2 (ENCLB772IIF)

description:
https://www.encodeproject.org/experiments/ENCSR997FOT/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SUB1 in HepG2 cells followed by RNA-seq. (SUB1 BGHLV14)
experiment encode accession: ENCSR997FOT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB772IIF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SUB1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4487e8a4-c722-45ae-8bf1-72d6745a6396/@@download/attachment/L-SUB1_BGHLV14-57.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUB1. (SUB1_BGHLV14-57)

value: ENCBS782BXQ at ENCODE; https://www.encodeproject.org/ENCBS782BXQ/


title: shRNA RNA-seq from HepG2 (ENCLB351TMV)

description:
https://www.encodeproject.org/experiments/ENCSR927JXU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FUS in HepG2 cells followed by RNA-seq. (FUS BGHLV14)
experiment encode accession: ENCSR927JXU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB351TMV
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/ca42a4a6-7865-4875-8489-938fd14eee49/@@download/attachment/L-FUS_BGHLV14-21.pdf

value: FUS

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FUS. (FUS_BGHLV14-21)

value: Brenton Graveley, UConn

value: ENCBS489ZQI at ENCODE; https://www.encodeproject.org/ENCBS489ZQI/

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


title: shRNA RNA-seq from HepG2 (ENCLB012XZP)

description:
https://www.encodeproject.org/experiments/ENCSR906WTM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RTF1 in HepG2 cells followed by RNA-seq. (RTF1 BGHLV14)
experiment encode accession: ENCSR906WTM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB012XZP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/be7bbdd9-879a-4e4f-9f4a-39a79537e09f/@@download/attachment/L-RTF1_BGHLV14-45.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RTF1. (RTF1_BGHLV14-45)

value: 15 year

value: child

value: male

value: ENCBS303VDB at ENCODE; https://www.encodeproject.org/ENCBS303VDB/

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


title: shRNA RNA-seq from K562 (ENCLB765ANP)

description:
https://www.encodeproject.org/experiments/ENCSR913CAE/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (Nontarget-LV08)
experiment encode accession: ENCSR913CAE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB765ANP
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/7a1f6d52-e536-4ca0-aa73-9318a524bac6/@@download/attachment/L-Nontarget-LV08-1-1.pdf

value: Control

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (nontarget-LV08-2)

value: 53 year

value: adult

value: female

value: ENCBS746YXR at ENCODE; https://www.encodeproject.org/ENCBS746YXR/

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 (ENCLB158EMI)

description:
https://www.encodeproject.org/experiments/ENCSR914WQV/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against CSTF2T in HepG2 cells followed by RNA-seq. (CSTF2T BGHLV14)
experiment encode accession: ENCSR914WQV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB158EMI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CSTF2T

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/49883c86-49af-45bc-85bf-ca11a44a2497/@@download/attachment/L-CSTF2T_BGHLV14-5.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CSTF2T. (CSTF2T_BGHLV14-5)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS044VWV at ENCODE; https://www.encodeproject.org/ENCBS044VWV/


title: shRNA RNA-seq from HepG2 (ENCLB854WUS)

description:
https://www.encodeproject.org/experiments/ENCSR914WQV/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against CSTF2T in HepG2 cells followed by RNA-seq. (CSTF2T BGHLV14)
experiment encode accession: ENCSR914WQV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB854WUS
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/a33b930f-8995-45eb-b671-eb50d00bd72d/@@download/attachment/L-CSTF2T_BGHLV14-6.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CSTF2T. (CSTF2T_BGHLV14-6)

value: 15 year

value: child

value: ENCBS900XSC at ENCODE; https://www.encodeproject.org/ENCBS900XSC/

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


title: shRNA RNA-seq from K562 (ENCLB265RRT)

description:
https://www.encodeproject.org/experiments/ENCSR913CAE/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (Nontarget-LV08)
experiment encode accession: ENCSR913CAE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB265RRT
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/861c6478-2fca-4c18-9c51-26d4ea0c85c8/@@download/attachment/L-Nontarget-LV08-1-2.pdf

value: Control

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (Nontarget-LV08-1)

value: chronic myelogenous leukemia (CML)

value: ENCBS366CLP at ENCODE; https://www.encodeproject.org/ENCBS366CLP/


title: shRNA RNA-seq from HepG2 (ENCLB347EEU)

description:
https://www.encodeproject.org/experiments/ENCSR906WTM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RTF1 in HepG2 cells followed by RNA-seq. (RTF1 BGHLV14)
experiment encode accession: ENCSR906WTM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB347EEU
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/f011acc2-b53e-4361-97c6-d9b596fef915/@@download/attachment/L-RTF1_BGHLV14-46.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RTF1. (RTF1_BGHLV14-46)

value: male

value: ENCBS628MMK at ENCODE; https://www.encodeproject.org/ENCBS628MMK/

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


title: Input_preB_WT

city: New York

first: Jane

last: Skok

state: NY

address: 550 First Ave, Smillow 307

institute: NYU

description: input taken before incubation with H3K27Ac antibody (after incubation with H3 and dsDNA antibodies and indexing)

library_source: genomic

data_processing:
Reads were aligned to the mouse genome mm10 using Bowtie2 with parameters --no-discordant --no-mixed -N 1.
Duplicated were removed
Enriched regions of H3K27Ac were identified using MACS 1.4.2 with parameters -p 1e-5 -g mm -B --single-profile with input libraries as background signal.
Genome_build: mm10
Supplementary_files_format_and_content: bw and bed (peaks called)

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Animals were bred and maintained in the animal facility. Animal care was approved by Institutional Animal Care and Use Committee (protocol number 150606-01, NYU School of Medicine).

extract_protocol:
Cells were crosslinked with 1% PFA 10 minutes on ice and lysed. Cross-linked DNA was incubated with H3 antibody. H3-bound chromatin was used to attach NEXTflexTM adapters. Chromatin with ligated adapters was incubated with H3K27Ac antibody.
H3K27Ac+ chromatin was decrosslinked and amplified with primers recognizing adapters.

treatment_protocol: Cells were sorted ex vivo and processed immediatelly.

tag: strain

tag: tissue

value: bone marrow

value: 5-7 weeks old

tag: cell type


title: H3K27Ac_preB_WT_rep2

description: chromatin enriched for H3K27Ac

value: anti-H3K27Ac (Abcam ab4729, lot number GR211895-1)


title: Input_ImmB_WT

source_name: CD19+IgD-B220+IgM+ immature B cells

value: CD19+IgD-B220+IgM+ immature B cells


title: Input_DN_WT

source_name: CD4-CD8- double negative (CD25+CD44-/+) T cells

value: thymus


title: shRNA RNA-seq from HepG2 (ENCLB370PLD)

description:
https://www.encodeproject.org/experiments/ENCSR939ZRA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RDBP in HepG2 cells followed by RNA-seq. (RDBP-BGHLV12)
experiment encode accession: ENCSR939ZRA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB370PLD
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/b57c52c5-016f-471f-9f2e-2b44d34f43b5/@@download/attachment/L-RDBP-BGHLV12-69.pdf

value: NELFE

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RDBP. (RDBP-BGHLV12-69)

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS315PDD at ENCODE; https://www.encodeproject.org/ENCBS315PDD/


title: shRNA RNA-seq from K562 (ENCLB566YIH)

description:
https://www.encodeproject.org/experiments/ENCSR906RHU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF5 in K562 cells followed by RNA-seq. (SRSF5-41-LV11)
experiment encode accession: ENCSR906RHU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB566YIH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 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/4e0f065a-4df1-4452-80c5-2889d23caffe/@@download/attachment/L-SRSF5-41-LV11-52.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF5. (SRSF5-41-LV11-52)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS741EFJ at ENCODE; https://www.encodeproject.org/ENCBS741EFJ/

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: H3K27Ac_ImmB_WT_rep2

description: chromatin enriched for H3K27Ac

value: bone marrow

value: 5-7 weeks old

value: CD19+IgD-B220+IgM+ immature B cells

value: anti-H3K27Ac (Abcam ab4729, lot number GR211895-1)


title: shRNA RNA-seq from K562 (ENCLB559ZSV)

description:
https://www.encodeproject.org/experiments/ENCSR916WOI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TRA2A in K562 cells followed by RNA-seq. (TRA2A-LV11)
experiment encode accession: ENCSR916WOI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB559ZSV
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/b19305f3-3f51-4826-b40e-899520905098/@@download/attachment/L-TRA2A-LV11-64.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against TRA2A. (TRA2A-LV11-64)

value: ENCBS905LQS at ENCODE; https://www.encodeproject.org/ENCBS905LQS/


title: shRNA RNA-seq from K562 (ENCLB559VUN)

description:
https://www.encodeproject.org/experiments/ENCSR906RHU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF5 in K562 cells followed by RNA-seq. (SRSF5-41-LV11)
experiment encode accession: ENCSR906RHU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB559VUN
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/844a76bf-b326-4b36-bda1-e37e5e928816/@@download/attachment/L-SRSF5-41-LV11-51.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF5. (SRSF5-41-LV11-51)

value: Brenton Graveley, UConn

value: ENCBS298QZZ at ENCODE; https://www.encodeproject.org/ENCBS298QZZ/


title: H3K27Ac_preB_WT_rep1

description: chromatin enriched for H3K27Ac


title: H3K27Ac_ImmB_WT_rep1

description: chromatin enriched for H3K27Ac


title: H3K27Ac_DN_WT_rep1

description: chromatin enriched for H3K27Ac

value: thymus

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: REIR_preB_WT_rep2

description:
cross-linked genomic DNA (preserved 3D organization)
4C bait at REIR (Rpia-Eif2ak3 Intergenic Region)

data_processing:
Library strategy: 4C-seq
Reads were mapped to a reduced genome derived from mm10 containing unique sequences adjacent to restriction enzyme sites with Bowtie2 (-N=0 and -5 was used to trim the barcode and primer sequences).
The counts for each fragment were obtained from the mapped SAM files.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Cells were crosslinked with 2% PFA 10 minutes at RT and lysed. Cross-linked DNA was digested and ligated with NlaIII and DpnII subsequently.
Resulting 4C templates were amplified with PCR primers specific for our bait regions (3'Ek, MiEk, Eb and REIR)

treatment_protocol: Cells were sorted ex vivo and processed immediately.


title: shRNA RNA-seq from K562 (ENCLB701BTR)

description:
https://www.encodeproject.org/experiments/ENCSR904CJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against U2AF2 in K562 cells followed by RNA-seq. (U2AF2-LV08)
experiment encode accession: ENCSR904CJQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB701BTR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting U2AF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f9a0ebe7-25f2-4cd9-9b11-63fddce1164e/@@download/attachment/L-U2AF2-LV08-64.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against U2AF2. (U2AF2-LV08-64)

value: 53 year

value: adult

value: female

value: ENCBS905JDP at ENCODE; https://www.encodeproject.org/ENCBS905JDP/


title: REIR_preB_WT_rep1

value: bone marrow


title: H3K27Ac_DN_WT_rep2

description: chromatin enriched for H3K27Ac

value: 5-7 weeks old


title: REIR_ImmB_WT_rep2

value: CD19+IgD-B220+IgM+ immature B cells


title: shRNA RNA-seq from K562 (ENCLB897TSL)

description:
https://www.encodeproject.org/experiments/ENCSR904CJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against U2AF2 in K562 cells followed by RNA-seq. (U2AF2-LV08)
experiment encode accession: ENCSR904CJQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB897TSL
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/1deb0375-dafd-4b5c-a7a3-06dd90a5cf77/@@download/attachment/L-U2AF2-LV08-63.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against U2AF2. (U2AF2-LV08-63)

value: chronic myelogenous leukemia (CML)

value: ENCBS443DUP at ENCODE; https://www.encodeproject.org/ENCBS443DUP/

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: REIR_DN_MiEk_rep1

source_name: CD4-CD8- double negative (CD25+CD44-/+) MiEk-/- T cells


title: REIR_DP_WT_rep2

source_name: CD4+CD8+ double positive T cells

value: CD4+CD8+ double positive T cells


title: REIR_ImmB_WT_rep1


title: REIR_DN_Eb_rep2

source_name: CD4-CD8- double negative (CD25+CD44-/+) Eb-/- T cells


title: REIR_DP_WT_rep1


title: shRNA RNA-seq from K562 (ENCLB496TCH)

description:
https://www.encodeproject.org/experiments/ENCSR904BCZ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RAVER1 in K562 cells followed by RNA-seq. (RAVER1-LV08)
experiment encode accession: ENCSR904BCZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB496TCH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RAVER1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cc95fd5d-0757-4794-983a-319659179d26/@@download/attachment/L-RAVER1-LV08-42.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RAVER1. (RAVER1-LV08-42)

value: Brenton Graveley, UConn

value: ENCBS169BBI at ENCODE; https://www.encodeproject.org/ENCBS169BBI/


title: Tcrb_Eb_preB_WT_rep1

description:
cross-linked genomic DNA (preserved 3D organization)
4C bait at Tcrb enhancer Eb


title: shRNA RNA-seq from K562 (ENCLB976KIO)

description:
https://www.encodeproject.org/experiments/ENCSR895BTE/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against CPSF6 in K562 cells followed by RNA-seq. (CPSF6-LV08)
experiment encode accession: ENCSR895BTE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB976KIO
size range: >200
spikeins used: /references/ENCSR449DXG/

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/ae448f4d-3677-4797-bcc3-bf88c2229c15/@@download/attachment/L-CPSF6-LV08-7.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF6. (CPSF6-LV08-7)

value: 53 year

value: ENCBS185RGL at ENCODE; https://www.encodeproject.org/ENCBS185RGL/


title: Tcrb_Eb_preB_WT_rep2


title: shRNA RNA-seq from K562 (ENCLB503JCK)

description:
https://www.encodeproject.org/experiments/ENCSR904BCZ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RAVER1 in K562 cells followed by RNA-seq. (RAVER1-LV08)
experiment encode accession: ENCSR904BCZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB503JCK
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/30c105d8-38fe-48e4-9082-3539c39dbfe1/@@download/attachment/L-RAVER1-LV08-41.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RAVER1. (RAVER1-LV08-41)

value: adult

value: female

value: ENCBS440DGS at ENCODE; https://www.encodeproject.org/ENCBS440DGS/


title: shRNA RNA-seq from HepG2 (ENCLB379PTA)

description:
https://www.encodeproject.org/experiments/ENCSR861ENA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF2S1 in HepG2 cells followed by RNA-seq. (EIF2S1-BGHLV12)
experiment encode accession: ENCSR861ENA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB379PTA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EIF2S1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8271c248-4e02-4675-a54f-e6a8f96f0c77/@@download/attachment/L-EIF2S1-BGHLV12-20.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2S1. (EIF2S1-BGHLV12-20)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS692HLB at ENCODE; https://www.encodeproject.org/ENCBS692HLB/

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 (ENCLB808GPN)

description:
https://www.encodeproject.org/experiments/ENCSR861ENA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF2S1 in HepG2 cells followed by RNA-seq. (EIF2S1-BGHLV12)
experiment encode accession: ENCSR861ENA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB808GPN
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/63ba5bc5-1fcd-40b6-b244-a0835166fc03/@@download/attachment/L-EIF2S1-BGHLV12-19.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF2S1. (EIF2S1-BGHLV12-19)

value: Brenton Graveley, UConn

value: ENCBS664KGZ at ENCODE; https://www.encodeproject.org/ENCBS664KGZ/


title: REIR_DN_WT_rep2

value: thymus

value: 5-7 weeks old

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: Tcrb_Eb_ImmB_WT_rep1

value: bone marrow

value: CD19+IgD-B220+IgM+ immature B cells


title: Tcrb_Eb_ImmB_WT_rep2


title: shRNA RNA-seq from K562 (ENCLB468NJK)

description:
https://www.encodeproject.org/experiments/ENCSR895BTE/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against CPSF6 in K562 cells followed by RNA-seq. (CPSF6-LV08)
experiment encode accession: ENCSR895BTE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB468NJK
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/9ade54cc-a0cd-4014-b1b9-8e2d6e79c0d7/@@download/attachment/L-CPSF6-LV08-8.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF6. (CPSF6-LV08-8)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS772SKD at ENCODE; https://www.encodeproject.org/ENCBS772SKD/

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 (ENCLB505FGD)

description:
https://www.encodeproject.org/experiments/ENCSR853ZJS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against HNRNPK in HepG2 cells followed by RNA-seq. (HNRNPK-BGHLV12)
experiment encode accession: ENCSR853ZJS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB505FGD
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f364b2c2-3bae-4aa9-9cb6-7014940fd846/@@download/attachment/L-HNRNPK-BGHLV12-37.pdf

value: HNRNPK

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPK. (HNRNPK-BGHLV12-37)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS172NZN at ENCODE; https://www.encodeproject.org/ENCBS172NZN/

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: Tcrb_Eb_DN_MiEk_rep2

value: thymus

value: 5-7 weeks old

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: Tcrb_Eb_DP_WT_rep1

value: CD4+CD8+ double positive T cells


title: Tcrb_Eb_DN_MiEk_rep1


title: shRNA RNA-seq from HepG2 (ENCLB604CIV)

description:
https://www.encodeproject.org/experiments/ENCSR853ZJS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against HNRNPK in HepG2 cells followed by RNA-seq. (HNRNPK-BGHLV12)
experiment encode accession: ENCSR853ZJS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB604CIV
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/f290d72c-f368-45c8-b25a-019c9acab83a/@@download/attachment/L-HNRNPK-BGHLV12-38.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPK. (HNRNPK-BGHLV12-38)

value: Brenton Graveley, UConn

value: ENCBS548DDM at ENCODE; https://www.encodeproject.org/ENCBS548DDM/


title: REIR_DN_MiEk_rep2


title: REIR_DN_Eb_rep1


title: REIR_DN_WT_rep1


title: Tcrb_Eb_DN_Eb_rep1


title: shRNA RNA-seq from HepG2 (ENCLB449JOE)

description:
https://www.encodeproject.org/experiments/ENCSR850CKU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against KHSRP in HepG2 cells followed by RNA-seq. (KHSRP-BGHLV12)
experiment encode accession: ENCSR850CKU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB449JOE
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/15521ffc-6549-448b-b001-2b20fd54bd14/@@download/attachment/L-KHSRP-BGHLV12-45.pdf

value: KHSRP

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against KHSRP. (KHSRP-BGHLV12-45)

value: ENCBS408JNN at ENCODE; https://www.encodeproject.org/ENCBS408JNN/


title: shRNA RNA-seq from HepG2 (ENCLB906UKX)

description:
https://www.encodeproject.org/experiments/ENCSR850CKU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against KHSRP in HepG2 cells followed by RNA-seq. (KHSRP-BGHLV12)
experiment encode accession: ENCSR850CKU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB906UKX
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/b84138c0-c3d6-414a-b22f-68ea6cabd114/@@download/attachment/L-KHSRP-BGHLV12-46.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against KHSRP. (KHSRP-BGHLV12-46)

value: 15 year

value: ENCBS486CUL at ENCODE; https://www.encodeproject.org/ENCBS486CUL/


title: Tcrb_Eb_DN_WT_rep2


title: shRNA RNA-seq from K562 (ENCLB062UPC)

description:
https://www.encodeproject.org/experiments/ENCSR849STR/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against MAGOH in K562 cells followed by RNA-seq. (MAGOH-LV11)
experiment encode accession: ENCSR849STR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB062UPC
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0ed3be45-acd8-4900-853e-28766657e3b6/@@download/attachment/L-MAGOH-LV11-26.pdf

value: MAGOH

value: RNA-seq on K562 cells treated with an shRNA knockdown against MAGOH. (MAGOH-LV11-26)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS133VWK at ENCODE; https://www.encodeproject.org/ENCBS133VWK/

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: Tcrb_Eb_DN_WT_rep1

value: thymus

value: 5-7 weeks old

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: Igk_MiEk_preB_3Ek_rep2

description:
cross-linked genomic DNA (preserved 3D organization)
4C bait at Igk enhancer MiEk

source_name: CD19+IgD-B220+IgM-CD25+ckit- 3'Ek-/- pre-B cells

value: bone marrow


title: shRNA RNA-seq from K562 (ENCLB202UGQ)

description:
https://www.encodeproject.org/experiments/ENCSR849STR/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against MAGOH in K562 cells followed by RNA-seq. (MAGOH-LV11)
experiment encode accession: ENCSR849STR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB202UGQ
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/c1c1bbb6-f34f-49db-adf5-c7d542b28961/@@download/attachment/L-MAGOH-LV11-25.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against MAGOH. (MAGOH-LV11-25)

value: Brenton Graveley, UConn

value: ENCBS918DLF at ENCODE; https://www.encodeproject.org/ENCBS918DLF/


title: Tcrb_Eb_DP_WT_rep2

value: CD4+CD8+ double positive T cells


title: Igk_MiEk_preB_MiEk_rep1

source_name: CD19+IgD-B220+IgM-CD25+ckit- MiEk-/- pre-B cells


title: Igk_MiEk_preB_3Ek_rep1


title: Igk_MiEk_preB_WT_rep2


title: shRNA RNA-seq from HepG2 (ENCLB012FCV)

description:
https://www.encodeproject.org/experiments/ENCSR840QFR/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DAZAP1 in HepG2 cells followed by RNA-seq. (DAZAP1 BGHLV14)
experiment encode accession: ENCSR840QFR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB012FCV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DAZAP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bf27a5ed-a7d6-4c5f-872e-c1317845c94a/@@download/attachment/L-DAZAP1_BGHLV14-7.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DAZAP1. (DAZAP1_BGHLV14-7)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS352ZNU at ENCODE; https://www.encodeproject.org/ENCBS352ZNU/

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: Igk_MiEk_ImmB_WT_rep2

value: CD19+IgD-B220+IgM+ immature B cells


title: Igk_MiEk_preB_MiEk_rep2

value: 5-7 weeks old


title: shRNA RNA-seq from HepG2 (ENCLB765GZR)

description:
https://www.encodeproject.org/experiments/ENCSR840QFR/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DAZAP1 in HepG2 cells followed by RNA-seq. (DAZAP1 BGHLV14)
experiment encode accession: ENCSR840QFR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB765GZR
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/fc579a6d-8327-4be6-b9c7-62a5209a174e/@@download/attachment/L-DAZAP1_BGHLV14-8.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DAZAP1. (DAZAP1_BGHLV14-8)

value: ENCBS550FNB at ENCODE; https://www.encodeproject.org/ENCBS550FNB/


title: Igk_MiEk_preB_WT_rep1

extract_protocol:
Cells were crosslinked with 2% PFA 10 minutes at RT and lysed. Cross-linked DNA was digested and ligated with NlaIII and DpnII subsequently.
Resulting 4C templates were amplified with PCR primers specific for our bait regions (3'Ek, MiEk, Eb and REIR)

value: bone marrow


title: Igk_MiEk_ImmB_WT_rep1


title: Igk_MiEk_DP_WT_rep1

value: thymus


title: Tcrb_Eb_DN_Eb_rep2

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: shRNA RNA-seq from K562 (ENCLB216GZS)

description:
https://www.encodeproject.org/experiments/ENCSR831YGP/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EWSR1 in K562 cells followed by RNA-seq. (EWSR1-LV08)
experiment encode accession: ENCSR831YGP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB216GZS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EWSR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/43190b8d-cab7-4716-841c-f88802ec50f3/@@download/attachment/L-EWSR1-LV08-26.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against EWSR1. (EWSR1-LV08-26)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS954RIE at ENCODE; https://www.encodeproject.org/ENCBS954RIE/

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: Igk_MiEk_DN_WT_rep2


title: Igk_MiEk_DP_WT_rep2

value: CD4+CD8+ double positive T cells


title: Igk_MiEk_DN_WT_rep1

value: 5-7 weeks old


title: shRNA RNA-seq from K562 (ENCLB289GAU)

description:
https://www.encodeproject.org/experiments/ENCSR831YGP/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EWSR1 in K562 cells followed by RNA-seq. (EWSR1-LV08)
experiment encode accession: ENCSR831YGP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB289GAU
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/d86f2a1c-7db1-444e-8344-c7f4f9f01d73/@@download/attachment/L-EWSR1-LV08-25.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EWSR1. (EWSR1-LV08-25)

value: ENCBS154XYR at ENCODE; https://www.encodeproject.org/ENCBS154XYR/


title: Igk_3Ek_preB_3Ek_rep2

description:
cross-linked genomic DNA (preserved 3D organization)
4C bait at Igk enhancer 3'Ek

value: bone marrow


title: Igk_3Ek_preB_MiEk_rep1


title: shRNA RNA-seq from K562 (ENCLB777NWA)

description:
https://www.encodeproject.org/experiments/ENCSR792XFP/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against MATR3 in K562 cells followed by RNA-seq. (MATR3-06-LV11)
experiment encode accession: ENCSR792XFP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB777NWA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting MATR3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b7ee4f16-bd71-4fb6-93ee-29a5dc1bafe8/@@download/attachment/L-MATR3-06-LV11-27.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against MATR3. (MATR3-06-LV11-27)

value: ENCBS174LOJ at ENCODE; https://www.encodeproject.org/ENCBS174LOJ/


title: Igk_3Ek_preB_3Ek_rep1


title: Igk_3Ek_preB_MiEk_rep2


title: shRNA RNA-seq from K562 (ENCLB005SCB)

description:
https://www.encodeproject.org/experiments/ENCSR792XFP/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against MATR3 in K562 cells followed by RNA-seq. (MATR3-06-LV11)
experiment encode accession: ENCSR792XFP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB005SCB
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/fcdeb19e-7f63-4494-8953-28c9017931fc/@@download/attachment/L-MATR3-06-LV11-28.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against MATR3. (MATR3-06-LV11-28)

value: ENCBS016YMK at ENCODE; https://www.encodeproject.org/ENCBS016YMK/


title: shRNA RNA-seq from K562 (ENCLB062IHT)

description:
https://www.encodeproject.org/experiments/ENCSR780YFF/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FXR1 in K562 cells followed by RNA-seq. (FXR1-LV08)
experiment encode accession: ENCSR780YFF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB062IHT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting FXR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ad8cc775-01ee-4861-9c4b-aa551f833921/@@download/attachment/L-FXR1-LV08-30.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FXR1. (FXR1-LV08-30)

value: 53 year

value: adult

value: ENCBS869IGF at ENCODE; https://www.encodeproject.org/ENCBS869IGF/


title: Igk_3Ek_preB_WT_rep2


title: ATAC_preB_WT_rep2

description: nucleosome-free chromatin

data_processing:
Library strategy: ATAC-seq
Reads were aligned to mm10 genome with Bowtie2 (parameters: --no-discordant -p 12 --no-mixed -N 1 -X 2000).
Potential PCR duplicates were removed from the reads with Picard-tools.
ATAC-seq peaks were called with PeaKDEck (parameters: -sig 0.0001 -PVAL ON).
Genome_build: mm10
Supplementary_files_format_and_content: tdf and bed (peaks called)

extract_protocol:
Cells were lysed and DNA was tagmented with Nextera transposon loaded with Illumina adapters.
Tagmented DNA was amplified with primers recognizing adapters.


title: ATAC_ImmB_WT_rep2

description: nucleosome-free chromatin

source_name: CD19+IgD-B220+IgM+ immature B cells

value: CD19+IgD-B220+IgM+ immature B cells


title: ATAC_preB_WT_rep1

description: nucleosome-free chromatin


title: shRNA RNA-seq from K562 (ENCLB953VYO)

description:
https://www.encodeproject.org/experiments/ENCSR792CBM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against G3BP1 in K562 cells followed by RNA-seq. (G3BP1-LV11)
experiment encode accession: ENCSR792CBM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB953VYO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting G3BP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3a9d060f-2a4f-442f-8377-a314de04ff59/@@download/attachment/L-G3BP1-LV11-13.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against G3BP1. (G3BP1-LV11-13)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS783PTA at ENCODE; https://www.encodeproject.org/ENCBS783PTA/

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


title: Igk_3Ek_preB_WT_rep1

value: bone marrow

value: 5-7 weeks old


title: ATAC_ImmB_WT_rep1

description: nucleosome-free chromatin


title: ATAC_DP_WT_rep2

description: nucleosome-free chromatin

value: thymus

value: CD4+CD8+ double positive T cells


title: ATAC_DN_WT_rep2

description: nucleosome-free chromatin

source_name: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: ATAC_DN_WT_rep1

description: nucleosome-free chromatin

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: RNA_preB_3Ek_rep1

description:
ribodepleted RNA
count data: htseq_counts_preB.txt

data_processing:
Paired-end reads were mapped to the mm10 genome using TopHat2 (parameters: --no-coverage-search --no-discordant --no-mixed --b2-very-sensitive –N 1).
Counts for Refseq genes were obtained using htseq-counts
Genome_build: mm10
Supplementary_files_format_and_content: tdf

extract_protocol:
Cells were lysed with RLT buffer, total RNA was extracted with Qiagen kit.
Ribo-depleted RNA was fragmented and reverse-transcribed.  Illumina adapters were attached to cDNA through T-A overhand ligation and the library was amplified.


title: shRNA RNA-seq from K562 (ENCLB197NWV)

description:
https://www.encodeproject.org/experiments/ENCSR780YFF/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FXR1 in K562 cells followed by RNA-seq. (FXR1-LV08)
experiment encode accession: ENCSR780YFF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB197NWV
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/966a4878-30b0-4dd4-83e5-7440aa04034b/@@download/attachment/L-FXR1-LV08-29.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against FXR1. (FXR1-LV08-29)

value: ENCBS013VIB at ENCODE; https://www.encodeproject.org/ENCBS013VIB/

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


title: shRNA RNA-seq from K562 (ENCLB337BBO)

description:
https://www.encodeproject.org/experiments/ENCSR774BXV/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF4B in K562 cells followed by RNA-seq. (EIF4B-LV08)
experiment encode accession: ENCSR774BXV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB337BBO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF4B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c590668f-c804-4a97-a5f8-999ad4ee7319/@@download/attachment/L-EIF4B-LV08-23.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4B. (EIF4B-LV08-23)

value: 53 year

value: adult

value: ENCBS984GCA at ENCODE; https://www.encodeproject.org/ENCBS984GCA/


title: RNA_preB_MiEk_rep2


title: shRNA RNA-seq from HepG2 (ENCLB644OJD)

description:
https://www.encodeproject.org/experiments/ENCSR778AJO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF3G in HepG2 cells followed by RNA-seq. (EIF3G BGHLV14)
experiment encode accession: ENCSR778AJO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB644OJD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EIF3G

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/afae3ba9-9ce6-44b4-916a-b2df7b212583/@@download/attachment/L-EIF3G_BGHLV14-16.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF3G. (EIF3G_BGHLV14-16)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS224CAS at ENCODE; https://www.encodeproject.org/ENCBS224CAS/

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: RNA_preB_3Ek_rep2

value: bone marrow

value: 5-7 weeks old


title: shRNA RNA-seq from K562 (ENCLB778YDT)

description:
https://www.encodeproject.org/experiments/ENCSR792CBM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against G3BP1 in K562 cells followed by RNA-seq. (G3BP1-LV11)
experiment encode accession: ENCSR792CBM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB778YDT
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/6b7769fc-c2b1-4262-a733-70fe8027dac3/@@download/attachment/L-G3BP1-LV11-14.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against G3BP1. (G3BP1-LV11-14)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS577QZL at ENCODE; https://www.encodeproject.org/ENCBS577QZL/

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


title: RNA_preB_Eb_rep2

source_name: CD19+IgD-B220+IgM-CD25+ckit- Eb-/- pre-B cells


title: RNA_preB_MiEk_rep1


title: shRNA RNA-seq from HepG2 (ENCLB821KHV)

description:
https://www.encodeproject.org/experiments/ENCSR746EKS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against MAGOH in HepG2 cells followed by RNA-seq. (MAGOH-BGHLV12)
experiment encode accession: ENCSR746EKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB821KHV
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/448e09a5-9504-4353-958e-7111ffe3aead/@@download/attachment/L-MAGOH-BGHLV12-48.pdf

value: MAGOH

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MAGOH. (MAGOH-BGHLV12-48)

value: ENCBS006INV at ENCODE; https://www.encodeproject.org/ENCBS006INV/


title: shRNA RNA-seq from HepG2 (ENCLB094YLM)

description:
https://www.encodeproject.org/experiments/ENCSR746EKS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against MAGOH in HepG2 cells followed by RNA-seq. (MAGOH-BGHLV12)
experiment encode accession: ENCSR746EKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB094YLM
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/6ddd785f-903a-440a-b86e-7514827f5ef3/@@download/attachment/L-MAGOH-BGHLV12-47.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MAGOH. (MAGOH-BGHLV12-47)

value: 15 year

value: child

value: male

value: ENCBS872GDG at ENCODE; https://www.encodeproject.org/ENCBS872GDG/


title: shRNA RNA-seq from K562 (ENCLB975VYQ)

description:
https://www.encodeproject.org/experiments/ENCSR774BXV/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF4B in K562 cells followed by RNA-seq. (EIF4B-LV08)
experiment encode accession: ENCSR774BXV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB975VYQ
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/7bb65f54-efb5-4aeb-8d16-6f712f4bb523/@@download/attachment/L-EIF4B-LV08-24.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4B. (EIF4B-LV08-24)

value: 53 year

value: adult

value: ENCBS680QCR at ENCODE; https://www.encodeproject.org/ENCBS680QCR/

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


title: RNA_preB_WT_rep1

value: bone marrow

value: 5-7 weeks old


title: RNA_preB_Eb_rep1


title: RNA_preB_WT_rep2


title: shRNA RNA-seq from HepG2 (ENCLB339AVD)

description:
https://www.encodeproject.org/experiments/ENCSR732IYM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against XRCC5 in HepG2 cells followed by RNA-seq. (XRCC5 BGHLV14)
experiment encode accession: ENCSR732IYM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB339AVD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting XRCC5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/43955fa4-be64-467e-bc3e-9e4be97c3540/@@download/attachment/L-XRCC5_BGHLV14-68.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRCC5. (XRCC5_BGHLV14-68)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS791FZV at ENCODE; https://www.encodeproject.org/ENCBS791FZV/

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: RNA_ImmB_3Ek_rep2

description:
ribodepleted RNA
count data: htseq_counts_ImmB.txt

source_name: CD19+IgD-B220+IgM+ 3'Ek-/- immature B cells

value: CD19+IgD-B220+IgM+ immature B cells


title: ATAC_DP_WT_rep1

description: nucleosome-free chromatin

source_name: CD4+CD8+ double positive T cells

value: thymus

value: CD4+CD8+ double positive T cells


title: RNA_ImmB_3Ek_rep1


title: RNA_ImmB_MiEk_rep1

source_name: CD19+IgD-B220+IgM+ MiEk-/- immature B cells


title: RNA_ImmB_Eb_rep2

source_name: CD19+IgD-B220+IgM+ Eb-/- immature B cells


title: RNA_ImmB_MiEk_rep2


title: shRNA RNA-seq from HepG2 (ENCLB339ESV)

description:
https://www.encodeproject.org/experiments/ENCSR732IYM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against XRCC5 in HepG2 cells followed by RNA-seq. (XRCC5 BGHLV14)
experiment encode accession: ENCSR732IYM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB339ESV
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/0aee9c91-6c3b-4b0b-984d-ccf4e87a9646/@@download/attachment/L-XRCC5_BGHLV14-67.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRCC5. (XRCC5_BGHLV14-67)

value: 15 year

value: child

value: male

value: ENCBS441XTP at ENCODE; https://www.encodeproject.org/ENCBS441XTP/


title: shRNA RNA-seq from HepG2 (ENCLB879QNQ)

description:
https://www.encodeproject.org/experiments/ENCSR778AJO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF3G in HepG2 cells followed by RNA-seq. (EIF3G BGHLV14)
experiment encode accession: ENCSR778AJO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB879QNQ
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/90a236e5-5d0f-473b-b1df-63549768f9f5/@@download/attachment/L-EIF3G_BGHLV14-15.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF3G. (EIF3G_BGHLV14-15)

value: ENCBS063CQL at ENCODE; https://www.encodeproject.org/ENCBS063CQL/


title: RNA_ImmB_WT_rep1

value: bone marrow

value: 5-7 weeks old


title: shRNA RNA-seq from HepG2 (ENCLB758LBA)

description:
https://www.encodeproject.org/experiments/ENCSR716WZH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FASTKD2 in HepG2 cells followed by RNA-seq. (FASTKD2 BGHLV14)
experiment encode accession: ENCSR716WZH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB758LBA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting FASTKD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/34e455e0-7c01-4371-8ca3-8351f80ea926/@@download/attachment/L-FASTKD2_BGHLV14-19.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FASTKD2. (FASTKD2_BGHLV14-19)

value: hepatocellular carcinoma

value: ENCBS791ETZ at ENCODE; https://www.encodeproject.org/ENCBS791ETZ/


title: RNA_DP_MiEk_rep2

description:
ribodepleted RNA
count data: htseq_counts_DP.txt

source_name: CD4+CD8+ double positive MiEk-/- T cells


title: shRNA RNA-seq from HepG2 (ENCLB781SUN)

description:
https://www.encodeproject.org/experiments/ENCSR716WZH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FASTKD2 in HepG2 cells followed by RNA-seq. (FASTKD2 BGHLV14)
experiment encode accession: ENCSR716WZH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB781SUN
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/484aa9b0-fe85-43d6-8112-dbe3256f5db5/@@download/attachment/L-FASTKD2_BGHLV14-20.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FASTKD2. (FASTKD2_BGHLV14-20)

value: Brenton Graveley, UConn

value: ENCBS217MRJ at ENCODE; https://www.encodeproject.org/ENCBS217MRJ/

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: RNA_DP_MiEk_rep1

value: thymus

value: CD4+CD8+ double positive T cells


title: RNA_DP_Eb_rep2

source_name: CD4+CD8+ double positive Eb-/- T cells


title: RNA_DP_3Ek_rep1

source_name: CD4+CD8+ double positive 3'Ek-/- T cells


title: RNA_DP_WT_rep2


title: shRNA RNA-seq from HepG2 (ENCLB965GMT)

description:
https://www.encodeproject.org/experiments/ENCSR708GKW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against IGF2BP1 in HepG2 cells followed by RNA-seq. (IGF2BP1 BGHLV14)
experiment encode accession: ENCSR708GKW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB965GMT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting IGF2BP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6adfed47-d600-4707-b3cb-9f57d7b53178/@@download/attachment/L-IGF2BP1_BGHLV14-27.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against IGF2BP1. (IGF2BP1_BGHLV14-27)

value: 15 year

value: child

value: male

value: ENCBS093QOO at ENCODE; https://www.encodeproject.org/ENCBS093QOO/


title: RNA_DP_WT_rep1

value: 5-7 weeks old


title: RNA_DN_3Ek_rep1

description:
ribodepleted RNA
count data: htseq_counts_DN.txt

source_name: CD4-CD8- double negative (CD25+CD44-/+) 3'Ek-/- T cells

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: RNA_DP_Eb_rep1


title: RNA_DN_3Ek_rep2


title: shRNA RNA-seq from K562 (ENCLB794BWG)

description:
https://www.encodeproject.org/experiments/ENCSR694LKY/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TIA1 in K562 cells followed by RNA-seq. (TIA1-LV11)
experiment encode accession: ENCSR694LKY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB794BWG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TIA1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/39f4f179-f392-49e4-8dd2-931633924eb0/@@download/attachment/L-TIA1-LV11-59.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against TIA1. (TIA1-LV11-59)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS138SLH at ENCODE; https://www.encodeproject.org/ENCBS138SLH/

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: RNA_DN_MiEk_rep2

source_name: CD4-CD8- double negative (CD25+CD44-/+) MiEk-/- T cells

value: thymus


title: shRNA RNA-seq from K562 (ENCLB258SZE)

description:
https://www.encodeproject.org/experiments/ENCSR648QFY/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PCBP2 in K562 cells followed by RNA-seq. (PCBP2-LV11)
experiment encode accession: ENCSR648QFY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB258SZE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PCBP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c8b4e9e9-2a32-49b1-b941-8a8cd65d3ea8/@@download/attachment/L-PCBP2-LV11-31.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PCBP2. (PCBP2-LV11-31)

value: Brenton Graveley, UConn

value: ENCBS324YAG at ENCODE; https://www.encodeproject.org/ENCBS324YAG/


title: shRNA RNA-seq from HepG2 (ENCLB719VTT)

description:
https://www.encodeproject.org/experiments/ENCSR637JLM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX3X in HepG2 cells followed by RNA-seq. (DDX3X-BGHLV12)
experiment encode accession: ENCSR637JLM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB719VTT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX3X

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/302b5267-7d6c-4e32-aa97-27dd4e677282/@@download/attachment/L-DDX3X-BGHLV12-16.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX3X. (DDX3X-BGHLV12-16)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS222ZOM at ENCODE; https://www.encodeproject.org/ENCBS222ZOM/

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: RNA_DN_MiEk_rep1

extract_protocol:
Cells were lysed with RLT buffer, total RNA was extracted with Qiagen kit.
Ribo-depleted RNA was fragmented and reverse-transcribed.  Illumina adapters were attached to cDNA through T-A overhand ligation and the library was amplified.

value: 5-7 weeks old

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: shRNA RNA-seq from K562 (ENCLB966LGF)

description:
https://www.encodeproject.org/experiments/ENCSR648QFY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PCBP2 in K562 cells followed by RNA-seq. (PCBP2-LV11)
experiment encode accession: ENCSR648QFY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB966LGF
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/8194509b-7acd-4928-8c98-f2800fb083e2/@@download/attachment/L-PCBP2-LV11-32.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PCBP2. (PCBP2-LV11-32)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS767HRR at ENCODE; https://www.encodeproject.org/ENCBS767HRR/


title: RNA_ImmB_WT_rep2

source_name: CD19+IgD-B220+IgM+ immature B cells

value: bone marrow

value: CD19+IgD-B220+IgM+ immature B cells


title: RNA_DN_Eb_rep2

source_name: CD4-CD8- double negative (CD25+CD44-/+) Eb-/- T cells

value: thymus


title: shRNA RNA-seq from HepG2 (ENCLB726SSL)

description:
https://www.encodeproject.org/experiments/ENCSR637JLM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX3X in HepG2 cells followed by RNA-seq. (DDX3X-BGHLV12)
experiment encode accession: ENCSR637JLM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB726SSL
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/c7b6e9c0-1f4e-4d1d-b72c-d4187db195ea/@@download/attachment/L-DDX3X-BGHLV12-15.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX3X. (DDX3X-BGHLV12-15)

value: 15 year

value: child

value: male

value: Brenton Graveley, UConn

value: ENCBS809KDQ at ENCODE; https://www.encodeproject.org/ENCBS809KDQ/


title: shRNA RNA-seq from HepG2 (ENCLB294EEG)

description:
https://www.encodeproject.org/experiments/ENCSR708GKW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against IGF2BP1 in HepG2 cells followed by RNA-seq. (IGF2BP1 BGHLV14)
experiment encode accession: ENCSR708GKW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB294EEG
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/844d6734-f0b5-4919-807d-5ef229979b48/@@download/attachment/L-IGF2BP1_BGHLV14-28.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against IGF2BP1. (IGF2BP1_BGHLV14-28)

value: hepatocellular carcinoma

value: ENCBS180UZG at ENCODE; https://www.encodeproject.org/ENCBS180UZG/

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: RNA_DN_WT_rep4

source_name: CD4-CD8- double negative (CD25+CD44-/+) T cells

value: 5-7 weeks old


title: shRNA RNA-seq from HepG2 (ENCLB435EJE)

description:
https://www.encodeproject.org/experiments/ENCSR635FRH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PCBP1 in HepG2 cells followed by RNA-seq. (PCBP1-BGHLV12)
experiment encode accession: ENCSR635FRH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB435EJE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PCBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bdfc9b40-450e-4d18-ac13-0808e9f854bc/@@download/attachment/L-PCBP1-BGHLV12-55.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PCBP1. (PCBP1-BGHLV12-55)

value: ENCBS435NIB at ENCODE; https://www.encodeproject.org/ENCBS435NIB/


title: RNA_DP_3Ek_rep2

value: CD4+CD8+ double positive T cells


title: RNA_DN_WT_rep3

value: thymus

value: CD4-CD8- double negative (CD25+CD44-/+) T cells


title: RNA_DN_WT_rep2


title: shRNA RNA-seq from HepG2 (ENCLB261RBD)

description:
https://www.encodeproject.org/experiments/ENCSR635FRH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PCBP1 in HepG2 cells followed by RNA-seq. (PCBP1-BGHLV12)
experiment encode accession: ENCSR635FRH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB261RBD
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/6970b9e8-c3ed-4e0a-af5e-3cb42e123d5b/@@download/attachment/L-PCBP1-BGHLV12-56.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PCBP1. (PCBP1-BGHLV12-56)

value: 15 year

value: ENCBS743ZMW at ENCODE; https://www.encodeproject.org/ENCBS743ZMW/


title: RNA_DN_WT_rep1


title: RNA_DN_MiEk_rep3


title: shRNA RNA-seq from K562 (ENCLB816NWR)

description:
https://www.encodeproject.org/experiments/ENCSR629EWX/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against IGF2BP1 in K562 cells followed by RNA-seq. (IGF2BP1-LV11)
experiment encode accession: ENCSR629EWX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB816NWR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting IGF2BP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ce627be9-344f-44f7-b609-cedc1a8013c0/@@download/attachment/L-IGF2BP1-LV11-18.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP1. (IGF2BP1-LV11-18)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS250IAJ at ENCODE; https://www.encodeproject.org/ENCBS250IAJ/

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: ChIP-BS_Input_Ser_1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: ChIP-BS-Seq

data_processing:
RNA-Seq: Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters) and mapped to the mouse GRCm38 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) applying transcript length correction and 75th percentile normalisation.
Genome_build: GRCm38
RRBS and ChIP-BS-Seq: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bismark (Krueger and Andrews, 2011) (v0.12.3); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts.
ChIP-Seq: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bowtie 2; Read counts over 2kb tiles were normalied for total reads and the largest data store and log2 transformed. Tiles with <3 normlized read counts in all input samples were excluded.
Genome_build: NCBIM37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following 17 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-17) log2 RPKM values for each sample
Supplementary_files_format_and_content: Quantitated H3K9me2 data file is tab delimited and contains the following 12 columns: (1) Chromosome; (2) Start; (3) End; (4-12) log2 readcount for each sample

source_name: ChIP-BS Input Ser 1

extract_protocol:
ChIP-BS-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then treated for WGBS as described before
Genomic DNA and total RNA were isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.
RNASeq: RNA was used for library preparation using TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed either using Illumina Indexes and 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.
RRBS-Seq was performed as described previously (Smallwood et al, 2011)
ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)
ChIP-BS-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then treated for WGBS as described before

tag: background strain

value: ESC

tag: genotype

value: Wild-type

tag: chip antibody


title: ChIP-BS_Input_Ser_2

description: ChIP-BS-Seq

source_name: ChIP-BS Input Ser 2


title: RNA_DN_Eb_rep1

value: 5-7 weeks old


title: ChIP-BS_Input_2i_2

description: ChIP-BS-Seq

source_name: ChIP-BS Input 2i 2


title: ChIP-BS_Input_2i_1

description: ChIP-BS-Seq

source_name: ChIP-BS Input 2i 1


title: shRNA RNA-seq from K562 (ENCLB042YPT)

description:
https://www.encodeproject.org/experiments/ENCSR629EWX/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against IGF2BP1 in K562 cells followed by RNA-seq. (IGF2BP1-LV11)
experiment encode accession: ENCSR629EWX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB042YPT
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/1c2923f5-f0ec-4325-9351-c42f2fd9fa1f/@@download/attachment/L-IGF2BP1-LV11-17.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP1. (IGF2BP1-LV11-17)

value: ENCBS004ALC at ENCODE; https://www.encodeproject.org/ENCBS004ALC/


title: shRNA RNA-seq from K562 (ENCLB286MYT)

description:
https://www.encodeproject.org/experiments/ENCSR627NVU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RBM15 in K562 cells followed by RNA-seq. (RBM15-LV08)
experiment encode accession: ENCSR627NVU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB286MYT
size range: >200
spikeins used: /references/ENCSR449DXG/

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/58c2c2a7-f832-4f8d-b4e9-0645e4211478/@@download/attachment/L-RBM15-LV08-43.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM15. (RBM15-LV08-43)

value: ENCBS476WAQ at ENCODE; https://www.encodeproject.org/ENCBS476WAQ/


title: ChIP-BS_H3K9me2_2i_2

description: ChIP-BS-Seq

source_name: ChIP-BS H3K9me2 2i 2

value: anti-H3K9me2; Abcam ab1220


title: ChIP-BS_H3K9me2_Ser_2

description: ChIP-BS-Seq

source_name: ChIP-BS H3K9me2 Ser 2


title: ChIP-BS_H3K9me2_2i_1

description: ChIP-BS-Seq

source_name: ChIP-BS H3K9me2 2i 1


title: shRNA RNA-seq from K562 (ENCLB609FQX)

description:
https://www.encodeproject.org/experiments/ENCSR627NVU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RBM15 in K562 cells followed by RNA-seq. (RBM15-LV08)
experiment encode accession: ENCSR627NVU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB609FQX
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/ec17341b-0cdb-4c3e-b596-2d232a30ab87/@@download/attachment/L-RBM15-LV08-44.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM15. (RBM15-LV08-44)

value: 53 year

value: ENCBS021PJN at ENCODE; https://www.encodeproject.org/ENCBS021PJN/