title: total RNA-seq from transverse colon (ENCLB584WWI)

description:
https://www.encodeproject.org/experiments/ENCSR630VJN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the transverse colon obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR630VJN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB584WWI
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1bf11642-f892-4104-b231-902808b3f16e/@@download/attachment/296163.pdf

value: transverse colon

value: tissue

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

value: 54 year

value: adult

value: Thomas Gingeras, CSHL

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

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


title: shRNA RNA-seq from HepG2 (ENCLB855MKK)

status: Public on Nov 08 2016

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR998MZP/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PRPF8 in HepG2 cells followed by RNA-seq. (PRPF8_BGHLV17)
experiment encode accession: ENCSR998MZP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB855MKK
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 HepG2 immortalized cell line transiently expressing shRNA targeting PRPF8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a962ac09-2937-4b01-92d2-8b8a674a18c4/@@download/attachment/L-PRPF8_BGHLV17_23.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PRPF8. (PRPF8_BGHLV17_23)

tag: biosample encode accession

tag: age

value: 15 year

tag: dev stage

value: child

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

tag: lab

value: Brenton Graveley, UConn

tag: link

value: ENCBS704TEF at ENCODE; https://www.encodeproject.org/ENCBS704TEF/

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: siRNA RNA-seq from K562 (ENCLB690PKX)

description:
https://www.encodeproject.org/experiments/ENCSR989NEA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting TBL1XR1.
experiment encode accession: ENCSR989NEA
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR561NXJ, ENCSR109YDL
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB690PKX
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting TBL1XR1

value: K562 cells treated with a siRNA knockdown against TBL1XR1, used in RNA-seq experiments.

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS701EZF at ENCODE; https://www.encodeproject.org/ENCBS701EZF/

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


title: siRNA RNA-seq from K562 (ENCLB543LRW)

description:
https://www.encodeproject.org/experiments/ENCSR989NEA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting TBL1XR1.
experiment encode accession: ENCSR989NEA
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR561NXJ, ENCSR109YDL
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB543LRW
size range: >200
spikeins used: /references/ENCSR866KGS/

value: immortalized cell line

value: adult

value: ENCBS699RAH at ENCODE; https://www.encodeproject.org/ENCBS699RAH/


title: shRNA RNA-seq from HepG2 (ENCLB014FHW)

description:
https://www.encodeproject.org/experiments/ENCSR629RUG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGHLV35)
experiment encode accession: ENCSR629RUG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB014FHW
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NSUN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b6e40288-dbbc-44a4-a915-efb59d9a9443/@@download/attachment/L-NSUN2_BGHLV35-30.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGHLV35-30)

value: 15 year

value: child

value: ENCBS794ZDV at ENCODE; https://www.encodeproject.org/ENCBS794ZDV/


title: shRNA RNA-seq from HepG2 (ENCLB577UVM)

description:
https://www.encodeproject.org/experiments/ENCSR995RPB/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SUPV3L1 in HepG2 cells followed by RNA-seq. (SUPV3L1_BGHLV17)
experiment encode accession: ENCSR995RPB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB577UVM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SUPV3L1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1ba29dcf-c446-4ddf-9ad9-0ce1d8b690a5/@@download/attachment/L-SUPV3L1_BGHLV17_32.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUPV3L1. (SUPV3L1_BGHLV17_32)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS505LMC at ENCODE; https://www.encodeproject.org/ENCBS505LMC/


title: shRNA RNA-seq from HepG2 (ENCLB052HNU)

description:
https://www.encodeproject.org/experiments/ENCSR992JGE/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against METAP2 in HepG2 cells followed by RNA-seq. (METAP2_BGHLV16)
experiment encode accession: ENCSR992JGE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB052HNU
size range: >200
spikeins used: /references/ENCSR449DXG/
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting METAP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/188d171e-7d79-4694-b846-dfe6424db4c0/@@download/attachment/L-METAP2_BGHLV16_34.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against METAP2. (METAP2_BGHLV16_34)

value: ENCBS554TEZ at ENCODE; https://www.encodeproject.org/ENCBS554TEZ/

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 (ENCLB918RQN)

description:
https://www.encodeproject.org/experiments/ENCSR629RUG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGHLV35)
experiment encode accession: ENCSR629RUG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB918RQN
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5729fd4c-8d17-4e80-b268-290c4b4607be/@@download/attachment/L-NSUN2_BGHLV35-29.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NSUN2. (NSUN2_BGHLV35-29)

value: ENCBS335MGQ at ENCODE; https://www.encodeproject.org/ENCBS335MGQ/


title: shRNA RNA-seq from HepG2 (ENCLB726PQW)

description:
https://www.encodeproject.org/experiments/ENCSR995RPB/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SUPV3L1 in HepG2 cells followed by RNA-seq. (SUPV3L1_BGHLV17)
experiment encode accession: ENCSR995RPB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB726PQW
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/65cf53a2-bc54-40c6-8e5c-edab71c4b65f/@@download/attachment/L-SUPV3L1_BGHLV17_31.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SUPV3L1. (SUPV3L1_BGHLV17_31)

value: ENCBS086XEN at ENCODE; https://www.encodeproject.org/ENCBS086XEN/


title: RAMPAGE from hepatocyte (ENCLB192PVM)

description:
https://www.encodeproject.org/experiments/ENCSR985XGK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from stem cells that were differentiated down a hepatocytic pathway. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR985XGK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR908ZAS
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB192PVM
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dd625e08-30e4-4406-8646-9d3484cf8b13/@@download/attachment/LID294717.pdf

value: hepatocyte

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/

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


title: RAMPAGE from hepatocyte (ENCLB951HUY)

description:
https://www.encodeproject.org/experiments/ENCSR985XGK/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from stem cells that were differentiated down a hepatocytic pathway. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR985XGK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR908ZAS
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB951HUY
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e511346d-6f0c-43a1-89a2-da9a7dc02220/@@download/attachment/LID294718.pdf

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/


title: shRNA RNA-seq from K562 (ENCLB753JHE)

description:
https://www.encodeproject.org/experiments/ENCSR618IQH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PUS1. (PUS1_BGKLV32)
experiment encode accession: ENCSR618IQH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB753JHE
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PUS1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a787e22d-1b8d-4547-88d2-45ada691eee9/@@download/attachment/L-PUS1_BGKLV32-51.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PUS1. (PUS1_BGKLV32-51)

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS284MJG at ENCODE; https://www.encodeproject.org/ENCBS284MJG/

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 (ENCLB715XRC)

description:
https://www.encodeproject.org/experiments/ENCSR620HAA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PPIG. (PPIG_BGHLV27)
experiment encode accession: ENCSR620HAA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB715XRC
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/16aa8455-08de-4187-9a14-00058b6d0a16/@@download/attachment/L-PPIG_BGHLV27-44.pdf

value: PPIG

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against PPIG (PPIG_BGHLV27-44)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS821PLV at ENCODE; https://www.encodeproject.org/ENCBS821PLV/

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

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


title: RAMPAGE from suprapubic skin (ENCLB844CWQ)

description:
https://www.encodeproject.org/experiments/ENCSR616JRI/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human suprapubic skin tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR616JRI
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR108MAU
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB844CWQ
size range: >200

source_name: Homo sapiens suprapubic skin tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be23074b-0bcb-40d3-bcf5-34cb877fb74e/@@download/attachment/296842.pdf

value: suprapubic skin

value: tissue

value: Suprapubic skin (not sun exposed) aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS368KLM at ENCODE; https://www.encodeproject.org/ENCBS368KLM/

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


title: shRNA RNA-seq from K562 (ENCLB233BKG)

description:
https://www.encodeproject.org/experiments/ENCSR984CLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against KIAA1967. (KIAA1967_BGKLV25)
experiment encode accession: ENCSR984CLJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB233BKG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CCAR2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1042d21f-b2ef-496e-b415-189cb9a79a8c/@@download/attachment/L-KIAA1967_BGKLV25-29.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against KIAA1967. (KIAA1967_BGKLV25-29)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS398SSI at ENCODE; https://www.encodeproject.org/ENCBS398SSI/

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 (ENCLB956ZHW)

description:
https://www.encodeproject.org/experiments/ENCSR631RFX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGKLV34)
experiment encode accession: ENCSR631RFX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR174OYC
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB956ZHW
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f1f36321-5b9e-47d5-b146-18f075384646/@@download/attachment/L-MTPAP_BGKLV34-24.pdf

value: MTPAP

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against MTPAP. (MTPAP_BGKLV34-24)

value: ENCBS966RJI at ENCODE; https://www.encodeproject.org/ENCBS966RJI/


title: siRNA RNA-seq from K562 (ENCLB310HOE)

description:
https://www.encodeproject.org/experiments/ENCSR977SOT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting CEBPZ.
experiment encode accession: ENCSR977SOT
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB310HOE
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: CEBPZ

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

value: Sherman Weissman, Yale

value: ENCBS750HYQ at ENCODE; https://www.encodeproject.org/ENCBS750HYQ/


title: shRNA RNA-seq from K562 (ENCLB463VYP)

description:
https://www.encodeproject.org/experiments/ENCSR618IQH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PUS1. (PUS1_BGKLV32)
experiment encode accession: ENCSR618IQH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB463VYP
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9a224247-cb55-4498-b7ec-8cf169c7148f/@@download/attachment/L-PUS1_BGKLV32-52.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PUS1. (PUS1_BGKLV32-52)

value: ENCBS495MNB at ENCODE; https://www.encodeproject.org/ENCBS495MNB/


title: total RNA-seq from esophagus muscularis mucosa (ENCLB391TZJ)

description:
https://www.encodeproject.org/experiments/ENCSR620LQN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's esophagal muscle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR620LQN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB391TZJ
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2ce59bfe-6815-42ea-82ef-bd0117d1ec03/@@download/attachment/296295.pdf

value: esophagus muscularis mucosa

value: tissue

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

value: 51 year

value: adult

value: Thomas Gingeras, CSHL

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

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


title: RAMPAGE from spleen (ENCLB392HUI)

description:
https://www.encodeproject.org/experiments/ENCSR627SPU/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human spleen tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR627SPU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR106SZN
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB392HUI
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5921c418-698d-472b-b9e2-a50924d218cb/@@download/attachment/296811.pdf

value: spleen

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

value: 54 year

value: male

value: ENCBS379XNT at ENCODE; https://www.encodeproject.org/ENCBS379XNT/

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


title: RAMPAGE from cardiac muscle cell (ENCLB550RSH)

description:
https://www.encodeproject.org/experiments/ENCSR613JNT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from hESC's that were differentiated into cardiomyocytes. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR613JNT
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR379YAE
encode release date: 2016-05-09
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB550RSH
size range: >200

source_name: Homo sapiens cardiac muscle in vitro differentiated cells fetal

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9bcf7902-8ace-4788-84c9-073f85965bc6/@@download/attachment/LID295887.pdf

value: cardiac muscle cell

value: in vitro differentiated cells

value: unknown

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

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

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


title: shRNA RNA-seq from HepG2 (ENCLB124UVF)

description:
https://www.encodeproject.org/experiments/ENCSR992JGE/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against METAP2 in HepG2 cells followed by RNA-seq. (METAP2_BGHLV16)
experiment encode accession: ENCSR992JGE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB124UVF
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/65c7b31e-c79e-4067-a4b0-b93b634eb9b3/@@download/attachment/L-METAP2_BGHLV16_33.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against METAP2. (METAP2_BGHLV16_33)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS849LND at ENCODE; https://www.encodeproject.org/ENCBS849LND/

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 (ENCLB998WKN)

description:
https://www.encodeproject.org/experiments/ENCSR620HAA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PPIG. (PPIG_BGHLV27)
experiment encode accession: ENCSR620HAA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR246RRQ
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB998WKN
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/707c72ae-ad6e-4db3-8101-de504ba94ad4/@@download/attachment/L-PPIG_BGHLV27-43.pdf

value: PPIG

value: RNA-seq on HepG2 cells treated with an Control shRNA against PPIG (PPIG_BGHLV27-43)

value: male

value: ENCBS544ETZ at ENCODE; https://www.encodeproject.org/ENCBS544ETZ/


title: shRNA RNA-seq from K562 (ENCLB475OEB)

description:
https://www.encodeproject.org/experiments/ENCSR973QSV/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against AATF in K562 cells followed by RNA-seq. (AATF BGKLV13)
experiment encode accession: ENCSR973QSV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB475OEB
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0914bc71-d93a-47f4-b21e-9e00760e9831/@@download/attachment/L-AATF_BGKLV13_13.pdf

value: AATF

value: RNA-seq on K562 cells treated with an shRNA knockdown against AATF.(AATF_BGKLV13_13)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS070OMK at ENCODE; https://www.encodeproject.org/ENCBS070OMK/

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

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


title: RAMPAGE from adrenal gland (ENCLB411VFR)

description:
https://www.encodeproject.org/experiments/ENCSR970OWZ/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR970OWZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR954PZB
encode release date: 2016-03-16
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB411VFR
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a753352a-f158-44bb-a6a4-047b657f6adb/@@download/attachment/295991.pdf

value: adrenal gland

value: tissue

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

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS724UYV at ENCODE; https://www.encodeproject.org/ENCBS724UYV/

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


title: RAMPAGE from cardiac muscle cell (ENCLB991EHH)

description:
https://www.encodeproject.org/experiments/ENCSR613JNT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this Experiment come from hESC's that were differentiated into cardiomyocytes. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR613JNT
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR379YAE
encode release date: 2016-05-09
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB991EHH
size range: >200

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/def6d6d6-7d68-4681-9a1f-fda4e346e9f5/@@download/attachment/LID295888.pdf

value: cardiac muscle cell

value: in vitro differentiated cells

value: unknown

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

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

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


title: siRNA RNA-seq from K562 (ENCLB789EJX)

description:
https://www.encodeproject.org/experiments/ENCSR965CCM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ZNF384.
experiment encode accession: ENCSR965CCM
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR561NXJ, ENCSR109YDL
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB789EJX
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting ZNF384

value: immortalized cell line

value: K562 cells treated with a siRNA knockdown against ZNF384, used in RNA-seq experiments.

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS800ECG at ENCODE; https://www.encodeproject.org/ENCBS800ECG/

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


title: shRNA RNA-seq from K562 (ENCLB055EBL)

description:
https://www.encodeproject.org/experiments/ENCSR624XHG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RNASEN. (RNASEN50_BGKLV28)
experiment encode accession: ENCSR624XHG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB055EBL
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2050ffc8-b117-46da-ac97-638528c01837/@@download/attachment/L-RNASEN50_BGKLV28-45.pdf

value: DROSHA

value: RNA-seq on K562 cells treated with an shRNA knockdown against DROSHA. (RNASEN50_BGKLV28-45)

value: Brenton Graveley, UConn

value: ENCBS272SXA at ENCODE; https://www.encodeproject.org/ENCBS272SXA/

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


title: siRNA RNA-seq from K562 (ENCLB197DTE)

description:
https://www.encodeproject.org/experiments/ENCSR965CCM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ZNF384.
experiment encode accession: ENCSR965CCM
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR561NXJ, ENCSR109YDL
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB197DTE
size range: >200
spikeins used: /references/ENCSR866KGS/

value: ENCBS931JLY at ENCODE; https://www.encodeproject.org/ENCBS931JLY/


title: shRNA RNA-seq from K562 (ENCLB111SMM)

description:
https://www.encodeproject.org/experiments/ENCSR973QSV/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against AATF in K562 cells followed by RNA-seq. (AATF BGKLV13)
experiment encode accession: ENCSR973QSV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB111SMM
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/29456619-f197-4c0c-8755-007a3312e877/@@download/attachment/L-AATF_BGKLV13_14.pdf

value: AATF

value: RNA-seq on K562 cells treated with an shRNA knockdown against AATF.(AATF_BGKLV13_14)

value: ENCBS478USZ at ENCODE; https://www.encodeproject.org/ENCBS478USZ/


title: shRNA RNA-seq from K562 (ENCLB779CXX)

description:
https://www.encodeproject.org/experiments/ENCSR624XHG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RNASEN. (RNASEN50_BGKLV28)
experiment encode accession: ENCSR624XHG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB779CXX
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/3e00ada8-29bd-4522-96b8-342aa1f77b2e/@@download/attachment/L-RNASEN50_BGKLV28-46.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DROSHA. (RNASEN50_BGKLV28-46)

value: ENCBS111RFA at ENCODE; https://www.encodeproject.org/ENCBS111RFA/


title: shRNA RNA-seq from K562 (ENCLB481PPA)

description:
https://www.encodeproject.org/experiments/ENCSR984CLJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against KIAA1967. (KIAA1967_BGKLV25)
experiment encode accession: ENCSR984CLJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB481PPA
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/55e6daf0-6b98-45b8-9c30-cbb9c5722280/@@download/attachment/L-KIAA1967_BGKLV25-30.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against KIAA1967. (KIAA1967_BGKLV25-30)

value: 53 year

value: adult

value: female

value: ENCBS836YTS at ENCODE; https://www.encodeproject.org/ENCBS836YTS/


title: RAMPAGE from omental fat pad (ENCLB813YYD)

description:
https://www.encodeproject.org/experiments/ENCSR611YXR/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human adipose tissue of omentum tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR611YXR
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR158KFO
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB813YYD
size range: >200

source_name: Homo sapiens omental fat pad tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b1a00354-fa1d-4c07-8ffc-0d1b6ba67002/@@download/attachment/296787.pdf

value: omental fat pad

value: tissue

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

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS689JVM at ENCODE; https://www.encodeproject.org/ENCBS689JVM/

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


title: siRNA RNA-seq from K562 (ENCLB324UKO)

description:
https://www.encodeproject.org/experiments/ENCSR977SOT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting CEBPZ.
experiment encode accession: ENCSR977SOT
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB324UKO
size range: >200
spikeins used: /references/ENCSR866KGS/

value: CEBPZ

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

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS402TOW at ENCODE; https://www.encodeproject.org/ENCBS402TOW/

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


title: shRNA RNA-seq from HepG2 (ENCLB400UBN)

description:
https://www.encodeproject.org/experiments/ENCSR610VTA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGHLV30)
experiment encode accession: ENCSR610VTA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB400UBN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ABCF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0a7fdf1d-6efb-416e-a643-c21e9e6b2dfd/@@download/attachment/L-ABCF1_BGHLV30-4.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGHLV30-4)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS923MFQ at ENCODE; https://www.encodeproject.org/ENCBS923MFQ/

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

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


title: total RNA-seq from gastrocnemius medialis (ENCLB669XXD)

description:
https://www.encodeproject.org/experiments/ENCSR609NZM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's skeletal muscle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR609NZM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB669XXD
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens gastrocnemius medialis tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/28ff0e84-60e8-4573-8db5-f851e96f0fcb/@@download/attachment/296331.pdf

value: gastrocnemius medialis

value: tissue

value: 51 year

value: adult

value: female

value: ENCODE Consortium

value: ENCBS094ENG at ENCODE; https://www.encodeproject.org/ENCBS094ENG/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/40a4131c-e9c4-4adc-b0f7-e5ec9c35571c/@@download/attachment/84265.svs


title: shRNA RNA-seq from HepG2 (ENCLB762ASE)

description:
https://www.encodeproject.org/experiments/ENCSR610VTA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGHLV30)
experiment encode accession: ENCSR610VTA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB762ASE
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/97e0ae80-21d3-4d5a-a3a0-e48b14e807be/@@download/attachment/L-ABCF1_BGHLV30-3.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGHLV30-3)

value: child

value: ENCBS786WUO at ENCODE; https://www.encodeproject.org/ENCBS786WUO/


title: shRNA RNA-seq from HepG2 (ENCLB139BJN)

description:
https://www.encodeproject.org/experiments/ENCSR964YTW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX55 in HepG2 cells followed by RNA-seq. (DDX55_BGHLV17)
experiment encode accession: ENCSR964YTW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB139BJN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX55

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/98496ffd-8cc9-4b73-87ce-35c386409877/@@download/attachment/L-DDX55_BGHLV17_59.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX55. (DDX55_BGHLV17_59)

value: 15 year

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS430PSA at ENCODE; https://www.encodeproject.org/ENCBS430PSA/


title: shRNA RNA-seq from K562 (ENCLB431QTM)

description:
https://www.encodeproject.org/experiments/ENCSR602AWR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TUFM. (TUFM-BGKLV25)
experiment encode accession: ENCSR602AWR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB431QTM
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7635c56b-fd80-425f-81e8-a89394064759/@@download/attachment/L-TUFM-BGKLV25-59.pdf

value: TUFM

value: RNA-seq on K562 cells treated with an shRNA knockdown against TUFM. (TUFM-BGKLV25-59)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS400CRG at ENCODE; https://www.encodeproject.org/ENCBS400CRG/

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

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


title: RAMPAGE from ovary (ENCLB181TQT)

description:
https://www.encodeproject.org/experiments/ENCSR601URL/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human female gonad tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR601URL
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR042GYH
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB181TQT
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7c985597-b2bc-4e95-b6b3-c3ac774d3c4e/@@download/attachment/296823.pdf

value: ovary

value: tissue

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

value: 51 year

value: adult

value: female

value: Thomas Gingeras, CSHL

value: ENCBS711CPB at ENCODE; https://www.encodeproject.org/ENCBS711CPB/

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


title: shRNA RNA-seq from HepG2 (ENCLB090BCK)

description:
https://www.encodeproject.org/experiments/ENCSR964YTW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX55 in HepG2 cells followed by RNA-seq. (DDX55_BGHLV17)
experiment encode accession: ENCSR964YTW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB090BCK
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/add74101-deb8-4dbc-9ab1-9ca8084430e6/@@download/attachment/L-DDX55_BGHLV17_60.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX55. (DDX55_BGHLV17_60)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS754KRB at ENCODE; https://www.encodeproject.org/ENCBS754KRB/

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 (ENCLB510KEQ)

description:
https://www.encodeproject.org/experiments/ENCSR602AWR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TUFM. (TUFM-BGKLV25)
experiment encode accession: ENCSR602AWR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB510KEQ
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/2128932d-7d22-4fcd-91d0-d7fa1b5f6582/@@download/attachment/L-TUFM-BGKLV25-60.pdf

value: TUFM

value: RNA-seq on K562 cells treated with an shRNA knockdown against TUFM. (TUFM-BGKLV25-60)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS123YCA at ENCODE; https://www.encodeproject.org/ENCBS123YCA/

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 (ENCLB556ZNK)

description:
https://www.encodeproject.org/experiments/ENCSR958NDU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against HLTF in K562 cells followed by RNA-seq. (HLTF BGKLV13)
experiment encode accession: ENCSR958NDU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB556ZNK
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/07745f20-899e-43d7-8c1b-cf7a11b1e270/@@download/attachment/L-HLTF_BGKLV13_4.pdf

value: HLTF

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HLTF.(HLTF_BGKLV13_4)

value: adult

value: female

value: ENCBS953YBZ at ENCODE; https://www.encodeproject.org/ENCBS953YBZ/


title: shRNA RNA-seq from K562 (ENCLB780TII)

description:
https://www.encodeproject.org/experiments/ENCSR963RLK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against APOBEC3C. (APOBEC3C_BGKLV25)
experiment encode accession: ENCSR963RLK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB780TII
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting APOBEC3C

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9e697962-da16-4cf6-abd3-f8f24dde5ec4/@@download/attachment/L-APOBEC3C_BGKLV25-3.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against APOBEC3C. (APOBEC3C_BGKLV25-3)

value: Brenton Graveley, UConn

value: ENCBS973MAW at ENCODE; https://www.encodeproject.org/ENCBS973MAW/


title: RAMPAGE from breast epithelium (ENCLB141XNK)

description:
https://www.encodeproject.org/experiments/ENCSR598TAK/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human mammary gland tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR598TAK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR438YPF
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB141XNK
size range: >200

source_name: Homo sapiens breast epithelium tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa93dead-c6c7-4789-88bc-7869b0f719cf/@@download/attachment/296822.pdf

value: breast epithelium

value: tissue

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

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS160KYO at ENCODE; https://www.encodeproject.org/ENCBS160KYO/

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


title: shRNA RNA-seq from K562 (ENCLB532LDG)

description:
https://www.encodeproject.org/experiments/ENCSR963RLK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against APOBEC3C. (APOBEC3C_BGKLV25)
experiment encode accession: ENCSR963RLK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB532LDG
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/7c6ae7e2-58d2-49dc-b179-bae5438b299e/@@download/attachment/L-APOBEC3C_BGKLV25-4.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against APOBEC3C. (APOBEC3C_BGKLV25-4)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS563BBS at ENCODE; https://www.encodeproject.org/ENCBS563BBS/

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 (ENCLB452VUW)

description:
https://www.encodeproject.org/experiments/ENCSR598GKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX59. (DDX59_BGHLV35)
experiment encode accession: ENCSR598GKQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB452VUW
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX59

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1c0f6146-f3a7-48d9-8a08-5f9f4bb28ba0/@@download/attachment/L-DDX59_BGHLV35-16.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX59. (DDX59_BGHLV35-16)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS021ZEK at ENCODE; https://www.encodeproject.org/ENCBS021ZEK/

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


title: shRNA RNA-seq from HepG2 (ENCLB782BJL)

description:
https://www.encodeproject.org/experiments/ENCSR598GKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX59. (DDX59_BGHLV35)
experiment encode accession: ENCSR598GKQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR264TUE
encode release date: 2016-09-29
lab: Brenton Graveley, UConn
library encode accession: ENCLB782BJL
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f7ebbdea-a673-4bb1-8f20-a7d0bae80b6c/@@download/attachment/L-DDX59_BGHLV35-15.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX59. (DDX59_BGHLV35-15)

value: Brenton Graveley, UConn

value: ENCBS574SLK at ENCODE; https://www.encodeproject.org/ENCBS574SLK/


title: shRNA RNA-seq from K562 (ENCLB543IEK)

description:
https://www.encodeproject.org/experiments/ENCSR958NDU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against HLTF in K562 cells followed by RNA-seq. (HLTF BGKLV13)
experiment encode accession: ENCSR958NDU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB543IEK
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/f5f9f76f-5004-4bcb-8cee-e1f9cc3b4c29/@@download/attachment/L-HLTF_BGKLV13_3.pdf

value: HLTF

value: RNA-seq on K562 cells treated with an shRNA knockdown against HLTF.(HLTF_BGKLV13_3)

value: adult

value: female

value: ENCBS519PER at ENCODE; https://www.encodeproject.org/ENCBS519PER/


title: shRNA RNA-seq from HepG2 (ENCLB536MRP)

description:
https://www.encodeproject.org/experiments/ENCSR599PXD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM15. (RBM15_BGHLV31)
experiment encode accession: ENCSR599PXD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR585KOJ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB536MRP
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RBM15

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c2359833-0bc6-4812-8d6e-ca65ec528643/@@download/attachment/L-RBM15_BGHLV31-54B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM15. (RBM15_BGHLV31-54B)

value: ENCBS755JGR at ENCODE; https://www.encodeproject.org/ENCBS755JGR/

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


title: shRNA RNA-seq from K562 (ENCLB677NTM)

description:
https://www.encodeproject.org/experiments/ENCSR954HAY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SART3. (SART3_BGKLV24_B)
experiment encode accession: ENCSR954HAY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB677NTM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SART3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a5783825-f019-4c2a-9a18-1915cab4c147/@@download/attachment/L-SART3_BGKLV24_54B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SART3. (SART3_BGKLV24_54B)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS415MYO at ENCODE; https://www.encodeproject.org/ENCBS415MYO/

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

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


title: RAMPAGE from fibroblast of arm (ENCLB365FXM)

description:
https://www.encodeproject.org/experiments/ENCSR949PHV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin fibroblasts from the PGP1 donor. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR949PHV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR797BPP
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB365FXM
size range: >200

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5dbf4238-514a-4798-a319-b08fdc45fc30/@@download/attachment/290913.pdf

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: male

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: total RNA-seq from adrenal gland (ENCLB325SDI)

description:
https://www.encodeproject.org/experiments/ENCSR954PZB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR954PZB
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB325SDI
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4452f73e-4af5-4977-9429-c5b43fa3e53d/@@download/attachment/295878.pdf

value: adrenal gland

value: tissue

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

value: 54 year

value: adult

value: ENCBS724UYV at ENCODE; https://www.encodeproject.org/ENCBS724UYV/

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


title: RAMPAGE from gastroesophageal sphincter (ENCLB452LXO)

description:
https://www.encodeproject.org/experiments/ENCSR590VCR/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human esophagogastric junction tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR590VCR
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR528ZKN
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB452LXO
size range: >200

source_name: Homo sapiens gastroesophageal sphincter tissue male adult (37 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e6aa26ae-6d3f-4af8-831e-d4a956539dc9/@@download/attachment/296776.pdf

value: gastroesophageal sphincter

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

value: 37 year

value: ENCBS581RWW at ENCODE; https://www.encodeproject.org/ENCBS581RWW/

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


title: RAMPAGE from fibroblast of arm (ENCLB351XBR)

description:
https://www.encodeproject.org/experiments/ENCSR949PHV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of skin fibroblasts from the PGP1 donor. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR949PHV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR797BPP
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB351XBR
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e991aba3-5bca-4df6-a213-ef9141a4b275/@@download/attachment/290912.pdf

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/


title: total RNA-seq from body of pancreas (ENCLB778YTC)

description:
https://www.encodeproject.org/experiments/ENCSR586SYA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's pancreas tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR586SYA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB778YTC
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens body of pancreas tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/de5da046-281d-4a29-ad3d-47af7c640d2e/@@download/attachment/296339.pdf

value: body of pancreas

value: tissue

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

value: female

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

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


title: shRNA RNA-seq from HepG2 (ENCLB172REZ)

description:
https://www.encodeproject.org/experiments/ENCSR599PXD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM15. (RBM15_BGHLV31)
experiment encode accession: ENCSR599PXD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR585KOJ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB172REZ
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/eca14e44-e4dd-4c8c-aa47-a9f8cc57cd0e/@@download/attachment/L-RBM15_BGHLV31-53B.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM15. (RBM15_BGHLV31-53B)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS413HHW at ENCODE; https://www.encodeproject.org/ENCBS413HHW/

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 (ENCLB340GSM)

description:
https://www.encodeproject.org/experiments/ENCSR594DNW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGHLV30)
experiment encode accession: ENCSR594DNW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB340GSM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CPSF7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1944527d-ed32-47df-8f20-e61bc891e9c8/@@download/attachment/L-CPSF7_BGHLV30-21.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGHLV30-21)

value: male

value: ENCBS250QAH at ENCODE; https://www.encodeproject.org/ENCBS250QAH/


title: shRNA RNA-seq from K562 (ENCLB954HKX)

description:
https://www.encodeproject.org/experiments/ENCSR954HAY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SART3. (SART3_BGKLV24_B)
experiment encode accession: ENCSR954HAY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB954HKX
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/75bb344d-e71b-4de0-a2f8-53213e574522/@@download/attachment/L-SART3_BGKLV24_53B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SART3. (SART3_BGKLV24_53B)

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS166SNL at ENCODE; https://www.encodeproject.org/ENCBS166SNL/

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 (ENCLB849HES)

description:
https://www.encodeproject.org/experiments/ENCSR585KOJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV31B)
experiment encode accession: ENCSR585KOJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB849HES
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f30aa265-0b36-469a-b2c5-064f7adde294/@@download/attachment/L-NT_BGHLV31-2B.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV31-2B)

value: 15 year

value: ENCBS730DQI at ENCODE; https://www.encodeproject.org/ENCBS730DQI/


title: shRNA RNA-seq from HepG2 (ENCLB273BQY)

description:
https://www.encodeproject.org/experiments/ENCSR945XKW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM1. (PUM1-BGHLV23)
experiment encode accession: ENCSR945XKW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB273BQY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PUM1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e8fc272d-96c9-47b2-b583-a0153f1d781b/@@download/attachment/L-PUM1-BGHLV23-33.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM1. (PUM1-BGHLV23-33)

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS844EBE at ENCODE; https://www.encodeproject.org/ENCBS844EBE/

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


title: shRNA RNA-seq from HepG2 (ENCLB828EHM)

description:
https://www.encodeproject.org/experiments/ENCSR585KOJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV31B)
experiment encode accession: ENCSR585KOJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB828EHM
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9d6b9b19-dcce-4812-ad69-f24abea89b89/@@download/attachment/L-NT_BGHLV31-1B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV31-1B)

value: male

value: ENCBS562WFV at ENCODE; https://www.encodeproject.org/ENCBS562WFV/

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


title: shRNA RNA-seq from HepG2 (ENCLB064MCD)

description:
https://www.encodeproject.org/experiments/ENCSR584JRB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NUFIP2. (NUFIP2_BGHLV26)
experiment encode accession: ENCSR584JRB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB064MCD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NUFIP2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4c93686c-2d41-4a2a-a34e-ff262c9817b8/@@download/attachment/L-NUFIP2_BGHLV26_30.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against NUFIP2 (NUFIP2_BGHLV26_30)

value: ENCBS310TGK at ENCODE; https://www.encodeproject.org/ENCBS310TGK/


title: shRNA RNA-seq from HepG2 (ENCLB204IVS)

description:
https://www.encodeproject.org/experiments/ENCSR946OFN/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TROVE2 in HepG2 cells followed by RNA-seq. (TROVE2_BGHLV16)
experiment encode accession: ENCSR946OFN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB204IVS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting TROVE2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3fcc43e6-d65e-4cbb-b9c4-1ce4af315836/@@download/attachment/L-TROVE2_BGHLV16_62.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TROVE2. (TROVE2_BGHLV16_62)

value: ENCBS210MLW at ENCODE; https://www.encodeproject.org/ENCBS210MLW/


title: shRNA RNA-seq from HepG2 (ENCLB740DDO)

description:
https://www.encodeproject.org/experiments/ENCSR584JRB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against NUFIP2. (NUFIP2_BGHLV26)
experiment encode accession: ENCSR584JRB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB740DDO
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/7e94dc5d-ff86-450c-9765-8cc96a0a445d/@@download/attachment/L-NUFIP2_BGHLV26_29.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against NUFIP2 (NUFIP2_BGHLV26_29)

value: ENCBS202CLF at ENCODE; https://www.encodeproject.org/ENCBS202CLF/


title: total RNA-seq from adrenal gland (ENCLB102CKX)

description:
https://www.encodeproject.org/experiments/ENCSR954PZB/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR954PZB
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB102CKX
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4809069a-864a-4b09-907a-6e25d312e398/@@download/attachment/295879.pdf

value: adrenal gland

value: tissue

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

value: 54 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS724UYV at ENCODE; https://www.encodeproject.org/ENCBS724UYV/

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


title: shRNA RNA-seq from HepG2 (ENCLB810NQE)

description:
https://www.encodeproject.org/experiments/ENCSR946OFN/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TROVE2 in HepG2 cells followed by RNA-seq. (TROVE2_BGHLV16)
experiment encode accession: ENCSR946OFN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB810NQE
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/618460ad-3dc2-4960-8fef-515658f83834/@@download/attachment/L-TROVE2_BGHLV16_61.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TROVE2. (TROVE2_BGHLV16_61)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS280KDG at ENCODE; https://www.encodeproject.org/ENCBS280KDG/

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


title: total RNA-seq from right atrium auricular region (ENCLB471FWT)

description:
https://www.encodeproject.org/experiments/ENCSR571RXE/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's heart tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR571RXE
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB471FWT
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens right atrium auricular region tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ccc5fe91-fad8-4410-a556-0298fdbe774a/@@download/attachment/296327.pdf

value: right atrium auricular region

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

value: 53 year

value: female

value: ENCBS357SRJ at ENCODE; https://www.encodeproject.org/ENCBS357SRJ/

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


title: shRNA RNA-seq from K562 (ENCLB900DNG)

description:
https://www.encodeproject.org/experiments/ENCSR942UNX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-30B)
experiment encode accession: ENCSR942UNX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB900DNG
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/c49bb423-a94b-4d7e-b9d4-746482454f44/@@download/attachment/L-K-NT-30B-1.pdf

value: Control

value: immortalized cell line

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (K-NT-30B-1)

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS023DBL at ENCODE; https://www.encodeproject.org/ENCBS023DBL/

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 (ENCLB876GVU)

description:
https://www.encodeproject.org/experiments/ENCSR594DNW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGHLV30)
experiment encode accession: ENCSR594DNW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB876GVU
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/734c1a48-ddce-4a73-8f93-e6c882db5076/@@download/attachment/L-CPSF7_BGHLV30-22.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGHLV30-22)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS875LKB at ENCODE; https://www.encodeproject.org/ENCBS875LKB/

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


title: shRNA RNA-seq from K562 (ENCLB171LFJ)

description:
https://www.encodeproject.org/experiments/ENCSR942UNX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-30B)
experiment encode accession: ENCSR942UNX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB171LFJ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/e7125af9-3236-4b6c-83b7-0b79857f046f/@@download/attachment/L-K-NT-30B-2.pdf

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (K-NT-30B-2)

value: 53 year

value: female

value: ENCBS020IUG at ENCODE; https://www.encodeproject.org/ENCBS020IUG/


title: shRNA RNA-seq from HepG2 (ENCLB635VFD)

description:
https://www.encodeproject.org/experiments/ENCSR945XKW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM1. (PUM1-BGHLV23)
experiment encode accession: ENCSR945XKW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB635VFD
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/5e2b14c6-34a6-445f-90c1-1129ff06580b/@@download/attachment/L-PUM1-BGHLV23-34.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM1. (PUM1-BGHLV23-34)

value: ENCBS464VEI at ENCODE; https://www.encodeproject.org/ENCBS464VEI/

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


title: shRNA RNA-seq from K562 (ENCLB361RYZ)

description:
https://www.encodeproject.org/experiments/ENCSR563YIS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL_BGKLV25)
experiment encode accession: ENCSR563YIS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR031RRO
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB361RYZ
size range: >200
spikeins used: /references/ENCSR358OMW/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6358cee0-7ee0-4ed2-9a80-f1dcb5d40350/@@download/attachment/L-HNRNPL_BGKLV25-26B.pdf

value: HNRNPL

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL_BGKLV25-26B)

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS958BUA at ENCODE; https://www.encodeproject.org/ENCBS958BUA/

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 (ENCLB928RTX)

description:
https://www.encodeproject.org/experiments/ENCSR563YIS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL_BGKLV25)
experiment encode accession: ENCSR563YIS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR031RRO
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB928RTX
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/54912890-9214-4c57-b3b1-15b4b5b28ec9/@@download/attachment/L-HNRNPL_BGKLV25-25B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL_BGKLV25-25B)

value: Brenton Graveley, UConn

value: ENCBS499ZBY at ENCODE; https://www.encodeproject.org/ENCBS499ZBY/


title: shRNA RNA-seq from HepG2 (ENCLB325AHL)

description:
https://www.encodeproject.org/experiments/ENCSR942MBU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ILF3. (ILF3-BGHLV22)
experiment encode accession: ENCSR942MBU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB325AHL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ILF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0250a77b-d2ac-4aa8-943f-b15ec00cd28c/@@download/attachment/L-ILF3-BGHLV22-29.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ILF3. (ILF3-BGHLV22-29)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS699OCX at ENCODE; https://www.encodeproject.org/ENCBS699OCX/

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


title: total RNA-seq from lower leg skin (ENCLB379JUW)

description:
https://www.encodeproject.org/experiments/ENCSR551NII/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's skin of the lower leg tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR551NII
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB379JUW
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens lower leg skin tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bf2e4692-1319-412a-ae36-72ce606ca208/@@download/attachment/296603.pdf

value: lower leg skin

value: tissue

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

value: 51 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS836VES at ENCODE; https://www.encodeproject.org/ENCBS836VES/

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


title: RAMPAGE from cardiac atrium fibroblast (ENCLB610UIW)

description:
https://www.encodeproject.org/experiments/ENCSR936TYP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of cardiac atrium fibroblast primary cell type (HCF-aa). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR936TYP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR110BDY
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB610UIW
size range: >200

source_name: Homo sapiens cardiac atrium fibroblast primary cell male child (2 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/16fda9de-e467-42d9-b65c-b92a78221c37/@@download/attachment/295344.pdf

value: cardiac atrium fibroblast

value: primary cell

value: Cardiac fibroblast (HCF-aa) from the atrial region of a 2 year old caucasian male.

value: 2 year

tag: passage number

value: ENCBS488CKE at ENCODE; https://www.encodeproject.org/ENCBS488CKE/

value: Derived from ENCODE donor ENCDO452MAH; https://www.encodeproject.org/ENCDO452MAH/

value: ScienCell sample source; http://sciencellonline.com/human-cardiac-fibroblast-adult-atrial-total-rna.html


title: shRNA RNA-seq from K562 (ENCLB554HNJ)

description:
https://www.encodeproject.org/experiments/ENCSR562CCA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SF1. (SF1_BGKLV28)
experiment encode accession: ENCSR562CCA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR164MUK
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB554HNJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e63e7c2e-d9a4-4deb-b9e6-e0c90003e859/@@download/attachment/L-SF1_BGKLV28-49.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SF1. (SF1_BGKLV28-49)

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS677BWZ at ENCODE; https://www.encodeproject.org/ENCBS677BWZ/

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 (ENCLB437TEQ)

description:
https://www.encodeproject.org/experiments/ENCSR942MBU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against ILF3. (ILF3-BGHLV22)
experiment encode accession: ENCSR942MBU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB437TEQ
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/26c7e25c-d673-4604-b6cb-609edf1a985e/@@download/attachment/L-ILF3-BGHLV22-30.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ILF3. (ILF3-BGHLV22-30)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS879MRD at ENCODE; https://www.encodeproject.org/ENCBS879MRD/

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

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


title: RAMPAGE from right atrium auricular region (ENCLB555BTG)

description:
https://www.encodeproject.org/experiments/ENCSR554TZR/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human right cardiac atrium tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR554TZR
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR457ENP
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555BTG
size range: >200

source_name: Homo sapiens right atrium auricular region tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d6a8bc23-f0ec-4a36-9f45-970c0bf5267a/@@download/attachment/296749.pdf

value: right atrium auricular region

value: tissue

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

value: 51 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS269BVG at ENCODE; https://www.encodeproject.org/ENCBS269BVG/

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


title: shRNA RNA-seq from K562 (ENCLB202ZWZ)

description:
https://www.encodeproject.org/experiments/ENCSR936VPP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (k562-shC)
experiment encode accession: ENCSR936VPP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB202ZWZ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/63bd57eb-e8ab-427a-9856-53492b8d0403/@@download/attachment/L-k562-shC-1.pdf

value: Control

value: immortalized cell line

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (k562-shC-1)

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS086JQA at ENCODE; https://www.encodeproject.org/ENCBS086JQA/

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

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


title: RAMPAGE from right lobe of liver (ENCLB144QUF)

description:
https://www.encodeproject.org/experiments/ENCSR543DIO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's right lobe of liver tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR543DIO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR226KML
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB144QUF
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ae2d3a80-5cac-4d29-8585-1258b55a8173/@@download/attachment/296700.pdf

value: right lobe of liver

value: tissue

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

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

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