title: shRNA RNA-seq from HepG2 (ENCLB098ZFJ)

description:
https://www.encodeproject.org/experiments/ENCSR398LZW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SND1 in HepG2 cells followed by RNA-seq. (SND1 BGHLV14)
experiment encode accession: ENCSR398LZW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB098ZFJ
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/4e1f8a2c-f45a-454d-8206-e87072aabca3/@@download/attachment/L-SND1_BGHLV14-52.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SND1. (SND1_BGHLV14-52)

value: child

value: hepatocellular carcinoma

value: ENCBS183QJT at ENCODE; https://www.encodeproject.org/ENCBS183QJT/


title: shRNA RNA-seq from K562 (ENCLB618XXP)

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/ENCSR373KOF/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FUBP3 in K562 cells followed by RNA-seq. (FUBP3-LV08)
experiment encode accession: ENCSR373KOF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB618XXP
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 FUBP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fe5016d5-fd4f-4b35-9a07-1e95a40d68ed/@@download/attachment/L-FUBP3-LV08-28.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against FUBP3. (FUBP3-LV08-28)

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

value: Brenton Graveley, UConn

tag: link

value: ENCBS719YVT at ENCODE; https://www.encodeproject.org/ENCBS719YVT/

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 (ENCLB401SBG)

description:
https://www.encodeproject.org/experiments/ENCSR485ZTC/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX21 in HepG2 cells followed by RNA-seq. (DDX21 BGHLV14)
experiment encode accession: ENCSR485ZTC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB401SBG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX21

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/170ea428-0d48-43c8-8c70-ca0ad64b717e/@@download/attachment/L-DDX21_BGHLV14-10.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX21. (DDX21_BGHLV14-10)

value: 15 year

value: male

value: ENCBS116IFC at ENCODE; https://www.encodeproject.org/ENCBS116IFC/

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 (ENCLB267EEQ)

description:
https://www.encodeproject.org/experiments/ENCSR361LBE/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against NCBP2 in K562 cells followed by RNA-seq. (NCBP2-LV08)
experiment encode accession: ENCSR361LBE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB267EEQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting NCBP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/894dc7d4-c1be-4a7a-8432-14b7a22899a0/@@download/attachment/L-NCBP2-LV08-36.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NCBP2. (NCBP2-LV08-36)

value: ENCBS630NVQ at ENCODE; https://www.encodeproject.org/ENCBS630NVQ/


title: shRNA RNA-seq from K562 (ENCLB005TNU)

description:
https://www.encodeproject.org/experiments/ENCSR361LBE/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against NCBP2 in K562 cells followed by RNA-seq. (NCBP2-LV08)
experiment encode accession: ENCSR361LBE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB005TNU
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/4096ea98-ef05-47f1-a0ff-3828c769dcae/@@download/attachment/L-NCBP2-LV08-35.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against NCBP2. (NCBP2-LV08-35)

value: ENCBS992SGT at ENCODE; https://www.encodeproject.org/ENCBS992SGT/


city: San Francisco

first: UCSF-UBC

last: CENTER

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: miRNA-Seq analysis of peripheral cd4 naive from TC014 (m00735) using Illumina Genome Analyzer IIx
library name: m00735
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN N/A
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: N/A ug
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN =>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

extract_protocol: library construction protocol: Refer to document 'miRNA3 - Plate Format miRNA Library Construction' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

tag: body site

value: Blood

tag: histological type

value: CD4 naive cell

tag: is tumor

value: No

value: primary cell


title: shRNA RNA-seq from K562 (ENCLB877HUQ)

description:
https://www.encodeproject.org/experiments/ENCSR344XID/
***************
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: ENCSR344XID
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB877HUQ
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/f7512bcd-eb7f-4b6e-89af-7890d50d8cc0/@@download/attachment/L-nontarget-LV08-2-1.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: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

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

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


title: shRNA RNA-seq from K562 (ENCLB393HBX)

description:
https://www.encodeproject.org/experiments/ENCSR344XID/
***************
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: ENCSR344XID
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB393HBX
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/296c2c90-2284-438f-9b96-e5b5b95cdce2/@@download/attachment/L-nontarget-LV08-2-2.pdf

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

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

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


title: shRNA RNA-seq from K562 (ENCLB055XDG)

description:
https://www.encodeproject.org/experiments/ENCSR342EDG/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against U2AF1 in K562 cells followed by RNA-seq. (U2AF1-LV08)
experiment encode accession: ENCSR342EDG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB055XDG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting U2AF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a71f7931-cbab-43b9-86ea-ccb96330f4b9/@@download/attachment/L-U2AF1-LV08-62.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against U2AF1. (U2AF1-LV08-62)

value: ENCBS222CHH at ENCODE; https://www.encodeproject.org/ENCBS222CHH/


title: shRNA RNA-seq from HepG2 (ENCLB039YQU)

description:
https://www.encodeproject.org/experiments/ENCSR410UHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPS10 in HepG2 cells followed by RNA-seq. (RPS10 BGHLV14)
experiment encode accession: ENCSR410UHJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB039YQU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RPS10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f2c02994-308c-443f-b754-c3fb95f765f3/@@download/attachment/L-RPS10_BGHLV14-41.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS10. (RPS10_BGHLV14-41)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS995NXW at ENCODE; https://www.encodeproject.org/ENCBS995NXW/

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 (ENCLB303VZR)

description:
https://www.encodeproject.org/experiments/ENCSR342EDG/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against U2AF1 in K562 cells followed by RNA-seq. (U2AF1-LV08)
experiment encode accession: ENCSR342EDG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB303VZR
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/22150eb4-8deb-4968-a49c-dd9151ddea69/@@download/attachment/L-U2AF1-LV08-61.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against U2AF1. (U2AF1-LV08-61)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS843LHE at ENCODE; https://www.encodeproject.org/ENCBS843LHE/


title: shRNA RNA-seq from HepG2 (ENCLB211ZUJ)

description:
https://www.encodeproject.org/experiments/ENCSR330YOU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against QKI in HepG2 cells followed by RNA-seq. (QKI-BGHLV12)
experiment encode accession: ENCSR330YOU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB211ZUJ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ce0d97ff-b118-4a34-ba1c-5a445faa24f6/@@download/attachment/L-QKI-BGHLV12-61.pdf

value: QKI

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against QKI. (QKI-BGHLV12-61)

value: ENCBS544WQP at ENCODE; https://www.encodeproject.org/ENCBS544WQP/


title: shRNA RNA-seq from K562 (ENCLB292HMQ)

description:
https://www.encodeproject.org/experiments/ENCSR338CON/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against AKAP1 in K562 cells followed by RNA-seq. (AKAP1-LV08)
experiment encode accession: ENCSR338CON
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB292HMQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting AKAP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1c88f119-0bfa-4690-92ef-f732f0494886/@@download/attachment/L-AKAP1-LV08-4.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP1. (AKAP1-LV08-4)

value: ENCBS014ZUQ at ENCODE; https://www.encodeproject.org/ENCBS014ZUQ/

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

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


title: shRNA RNA-seq from K562 (ENCLB659HCY)

description:
https://www.encodeproject.org/experiments/ENCSR338CON/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against AKAP1 in K562 cells followed by RNA-seq. (AKAP1-LV08)
experiment encode accession: ENCSR338CON
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB659HCY
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/48ba1e3e-d1e1-4b9f-abce-a99330b2729a/@@download/attachment/L-AKAP1-LV08-3.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP1. (AKAP1-LV08-3)

value: ENCBS132EBC at ENCODE; https://www.encodeproject.org/ENCBS132EBC/


title: shRNA RNA-seq from HepG2 (ENCLB091TPK)

description:
https://www.encodeproject.org/experiments/ENCSR330YOU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against QKI in HepG2 cells followed by RNA-seq. (QKI-BGHLV12)
experiment encode accession: ENCSR330YOU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB091TPK
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/3232670d-00fe-4299-8273-b18acf01e133/@@download/attachment/L-QKI-BGHLV12-62.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against QKI. (QKI-BGHLV12-62)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS158NUW at ENCODE; https://www.encodeproject.org/ENCBS158NUW/

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 (ENCLB048ACT)

description:
https://www.encodeproject.org/experiments/ENCSR310VND/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RECQL in K562 cells followed by RNA-seq. (RECQL-LV08)
experiment encode accession: ENCSR310VND
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB048ACT
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8ec56e90-1495-42b3-a4a0-361a498d593d/@@download/attachment/L-RECQL-LV08-49.pdf

value: RECQL

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RECQL. (RECQL-LV08-49)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS555BIW at ENCODE; https://www.encodeproject.org/ENCBS555BIW/


title: shRNA RNA-seq from HepG2 (ENCLB393XCE)

description:
https://www.encodeproject.org/experiments/ENCSR313CHR/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF4B in HepG2 cells followed by RNA-seq. (EIF4B-BGHLV12)
experiment encode accession: ENCSR313CHR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB393XCE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/d4084a86-fa9b-491f-8393-3ab02596d5ee/@@download/attachment/L-EIF4B-BGHLV12-23.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4B. (EIF4B-BGHLV12-23)

value: ENCBS275NVW at ENCODE; https://www.encodeproject.org/ENCBS275NVW/


title: shRNA RNA-seq from HepG2 (ENCLB159DRV)

description:
https://www.encodeproject.org/experiments/ENCSR318HAT/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RBM34 in HepG2 cells followed by RNA-seq. (RBM34 BGHLV14)
experiment encode accession: ENCSR318HAT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB159DRV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RBM34

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6d96a876-9cf7-4e8d-b7ab-47fec1dc8479/@@download/attachment/L-RBM34_BGHLV14-39.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM34. (RBM34_BGHLV14-39)

value: 15 year

value: child

value: ENCBS741YEQ at ENCODE; https://www.encodeproject.org/ENCBS741YEQ/


title: shRNA RNA-seq from K562 (ENCLB346MZQ)

description:
https://www.encodeproject.org/experiments/ENCSR373KOF/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FUBP3 in K562 cells followed by RNA-seq. (FUBP3-LV08)
experiment encode accession: ENCSR373KOF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB346MZQ
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/04c44570-59de-4df2-811e-3d9fbf516a43/@@download/attachment/L-FUBP3-LV08-27.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FUBP3. (FUBP3-LV08-27)

value: ENCBS060HRB at ENCODE; https://www.encodeproject.org/ENCBS060HRB/

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 (ENCLB913UJX)

description:
https://www.encodeproject.org/experiments/ENCSR318HAT/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RBM34 in HepG2 cells followed by RNA-seq. (RBM34 BGHLV14)
experiment encode accession: ENCSR318HAT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB913UJX
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/227e7722-fbd3-4693-ba1a-fdd7bd5ce8fd/@@download/attachment/L-RBM34_BGHLV14-40.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM34. (RBM34_BGHLV14-40)

value: male

value: hepatocellular carcinoma

value: ENCBS148AQX at ENCODE; https://www.encodeproject.org/ENCBS148AQX/

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 (ENCLB826MKC)

description:
https://www.encodeproject.org/experiments/ENCSR313CHR/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF4B in HepG2 cells followed by RNA-seq. (EIF4B-BGHLV12)
experiment encode accession: ENCSR313CHR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB826MKC
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/6592ad19-8268-483e-8225-1dcf933dbd50/@@download/attachment/L-EIF4B-BGHLV12-24.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4B. (EIF4B-BGHLV12-24)

value: Brenton Graveley, UConn

value: ENCBS656AXT at ENCODE; https://www.encodeproject.org/ENCBS656AXT/


title: shRNA RNA-seq from HepG2 (ENCLB962LBA)

description:
https://www.encodeproject.org/experiments/ENCSR295XKC/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against GTF2F1 in HepG2 cells followed by RNA-seq. (GTF2F1 BGHLV14)
experiment encode accession: ENCSR295XKC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB962LBA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting GTF2F1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5030e1a1-da35-48e7-84d7-0dd41dcb829a/@@download/attachment/L-GTF2F1_BGHLV14-23.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GTF2F1. (GTF2F1_BGHLV14-23)

value: 15 year

value: ENCBS824QCP at ENCODE; https://www.encodeproject.org/ENCBS824QCP/


title: shRNA RNA-seq from K562 (ENCLB638TBP)

description:
https://www.encodeproject.org/experiments/ENCSR246SOU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against G3BP2 in K562 cells followed by RNA-seq. (G3BP2-LV08)
experiment encode accession: ENCSR246SOU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB638TBP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 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/3c5471cd-693f-4b91-9aef-09d5fe78e762/@@download/attachment/L-G3BP2-LV08-33.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against G3BP2. (G3BP2-LV08-33)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS822TRA at ENCODE; https://www.encodeproject.org/ENCBS822TRA/


title: shRNA RNA-seq from K562 (ENCLB863NAD)

description:
https://www.encodeproject.org/experiments/ENCSR253DCB/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against ASCC1 in K562 cells followed by RNA-seq. (ASCC1-LV08)
experiment encode accession: ENCSR253DCB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB863NAD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting ASCC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b4c4890f-b296-4dbf-85c6-fc909472ebc7/@@download/attachment/L-ASCC1-LV08-5.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against ASCC1. (ASCC1-LV08-5)

value: ENCBS904ULB at ENCODE; https://www.encodeproject.org/ENCBS904ULB/

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

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


title: shRNA RNA-seq from K562 (ENCLB657YMB)

description:
https://www.encodeproject.org/experiments/ENCSR310VND/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RECQL in K562 cells followed by RNA-seq. (RECQL-LV08)
experiment encode accession: ENCSR310VND
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB657YMB
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/9eb01628-0ba3-4bc4-b3cb-a2b19ac4483b/@@download/attachment/L-RECQL-LV08-50.pdf

value: RECQL

value: RNA-seq on K562 cells treated with an shRNA knockdown against RECQL. (RECQL-LV08-50)

value: ENCBS152WCA at ENCODE; https://www.encodeproject.org/ENCBS152WCA/


title: shRNA RNA-seq from K562 (ENCLB817RVR)

description:
https://www.encodeproject.org/experiments/ENCSR302JQA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against IGF2BP3 in K562 cells followed by RNA-seq. (IGF2BP3-LV11)
experiment encode accession: ENCSR302JQA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB817RVR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting IGF2BP3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8ff72c3a-2f7d-480d-a12c-0852160e3b50/@@download/attachment/L-IGF2BP3-LV11-19.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP3. (IGF2BP3-LV11-19)

value: Brenton Graveley, UConn

value: ENCBS275HBP at ENCODE; https://www.encodeproject.org/ENCBS275HBP/


title: shRNA RNA-seq from K562 (ENCLB425MTV)

description:
https://www.encodeproject.org/experiments/ENCSR302JQA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against IGF2BP3 in K562 cells followed by RNA-seq. (IGF2BP3-LV11)
experiment encode accession: ENCSR302JQA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB425MTV
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/c6948207-a258-4c59-8469-49f9bf9c400c/@@download/attachment/L-IGF2BP3-LV11-20.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP3. (IGF2BP3-LV11-20)

value: ENCBS198YII at ENCODE; https://www.encodeproject.org/ENCBS198YII/


title: shRNA RNA-seq from HepG2 (ENCLB392DCN)

description:
https://www.encodeproject.org/experiments/ENCSR230ORC/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against CIRBP in HepG2 cells followed by RNA-seq. (CIRBP-BGHLV12)
experiment encode accession: ENCSR230ORC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB392DCN
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/65ed6b55-1228-4f6b-bc28-0ecf04bb4dd4/@@download/attachment/L-CIRBP-BGHLV12-7.pdf

value: CIRBP

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CIRBP. (CIRBP-BGHLV12-7)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS530LIV at ENCODE; https://www.encodeproject.org/ENCBS530LIV/

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 (ENCLB781BJK)

description:
https://www.encodeproject.org/experiments/ENCSR237YZT/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-01-02)
experiment encode accession: ENCSR237YZT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB781BJK
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0c566775-ed1c-41f0-b1b8-6a0e7de612be/@@download/attachment/L-NT-BGHLV12-02.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target (NT-BGHLV12-02-94)

value: ENCBS638ASL at ENCODE; https://www.encodeproject.org/ENCBS638ASL/


title: shRNA RNA-seq from K562 (ENCLB613NXQ)

description:
https://www.encodeproject.org/experiments/ENCSR201WFU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RDBP in K562 cells followed by RNA-seq. (RDBP-LV11)
experiment encode accession: ENCSR201WFU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB613NXQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 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/f5d9c4dd-ec6a-438e-b127-9a372f324e3e/@@download/attachment/L-RDBP-LV11-46.pdf

value: NELFE

value: RNA-seq on K562 cells treated with an shRNA knockdown against RDBP. (RDBP-LV11-46)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS450ITK at ENCODE; https://www.encodeproject.org/ENCBS450ITK/

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 (ENCLB764JNY)

description:
https://www.encodeproject.org/experiments/ENCSR193FFA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against ASCC1 in HepG2 cells followed by RNA-seq. (ASCC1-BGHLV12)
experiment encode accession: ENCSR193FFA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB764JNY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ASCC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f8c74427-35f0-4c50-8c87-4e2eb8ccd3ad/@@download/attachment/L-ASCC--BGHLV12-6.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ASCC1. (ASCC--BGHLV12-6)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS869GQP at ENCODE; https://www.encodeproject.org/ENCBS869GQP/


title: shRNA RNA-seq from K562 (ENCLB714ABY)

description:
https://www.encodeproject.org/experiments/ENCSR256PLH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against QKI in K562 cells followed by RNA-seq. (QKI-LV08)
experiment encode accession: ENCSR256PLH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB714ABY
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3824b2d0-ec10-4f9b-b95a-f7fa5d8c6110/@@download/attachment/L-QKI-LV08-40.pdf

value: QKI

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against QKI. (QKI-LV08-40)

value: ENCBS960IYL at ENCODE; https://www.encodeproject.org/ENCBS960IYL/


title: shRNA RNA-seq from K562 (ENCLB781JZS)

description:
https://www.encodeproject.org/experiments/ENCSR256PLH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against QKI in K562 cells followed by RNA-seq. (QKI-LV08)
experiment encode accession: ENCSR256PLH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB781JZS
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/2a6309ed-1b27-4ccd-ac72-3f34d0efcadc/@@download/attachment/L-QKI-LV08-39.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against QKI. (QKI-LV08-39)

value: 53 year

value: adult

value: ENCBS152XKV at ENCODE; https://www.encodeproject.org/ENCBS152XKV/


title: shRNA RNA-seq from HepG2 (ENCLB560QUJ)

description:
https://www.encodeproject.org/experiments/ENCSR300IEW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX24 in HepG2 cells followed by RNA-seq. (DDX24 BGHLV14)
experiment encode accession: ENCSR300IEW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB560QUJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX24

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/691e8baa-e077-434b-8aa4-c2779b72749b/@@download/attachment/L-DDX24_BGHLV14-12.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX24. (DDX24_BGHLV14-12)

value: Brenton Graveley, UConn

value: ENCBS664MRR at ENCODE; https://www.encodeproject.org/ENCBS664MRR/

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: WGBS from H1-hESC (ENCLB167QQW)

description:
https://www.encodeproject.org/experiments/ENCSR617FKV/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing H1-hESC
experiment encode accession: ENCSR617FKV
assay title: WGBS
assembly: GRCh38
encode release date: 2015-10-13
lab: Richard Myers, HAIB
library encode accession: ENCLB167QQW

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

value: Embryonic stem cells

value: unknown

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS345JIP at ENCODE; https://www.encodeproject.org/ENCBS345JIP/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771

value: WiCell sample source; http://www.wicell.org


title: shRNA RNA-seq from HepG2 (ENCLB224EFN)

description:
https://www.encodeproject.org/experiments/ENCSR295XKC/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against GTF2F1 in HepG2 cells followed by RNA-seq. (GTF2F1 BGHLV14)
experiment encode accession: ENCSR295XKC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB224EFN
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/59761230-ae07-4f3e-abcc-ab2c5eee930e/@@download/attachment/L-GTF2F1_BGHLV14-24.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GTF2F1. (GTF2F1_BGHLV14-24)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS466PDL at ENCODE; https://www.encodeproject.org/ENCBS466PDL/


title: shRNA RNA-seq from K562 (ENCLB501PDX)

description:
https://www.encodeproject.org/experiments/ENCSR246SOU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against G3BP2 in K562 cells followed by RNA-seq. (G3BP2-LV08)
experiment encode accession: ENCSR246SOU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB501PDX
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/163527cd-c432-450d-96ed-1297e381d52b/@@download/attachment/L-G3BP2-LV08-34.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against G3BP2. (G3BP2-LV08-34)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS964MCW at ENCODE; https://www.encodeproject.org/ENCBS964MCW/

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 (ENCLB792HAC)

description:
https://www.encodeproject.org/experiments/ENCSR148MQK/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SF3B4 in HepG2 cells followed by RNA-seq. (SF3B4-BGHLV12)
experiment encode accession: ENCSR148MQK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB792HAC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SF3B4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d1f0cee0-7de3-4230-8822-a6b4e0001610/@@download/attachment/L-SF3B4-BGHLV12-73.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3B4. (SF3B4-BGHLV12-73)

value: ENCBS650SLE at ENCODE; https://www.encodeproject.org/ENCBS650SLE/

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 (ENCLB278CGF)

description:
https://www.encodeproject.org/experiments/ENCSR300IEW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX24 in HepG2 cells followed by RNA-seq. (DDX24 BGHLV14)
experiment encode accession: ENCSR300IEW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR003EKR
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB278CGF
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/9a936daa-4fae-45a5-95e5-7533cebbd4c2/@@download/attachment/L-DDX24_BGHLV14-11.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX24. (DDX24_BGHLV14-11)

value: 15 year

value: child

value: ENCBS721RXI at ENCODE; https://www.encodeproject.org/ENCBS721RXI/


title: shRNA RNA-seq from HepG2 (ENCLB807KAY)

description:
https://www.encodeproject.org/experiments/ENCSR237YZT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-01-02)
experiment encode accession: ENCSR237YZT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB807KAY
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/b2fd1115-44f3-4b38-9b75-050ac3272e78/@@download/attachment/L-NT-BGHLV12-01.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target (NT-BGHLV12-01-93)

value: male

value: hepatocellular carcinoma

value: ENCBS623BZF at ENCODE; https://www.encodeproject.org/ENCBS623BZF/


title: shRNA RNA-seq from HepG2 (ENCLB581PTX)

description:
https://www.encodeproject.org/experiments/ENCSR147ZBD/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX6 in HepG2 cells followed by RNA-seq. (DDX6-BGHLV12)
experiment encode accession: ENCSR147ZBD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB581PTX
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/406f4fda-ffcd-459f-8a10-a4180f33c089/@@download/attachment/L-DDX6-BGHLV12-18.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX6. (DDX6-BGHLV12-18)

value: Brenton Graveley, UConn

value: ENCBS924KDO at ENCODE; https://www.encodeproject.org/ENCBS924KDO/


title: shRNA RNA-seq from K562 (ENCLB447KVC)

description:
https://www.encodeproject.org/experiments/ENCSR149DMY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RBM25 in K562 cells followed by RNA-seq. (RBM25-LV08)
experiment encode accession: ENCSR149DMY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB447KVC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RBM25

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/322bb771-bb82-474c-b957-c543eb40bc45/@@download/attachment/L-RBM25-LV08-46.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM25. (RBM25-LV08-46)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS994NNW at ENCODE; https://www.encodeproject.org/ENCBS994NNW/

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

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


title: shRNA RNA-seq from K562 (ENCLB734TNI)

description:
https://www.encodeproject.org/experiments/ENCSR201WFU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RDBP in K562 cells followed by RNA-seq. (RDBP-LV11)
experiment encode accession: ENCSR201WFU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB734TNI
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/80e38585-db55-4999-bb2b-59a9324f781b/@@download/attachment/L-RDBP-LV11-45.pdf

value: NELFE

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RDBP. (RDBP-LV11-45)

value: ENCBS530JOQ at ENCODE; https://www.encodeproject.org/ENCBS530JOQ/


title: shRNA RNA-seq from K562 (ENCLB468ZAX)

description:
https://www.encodeproject.org/experiments/ENCSR253DCB/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against ASCC1 in K562 cells followed by RNA-seq. (ASCC1-LV08)
experiment encode accession: ENCSR253DCB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB468ZAX
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/5908a996-23f2-4cb4-8b7a-d7b35ebda043/@@download/attachment/L-ASCC1-LV08-6.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ASCC1. (ASCC1-LV08-6)

value: ENCBS551TRA at ENCODE; https://www.encodeproject.org/ENCBS551TRA/


title: shRNA RNA-seq from HepG2 (ENCLB713YAZ)

description:
https://www.encodeproject.org/experiments/ENCSR193FFA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against ASCC1 in HepG2 cells followed by RNA-seq. (ASCC1-BGHLV12)
experiment encode accession: ENCSR193FFA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB713YAZ
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/d6d665b1-1e1c-461b-a2cf-72313cf04820/@@download/attachment/L-ASCC1-BGHLV12-5.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ASCC1. (ASCC1-BGHLV12-5)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS985WFY at ENCODE; https://www.encodeproject.org/ENCBS985WFY/

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 (ENCLB419TCX)

description:
https://www.encodeproject.org/experiments/ENCSR134JRE/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TARDBP in K562 cells followed by RNA-seq. (TARDBP-LV11)
experiment encode accession: ENCSR134JRE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB419TCX
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/755cfd2b-a770-45e3-88f0-a8e82b4f4df3/@@download/attachment/L-TARDBP-LV11-57.pdf

value: TARDBP

value: RNA-seq on K562 cells treated with an shRNA knockdown against TARDBP. (TARDBP-LV11-57)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS512JXB at ENCODE; https://www.encodeproject.org/ENCBS512JXB/


title: shRNA RNA-seq from HepG2 (ENCLB123XMP)

description:
https://www.encodeproject.org/experiments/ENCSR185JGT/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SLTM in HepG2 cells followed by RNA-seq. (SLTM BGHLV14)
experiment encode accession: ENCSR185JGT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB123XMP
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5734f3fa-ba6f-4eb6-8a11-75f67eb3f3ac/@@download/attachment/L-SLTM_BGHLV14-47.pdf

value: SLTM

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SLTM. (SLTM_BGHLV14-47)

value: ENCBS738ADY at ENCODE; https://www.encodeproject.org/ENCBS738ADY/


title: shRNA RNA-seq from HepG2 (ENCLB242LJF)

description:
https://www.encodeproject.org/experiments/ENCSR147ZBD/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX6 in HepG2 cells followed by RNA-seq. (DDX6-BGHLV12)
experiment encode accession: ENCSR147ZBD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB242LJF
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/4df2b79a-aec2-4b11-9a2c-bf77ef601ad4/@@download/attachment/L-DDX6-BGHLV12-17.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX6. (DDX6-BGHLV12-17)

value: 15 year

value: child

value: male

value: ENCBS798PZJ at ENCODE; https://www.encodeproject.org/ENCBS798PZJ/


title: shRNA RNA-seq from HepG2 (ENCLB157NQV)

description:
https://www.encodeproject.org/experiments/ENCSR230ORC/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against CIRBP in HepG2 cells followed by RNA-seq. (CIRBP-BGHLV12)
experiment encode accession: ENCSR230ORC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB157NQV
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/6d8af0d5-f549-4521-9ff3-3a876d407f64/@@download/attachment/L-CIRBP-BGHLV12-8.pdf

value: CIRBP

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CIRBP. (CIRBP-BGHLV12-8)

value: hepatocellular carcinoma

value: ENCBS263MSZ at ENCODE; https://www.encodeproject.org/ENCBS263MSZ/

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 (ENCLB076ADA)

description:
https://www.encodeproject.org/experiments/ENCSR148MQK/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SF3B4 in HepG2 cells followed by RNA-seq. (SF3B4-BGHLV12)
experiment encode accession: ENCSR148MQK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB076ADA
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/c684341c-775f-44d1-b0e9-5994e54e8185/@@download/attachment/L-SF3B4-BGHLV12-74.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SF3B4. (SF3B4-BGHLV12-74)

value: Brenton Graveley, UConn

value: ENCBS895EOS at ENCODE; https://www.encodeproject.org/ENCBS895EOS/


title: shRNA RNA-seq from K562 (ENCLB315MQB)

description:
https://www.encodeproject.org/experiments/ENCSR134JRE/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TARDBP in K562 cells followed by RNA-seq. (TARDBP-LV11)
experiment encode accession: ENCSR134JRE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB315MQB
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/f4c1c672-d26c-4a86-839b-615681f59108/@@download/attachment/L-TARDBP-LV11-58.pdf

value: TARDBP

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against TARDBP. (TARDBP-LV11-58)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS011IBX at ENCODE; https://www.encodeproject.org/ENCBS011IBX/

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 (ENCLB871VGV)

description:
https://www.encodeproject.org/experiments/ENCSR185JGT/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SLTM in HepG2 cells followed by RNA-seq. (SLTM BGHLV14)
experiment encode accession: ENCSR185JGT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB871VGV
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/a3fd659f-514c-4726-9fee-eb769176cf3f/@@download/attachment/L-SLTM_BGHLV14-48.pdf

value: SLTM

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SLTM. (SLTM_BGHLV14-48)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS668RFG at ENCODE; https://www.encodeproject.org/ENCBS668RFG/


title: shRNA RNA-seq from K562 (ENCLB005FQE)

description:
https://www.encodeproject.org/experiments/ENCSR113HRG/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF9 in K562 cells followed by RNA-seq. (SRSF9-LV11)
experiment encode accession: ENCSR113HRG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB005FQE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SRSF9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0a2c2110-2244-4b8e-8bf4-8fb9808833de/@@download/attachment/L-SRSF9-LV11-55.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF9. (SRSF9-LV11-55)

value: Brenton Graveley, UConn

value: ENCBS851WPL at ENCODE; https://www.encodeproject.org/ENCBS851WPL/


title: shRNA RNA-seq from K562 (ENCLB958PSD)

description:
https://www.encodeproject.org/experiments/ENCSR149DMY/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RBM25 in K562 cells followed by RNA-seq. (RBM25-LV08)
experiment encode accession: ENCSR149DMY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB958PSD
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/31f605f7-ccb6-4921-a4d9-dec88b712c06/@@download/attachment/L-RBM25-LV08-45.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBM25. (RBM25-LV08-45)

value: 53 year

value: ENCBS739ZIJ at ENCODE; https://www.encodeproject.org/ENCBS739ZIJ/


title: shRNA RNA-seq from K562 (ENCLB807NXT)

description:
https://www.encodeproject.org/experiments/ENCSR129RWD/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (Nontarget-LV11)
experiment encode accession: ENCSR129RWD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB807NXT
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/04b66118-6efe-4a7f-8b6e-82b74284292a/@@download/attachment/L-nontarget-LV11-2.pdf

value: Control

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (nontarget-LV11-2)

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS280PHL at ENCODE; https://www.encodeproject.org/ENCBS280PHL/


title: shRNA RNA-seq from K562 (ENCLB079YXP)

description:
https://www.encodeproject.org/experiments/ENCSR119QWQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX6 in K562 cells followed by RNA-seq. (DDX6-LV08)
experiment encode accession: ENCSR119QWQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB079YXP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c3f18a32-a115-447f-a891-321d63936aaa/@@download/attachment/L-DDX6-LV08-18.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX6. (DDX6-LV08-18)

value: ENCBS014ZBK at ENCODE; https://www.encodeproject.org/ENCBS014ZBK/

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

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


title: shRNA RNA-seq from K562 (ENCLB685TGO)

description:
https://www.encodeproject.org/experiments/ENCSR113HRG/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF9 in K562 cells followed by RNA-seq. (SRSF9-LV11)
experiment encode accession: ENCSR113HRG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB685TGO
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/2c6a5b39-cd94-49ad-b523-d6a8e7efe60f/@@download/attachment/L-SRSF9-LV11-56.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF9. (SRSF9-LV11-56)

value: ENCBS877QTV at ENCODE; https://www.encodeproject.org/ENCBS877QTV/


title: shRNA RNA-seq from K562 (ENCLB751ONS)

description:
https://www.encodeproject.org/experiments/ENCSR129RWD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (Nontarget-LV11)
experiment encode accession: ENCSR129RWD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB751ONS
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/51577bcb-f38b-4274-9702-5f1a07092515/@@download/attachment/L-Nontarget-LV11-1.pdf

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (Nontarget-LV11-1)

value: Brenton Graveley, UConn

value: ENCBS460WQH at ENCODE; https://www.encodeproject.org/ENCBS460WQH/


title: shRNA RNA-seq from HepG2 (ENCLB042LJY)

description:
https://www.encodeproject.org/experiments/ENCSR081QQH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against ZRANB2 in HepG2 cells followed by RNA-seq. (ZRANB2 BGHLV14)
experiment encode accession: ENCSR081QQH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB042LJY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ZRANB2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f329dfc7-2fbc-4dbb-ac94-f0be9029555a/@@download/attachment/L-ZRANB2_27_BGHLV14-72.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZRANB2. (ZRANB2_27_BGHLV14-72)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS074GMS at ENCODE; https://www.encodeproject.org/ENCBS074GMS/

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 (ENCLB148NQP)

description:
https://www.encodeproject.org/experiments/ENCSR081XRA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SF3B4 in K562 cells followed by RNA-seq. (SF3B4-LV08)
experiment encode accession: ENCSR081XRA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB148NQP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SF3B4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/09406c0b-9594-4463-acb5-4c64c001e73b/@@download/attachment/L-SF3B4-LV08-52.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SF3B4. (SF3B4-LV08-52)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS642DEU at ENCODE; https://www.encodeproject.org/ENCBS642DEU/


title: shRNA RNA-seq from HepG2 (ENCLB556DKZ)

description:
https://www.encodeproject.org/experiments/ENCSR094KBY/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF1 in HepG2 cells followed by RNA-seq. (SRSF1-BGHLV12)
experiment encode accession: ENCSR094KBY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB556DKZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SRSF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/958305e2-00ce-4877-88c4-7eac630060fc/@@download/attachment/L-SRSF1-BGHLV12-75.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF1. (SRSF1-BGHLV12-75)

value: Brenton Graveley, UConn

value: ENCBS066SXT at ENCODE; https://www.encodeproject.org/ENCBS066SXT/


title: M063.X1

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Read mapping was performed using TopHat version 2.0.9
Read counts per gene were quantified using HTSeq version 0.5.4
Read counts were normalised to 10Million reads per sample.
Genome_build: hg19
Supplementary_files_format_and_content: Read count table

source_name: Melanoma PDX

growth_protocol: Tumor fragments of ~5mm3 were used for subcutaneous transplantation into NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice, which was performed under anesthesia. Tumor outgrowth was measured twice a week with a caliper. Before reaching the maximum allowed tumor size of 1000 mm3, mice were sacrificed, tumors were removed and tumor pieces were snap-frozen and stored at -80°C for RNAseq analysis.

extract_protocol:
RNA isolated by Trizol, according to manufacturers protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: origin

value: Patient derived xenograft (PSX) sample

tag: derived from

value: BRAFV600E melanoma metastases

tag: host strain

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse

tag: drug resistance

value: Vemurafenib resistant

tag: passage

value: Human tumor samples after first passage in a mouse


title: shRNA RNA-seq from K562 (ENCLB503NZF)

description:
https://www.encodeproject.org/experiments/ENCSR081XRA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SF3B4 in K562 cells followed by RNA-seq. (SF3B4-LV08)
experiment encode accession: ENCSR081XRA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB503NZF
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/fae938f5-383f-484d-a5b5-ef840a00bfd4/@@download/attachment/L-SF3B4-LV08-51.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against SF3B4. (SF3B4-LV08-51)

value: ENCBS182SAO at ENCODE; https://www.encodeproject.org/ENCBS182SAO/

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

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


title: shRNA RNA-seq from K562 (ENCLB619RKQ)

description:
https://www.encodeproject.org/experiments/ENCSR119QWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX6 in K562 cells followed by RNA-seq. (DDX6-LV08)
experiment encode accession: ENCSR119QWQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB619RKQ
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/d1695351-2904-4dbe-9c51-8d2b816cbe86/@@download/attachment/L-DDX6-LV08-17.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX6. (DDX6-LV08-17)

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

value: ENCBS107DSY at ENCODE; https://www.encodeproject.org/ENCBS107DSY/


title: shRNA RNA-seq from HepG2 (ENCLB146QCP)

description:
https://www.encodeproject.org/experiments/ENCSR094KBY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF1 in HepG2 cells followed by RNA-seq. (SRSF1-BGHLV12)
experiment encode accession: ENCSR094KBY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB146QCP
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/7e22af64-08ab-4f7e-a9bb-d885ce9fae9d/@@download/attachment/L-SRSF1-BGHLV12-76.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF1. (SRSF1-BGHLV12-76)

value: 15 year

value: child

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

tag: lab

value: ENCBS148BFZ at ENCODE; https://www.encodeproject.org/ENCBS148BFZ/

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 (ENCLB961LKY)

description:
https://www.encodeproject.org/experiments/ENCSR079IPT/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TBRG4 in K562 cells followed by RNA-seq. (TBRG4-LV08)
experiment encode accession: ENCSR079IPT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB961LKY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TBRG4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1e21b32f-7b80-4a68-b58f-bd361ecdf6c2/@@download/attachment/L-TBRG4-LV08-59.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against TBRG4. (TBRG4-LV08-59)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

tag: link

value: ENCBS843ZIK at ENCODE; https://www.encodeproject.org/ENCBS843ZIK/


title: M048R2.X1

value: Patient derived xenograft (PSX) sample

value: BRAFV600E melanoma metastases

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse

value: Vemurafenib resistant

value: Human tumor samples after first passage in a mouse


title: M033.X1


title: shRNA RNA-seq from HepG2 (ENCLB745TJJ)

description:
https://www.encodeproject.org/experiments/ENCSR081QQH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against ZRANB2 in HepG2 cells followed by RNA-seq. (ZRANB2 BGHLV14)
experiment encode accession: ENCSR081QQH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB745TJJ
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/7c2ffabe-bfb0-43c1-b863-089a085f8ffd/@@download/attachment/L-ZRANB2_27_BGHLV14-71.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ZRANB2. (ZRANB2_27_BGHLV14-71)

value: 15 year

value: child

value: ENCBS213GIX at ENCODE; https://www.encodeproject.org/ENCBS213GIX/


title: M010.X1


title: Wildtype Replicate 3

city: Brisbane

first: Charles

middle: Cameron

last: Bell

state: Queensland

address: 37 Kent Street

country: Australia

institute: Mater Research

description: Differentiation performed in serum

data_processing:
RNAseq data was mapped to the Mus musculus reference genome (mm9) using TopHat2 and then TMAP (Kim et al. 2013). Tophat2 is required to map spliced junctions, while TMAP is designed for IonTorrent sequencing data and therefore performs better with IonTorrent data. Transcript counts were obtained by using HTSeq on the mapped data using the standard settings (Anders et al. 2013). Differential gene expression analysis was performed on the HTSeq output using DESeq2 using the standard settings (Love et al. 2014).
Genome_build: mm9
Supplementary_files_format_and_content: CSV file containing normalized counts for each replicate as calculated by DESeq2.

organism: Mus musculus

source_name: D4 Embryoid Bodies

growth_protocol: W9.5 and Evx1Δfs mESCs were maintained in 1000U/ml LIF on gelatanized plates in standard embryonic stem cell media at 37 degrees C and 5% CO2.

extract_protocol:
RNA was extracted from the embryoid bodies using Trizol according to manufactors instructions.
Total RNA was analysed on the Bioanalyser (Agilent) to confirm high RNA quality (Rinn value > 8). mRNA selection of total RNA was performed using Ambion Dynabeads© mRNA DIRECT Micro Purification Kit (#61021, Life Technologies). Barcoded RNAseq libraries were generated from the mRNA using the Ion Total RNAseq Kit v3 (#4475936) and Ion Xpress RNAseq Barcode 1-16 Kit (#4475485, Life Technologies). RNAseq libraries were sequenced on the Ion Proton sequencing instrument using the Ion P1 Hi-Q Sequencing 200 Kit with the Ion P1 v2 chip. Each sample was sequenced to a depth of least 15 million reads.

treatment_protocol: Cells were seeded at 2x104 cells/ml in embryonic stem cell media without LIF, as described previously (Bruce et al. 2007). Cells were then grown in this serum containing media for 4 days. Samples being compared were set up on the same day at the same time.

tag: tissue

value: Day 4 embryoid bodies

tag: cell type

value: W9.5 mESCs


title: Evx1Δfs Clone 14 Replicate 3

description: Differentiation performed in serum

value: W9.5 mESCs (derived from)


title: Control 2

city: Galveston

first: Muge

middle: N

last: Kuyumcu-Martinez

state: TX

address: 301 University Blvd

department: Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

data_processing:
Base calling was performed with CASAVA 1.8.2
Sequences were trimmed then aligned to the mm9 mouse genome using TOPHAT
Probabilities of isoform abundances were computed using MISO
Data was filtered based on a Bayes factor of at least 1
Additional details are included in Verma, S.K., Deshmukh, V., Liu, P., Nutter, C.A., Espejo, R., Hung, M.L., Wang, G.S., Yeo, G.W., and Kuyumcu-Martinez, M.N. (2013). Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling. The Journal of biological chemistry 288, 35372-35386.
genome build: mm9
processed data files format and content: Proccessed data is MISO analysis of skipped exons in comparisions between control and diabetic samples. The proccessed data format is tab deliniated .txt files.

source_name: Heart

extract_protocol:
Hearts were removed, cut into quarters, and flash frozen in liquid nitrogen. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were intraperitoneally injected at 8 weeks of age for 5 consequative days with either citrate buffer as a control or Streptozotocin suspended in citrate buffer to induce diabetes. Specific details on dose are included above.

tag: strain

value: Left Ventricle Heart

value: 12 weeks

tag: treatment

value: Mock treatment:IP injection of citrate buffer


title: shRNA RNA-seq from HepG2 (ENCLB373NLL)

description:
https://www.encodeproject.org/experiments/ENCSR074UZM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against G3BP1 in HepG2 cells followed by RNA-seq. (G3BP1-BGHLV12)
experiment encode accession: ENCSR074UZM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB373NLL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/8800f49d-3b0f-461f-a88e-6e12736e305a/@@download/attachment/L-G3BP1-BGHLV12-33.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against G3BP1. (G3BP1-BGHLV12-33)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS943ASZ at ENCODE; https://www.encodeproject.org/ENCBS943ASZ/

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: STZ:T1D 1

value: STZ treatment:IP injection of 70mg/kg streptezotocin 1/per day for 5 days.


title: Wildtype Replicate 2

description: Differentiation performed in serum


title: Wildtype Replicate 1

description: Differentiation performed in serum


title: shRNA RNA-seq from K562 (ENCLB191WPP)

description:
https://www.encodeproject.org/experiments/ENCSR066VOO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF1 in K562 cells followed by RNA-seq. (SRSF1-LV11)
experiment encode accession: ENCSR066VOO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB191WPP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SRSF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/94440443-4893-4cc7-86e0-cc4a3225f3a8/@@download/attachment/L-SRSF1-LV11-49.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF1. (SRSF1-LV11-49)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS655HQL at ENCODE; https://www.encodeproject.org/ENCBS655HQL/

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 (ENCLB354JUZ)

description:
https://www.encodeproject.org/experiments/ENCSR074UZM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against G3BP1 in HepG2 cells followed by RNA-seq. (G3BP1-BGHLV12)
experiment encode accession: ENCSR074UZM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR237YZT
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB354JUZ
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/2ad4f566-72d9-4b54-968b-22f8b9388760/@@download/attachment/L-G3BP1-BGHLV12-34.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against G3BP1. (G3BP1-BGHLV12-34)

value: 15 year

value: child

value: ENCBS995WFW at ENCODE; https://www.encodeproject.org/ENCBS995WFW/


title: Control 1

value: Left Ventricle Heart

value: 12 weeks

value: Mock treatment:IP injection of citrate buffer


title: Del3 (Evx1/Evx1asΔ2.6kb) Rep3

description: Differentiation performed in serum

growth_protocol: Evx1Δfs and Del#3 mESCs were maintained in 1000U/ml LIF on gelatanized plates in standard embryonic stem cell media at 37 degrees C and 5% CO2.

value: Day 4 embryoid bodies

value: W9.5 mESCs (derived from)


title: shRNA RNA-seq from K562 (ENCLB420CAX)

description:
https://www.encodeproject.org/experiments/ENCSR067LLB/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX24 in K562 cells followed by RNA-seq. (DDX24-LV08)
experiment encode accession: ENCSR067LLB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB420CAX
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX24

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d9ad0442-eea0-47a4-bfdd-b73c687e3689/@@download/attachment/L-DDX24-LV08-13.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX24. (DDX24-LV08-13)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS463GGK at ENCODE; https://www.encodeproject.org/ENCBS463GGK/


title: Del3 (Evx1/Evx1asΔ2.6kb) Rep2

description: Differentiation performed in serum


title: shRNA RNA-seq from K562 (ENCLB008YNW)

description:
https://www.encodeproject.org/experiments/ENCSR067LLB/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX24 in K562 cells followed by RNA-seq. (DDX24-LV08)
experiment encode accession: ENCSR067LLB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR913CAE
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB008YNW
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/a74456b7-7799-4e79-bd5f-db4bdebfc5ba/@@download/attachment/L-DDX24-LV08-14.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX24. (DDX24-LV08-14)

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS243YEC at ENCODE; https://www.encodeproject.org/ENCBS243YEC/


title: shRNA RNA-seq from K562 (ENCLB659IOG)

description:
https://www.encodeproject.org/experiments/ENCSR066VOO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF1 in K562 cells followed by RNA-seq. (SRSF1-LV11)
experiment encode accession: ENCSR066VOO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB659IOG
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/53dcc06e-7564-4e2b-b4e3-3fd2530667aa/@@download/attachment/L-SRSF1-LV11-50.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRSF1. (SRSF1-LV11-50)

value: ENCBS659SAO at ENCODE; https://www.encodeproject.org/ENCBS659SAO/

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 (ENCLB983JAP)

description:
https://www.encodeproject.org/experiments/ENCSR057GCF/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TIA1 in HepG2 cells followed by RNA-seq. (TIA1-BGHLV12)
experiment encode accession: ENCSR057GCF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB983JAP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/48044334-b501-45e8-86bd-8afe4ceb055b/@@download/attachment/L-TIA1-BGHLV12-88.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TIA1. (TIA1-BGHLV12-88)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS555IZN at ENCODE; https://www.encodeproject.org/ENCBS555IZN/

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 (ENCLB852CHH)

description:
https://www.encodeproject.org/experiments/ENCSR056QEW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against CIRBP in K562 cells followed by RNA-seq. (CIRBP-LV11)
experiment encode accession: ENCSR056QEW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR129RWD
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB852CHH
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7b50076c-75ff-467e-8f98-ffb709b7ab18/@@download/attachment/L-CIRBP-LV11-4.pdf

value: CIRBP

value: RNA-seq on K562 cells treated with an shRNA knockdown against CIRBP. (CIRBP-LV11-4)

value: 53 year

value: adult

value: Brenton Graveley, UConn

value: ENCBS370QIM at ENCODE; https://www.encodeproject.org/ENCBS370QIM/


title: STZ:T1D 3

value: Left Ventricle Heart

value: 12 weeks

value: STZ treatment:IP injection of 70mg/kg streptezotocin 1/per day for 5 days.


title: Evx1Δfs Clone 14 Replicate 2

description: Differentiation performed in serum

value: Day 4 embryoid bodies

value: W9.5 mESCs (derived from)


title: shRNA RNA-seq from HepG2 (ENCLB214ONW)

description:
https://www.encodeproject.org/experiments/ENCSR064DXG/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PTBP1 in HepG2 cells followed by RNA-seq. (PTBP1-BGHLV12)
experiment encode accession: ENCSR064DXG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR603TCV
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB214ONW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PTBP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/46e290c3-c1a8-4c18-9380-4f27fcd534dd/@@download/attachment/L-PTBP1-BGHLV12-60.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PTBP1. (PTBP1-BGHLV12-60)

value: 15 year

value: child

value: ENCBS757QFO at ENCODE; https://www.encodeproject.org/ENCBS757QFO/


title: Evx1Δfs Clone 14 Replicate 1

description: Differentiation performed in serum


title: STZ:T1D 2


title: shRNA RNA-seq from K562 (ENCLB271WKE)

description:
https://www.encodeproject.org/experiments/ENCSR047EEG/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PABPC4 in K562 cells followed by RNA-seq. (PABPC4-LV08)
experiment encode accession: ENCSR047EEG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB271WKE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PABPC4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1587c3ce-08bc-47d5-acf5-ffbeb2fa74d1/@@download/attachment/L-PABPC4-LV08-37.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PABPC4. (PABPC4-LV08-37)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS482NAM at ENCODE; https://www.encodeproject.org/ENCBS482NAM/

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

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


title: shRNA RNA-seq from K562 (ENCLB168GSM)

description:
https://www.encodeproject.org/experiments/ENCSR079IPT/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TBRG4 in K562 cells followed by RNA-seq. (TBRG4-LV08)
experiment encode accession: ENCSR079IPT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR344XID
encode release date: 2014-10-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB168GSM
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/1df655db-b0f7-414c-a3ba-18b283f2007d/@@download/attachment/L-TBRG4-LV08-60.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TBRG4. (TBRG4-LV08-60)

value: 53 year

value: adult

value: Brenton Graveley, UConn

value: ENCBS488IUR at ENCODE; https://www.encodeproject.org/ENCBS488IUR/


title: Evx1Δfs Clone 14 Rep3

description: Differentiation performed in serum

value: Day 4 embryoid bodies

value: W9.5 mESCs (derived from)


title: shRNA RNA-seq from HepG2 (ENCLB248CIZ)

description:
https://www.encodeproject.org/experiments/ENCSR030GZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TRA2A in HepG2 cells followed by RNA-seq. (TRA2A BGHLV14)
experiment encode accession: ENCSR030GZQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB248CIZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/211a5cd2-651d-4aae-b82d-6332c6a5c1fa/@@download/attachment/L-TRA2A_BGHLV14-61.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TRA2A. (TRA2A_BGHLV14-61)

value: male

value: hepatocellular carcinoma

value: ENCBS074IZI at ENCODE; https://www.encodeproject.org/ENCBS074IZI/

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

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