title: shRNA RNA-seq from HepG2 (ENCLB675NYL)

description:
https://www.encodeproject.org/experiments/ENCSR003LSA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SNRNP200. (SNRNP200_BGHLV26)
experiment encode accession: ENCSR003LSA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB675NYL
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SNRNP200

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/739723d9-0b86-44bf-bc58-ff1faeb928d8/@@download/attachment/L-SNRNP200_BGHLV26_57.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against SNRNP200 (SNRNP200_BGHLV26_57)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS344VFK at ENCODE; https://www.encodeproject.org/ENCBS344VFK/

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 (ENCLB839CZO)

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/ENCSR000YYN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8. (AKAP8_BGKLV32)
experiment encode accession: ENCSR000YYN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB839CZO
size range: >200
spikeins used: /references/ENCSR358OMW/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting AKAP8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a480b9a3-0946-492e-bc09-b496c8906faa/@@download/attachment/L-AKAP8_BGKLV32-7.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8. (AKAP8_BGKLV32-7)

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

tag: link

value: ENCBS449PYL at ENCODE; https://www.encodeproject.org/ENCBS449PYL/

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 (ENCLB137CIN)

description:
https://www.encodeproject.org/experiments/ENCSR000YYN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8. (AKAP8_BGKLV32)
experiment encode accession: ENCSR000YYN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB137CIN
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/33193358-a34c-42f1-ad23-6702a4cce413/@@download/attachment/L-AKAP8_BGKLV32-8.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against AKAP8. (AKAP8_BGKLV32-8)

value: ENCBS250CMV at ENCODE; https://www.encodeproject.org/ENCBS250CMV/


title: 400nM_2_Rep1

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

library_source: genomic

data_processing:
Library strategy: COSMIC-seq
Base pairs were called with Casava v.1.8.2 (Illumina).
Reads were de-multiplexed with the barcode to yield only the 51 bp genomic fragment. Reads were filtered and trimmed to eliminate low-quality reads and adapter sequences, and mapped to the human genome (hg19) with Bowtie v 1.0 (best -m 1) to yield unique alignments.
HOMER (http://biowhat.ucsd.edu/homer/) was used to produce a signal track. The tag density for each factor was normalized to 10^7 tags and Input DNA. Peaks were called with SPP v 1.10.1 with the default parameters of the IDR methodology according to ENCODE guidelines (Landt et al Genome Res. 2012, 22, 1813).
Genome_build: hg19
Supplementary_files_format_and_content: *.bed files contain the COSMIC-seq peak locations. *.bedgraph files contain signal tracks.

molecule: genomic DNA

growth_protocol: E8 with Matrigel-coated plates

extract_protocol:
Cells were washed again with PBS, and isolated with Accutase per manufacturer’s directions. COSMIC was performed as described previously (Erwin et al. Angew. Chem. Int. Ed. 2014, 53, 38, 10124).
Sequencing libraries for Input and AP DNA were labeled with a DNA barcode for multiplexing, and prepared for sequencing with the TruSeq ChIP Sample Prep Kit (Illumina, Inc., San Diego, CA) per manufacturer’s directions.

treatment_protocol: H1-hESCs were treated with molecule for 24 h.

tag: cell line

tag: treatment


title: polyA mRNA RNA-seq from K562 (ENCLB486WAD)

description:
https://www.encodeproject.org/experiments/ENCSR596ACL/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial membrane fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR596ACL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB486WAD
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line membrane fraction

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

value: Eric Lécuyer, IRCM

tag: subcellular fraction term name

value: membrane

value: ENCBS985INM at ENCODE; https://www.encodeproject.org/ENCBS985INM/


title: Input_ChIPSeq

city: Hangzhou

first: Xinhua

last: Liu

state: Zhejiang

address: NO.2318, Yuhangtang road

department: School of Basic Medicine

country: China

institute: Hangzhou Normal University

data_processing:
Base-Calling was conducted by CASAVA software.
ChIP Seq reads were aligned to the hg19 genome assembly by Bowtie2.
Peaks were called by MACS14 with the thresholds of fragments size=300 and P-Value<1e-5.
Genome_build: hg19
Supplementary_files_format_and_content: bed file represents the binding coordinates in the whole genome of FOXK2.

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Cells were maintained in a humidified incubator equilibrated with 5% CO2 at 37°C. MDA-MB-231 cells were cultured in L-15 medium supplemented with 10% FBS and without CO2.

extract_protocol:
MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum. Approximately 5 x 107 cells were used for each ChIP-seq assay. The chromatin DNA precipitated by either normal goat IgG (control) or polyclonal antibodies against FOXK2. The DNA was purified with the Qiagen PCR purification kit.
DNA libraries were prepared for sequencing using standard Illumina protocols


title: RAMPAGE from gastrocnemius medialis (ENCLB652DUP)

description:
https://www.encodeproject.org/experiments/ENCSR024MNP/
***************
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 RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR024MNP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR609NZM
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB652DUP
size range: >200

source_name: Homo sapiens gastrocnemius medialis 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/1c1c33dd-ee47-4d4a-8eaf-4008f8ddd0bf/@@download/attachment/296728.pdf

value: gastrocnemius medialis

value: tissue

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

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS691OIE at ENCODE; https://www.encodeproject.org/ENCBS691OIE/

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


title: polyA mRNA RNA-seq from K562 (ENCLB162VAK)

description:
https://www.encodeproject.org/experiments/ENCSR594NJP/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial insoluble fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR594NJP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB162VAK
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line insoluble cytoplasmic fraction

value: immortalized cell line

value: 53 year

value: adult

value: female

value: insoluble cytoplasmic fraction

value: ENCBS636RQT at ENCODE; https://www.encodeproject.org/ENCBS636RQT/


title: polyA mRNA RNA-seq from K562 (ENCLB072OHO)

description:
https://www.encodeproject.org/experiments/ENCSR594NJP/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial insoluble fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR594NJP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB072OHO
size range: >200
spikeins used: /references/ENCSR866KGS/

value: chronic myelogenous leukemia (CML)

value: ENCBS569WDT at ENCODE; https://www.encodeproject.org/ENCBS569WDT/

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 (ENCLB650MYJ)

description:
https://www.encodeproject.org/experiments/ENCSR598YQX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against LIN28B. (LIN28B_BGKLV21)
experiment encode accession: ENCSR598YQX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB650MYJ
size range: >200
spikeins used: /references/ENCSR449DXG/
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting LIN28B

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4d1840ac-a3e2-4e0e-a0a3-a2d7a3ce1a97/@@download/attachment/L-LIN28B_BGKLV21_28_17574.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against LIN28B. (LIN28B_BGKLV21_28_17574)

value: Brenton Graveley, UConn

value: ENCBS521FNT at ENCODE; https://www.encodeproject.org/ENCBS521FNT/


title: input

data_processing:
Library strategy: COSMIC-seq
Base pairs were called with Casava v.1.8.2 (Illumina).
Reads were de-multiplexed with the barcode to yield only the 51 bp genomic fragment. Reads were filtered and trimmed to eliminate low-quality reads and adapter sequences, and mapped to the human genome (hg19) with Bowtie v 1.0 (best -m 1) to yield unique alignments.
HOMER (http://biowhat.ucsd.edu/homer/) was used to produce a signal track. The tag density for each factor was normalized to 10^7 tags and Input DNA. Peaks were called with SPP v 1.10.1 with the default parameters of the IDR methodology according to ENCODE guidelines (Landt et al Genome Res. 2012, 22, 1813).
Genome_build: hg19
Supplementary_files_format_and_content: *.bed files contain peak locations. *.bedgraph files contain signal tracks.


title: FOXK2_ChIPSeq


title: 400nM_6_Rep2


title: shRNA RNA-seq from HepG2 (ENCLB108EAM)

description:
https://www.encodeproject.org/experiments/ENCSR003LSA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SNRNP200. (SNRNP200_BGHLV26)
experiment encode accession: ENCSR003LSA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR104ABF
encode release date: 2016-02-11
lab: Brenton Graveley, UConn
library encode accession: ENCLB108EAM
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/ec4ca64c-70b6-414d-bb11-c578ab8abbb0/@@download/attachment/L-SNRNP200_BGHLV26_58.pdf

value: RNA-seq on HepG2 cells treated with an Control shRNA against SNRNP200 (SNRNP200_BGHLV26_58)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS178ASF at ENCODE; https://www.encodeproject.org/ENCBS178ASF/

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 (ENCLB980OFO)

description:
https://www.encodeproject.org/experiments/ENCSR598YQX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against LIN28B. (LIN28B_BGKLV21)
experiment encode accession: ENCSR598YQX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB980OFO
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/dbe2a5e3-ac2e-4f7c-97ae-8d2a941af9ad/@@download/attachment/L-LIN28B_BGKLV21_27_17573.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against LIN28B. (LIN28B_BGKLV21_27_17573)

value: 53 year

value: adult

value: female

value: ENCBS396JPQ at ENCODE; https://www.encodeproject.org/ENCBS396JPQ/


title: 400nM_6_Rep1


title: RAMPAGE from PC-3 (ENCLB754USB)

description:
https://www.encodeproject.org/experiments/ENCSR585QYX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line PC-3. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR585QYX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR420NLC
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB754USB
size range: >200

source_name: Homo sapiens PC-3 immortalized cell line

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/544e46e4-70f1-4926-b8a6-9bc24338e4cc/@@download/attachment/289919.pdf

value: prostate cancer cell line

value: 62 year

tag: passage number

value: grade IV, adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS608AAA at ENCODE; https://www.encodeproject.org/ENCBS608AAA/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: 20nM_4_Rep1


title: 20nM_4_Rep2


title: RAMPAGE from PC-3 (ENCLB052UXN)

description:
https://www.encodeproject.org/experiments/ENCSR585QYX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line PC-3. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR585QYX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR420NLC
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB052UXN
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/ecb8af39-d9f0-453c-adb3-6e4be99d8931/@@download/attachment/289920.pdf

value: male

value: ENCBS609AAA at ENCODE; https://www.encodeproject.org/ENCBS609AAA/


title: 20nM_2_Rep2


title: 20nM_2_Rep1


title: siRNA RNA-seq from K562 (ENCLB327RLE)

description:
https://www.encodeproject.org/experiments/ENCSR576FFB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting KAT2B.
experiment encode accession: ENCSR576FFB
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR401RKW, ENCSR109YDL
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB327RLE
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting KAT2B

value: K562 cells treated with a siRNA knockdown against KAT2B, used in RNA-seq experiments.

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS115MXS at ENCODE; https://www.encodeproject.org/ENCBS115MXS/

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

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: 400nM_5_Rep1


title: shRNA RNA-seq from K562 (ENCLB952LVV)

description:
https://www.encodeproject.org/experiments/ENCSR584LDM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX27 in K562 cells followed by RNA-seq. (DDX27_BGKLV19)
experiment encode accession: ENCSR584LDM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR245BNJ
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB952LVV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX27

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/81b2c12d-7cfe-4d5b-8f4d-645e0e45bb88/@@download/attachment/L-DDX27_BGKLV19_11A.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX27. (DDX27_BGKLV19_11A)

value: adult

value: female

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS983TNS at ENCODE; https://www.encodeproject.org/ENCBS983TNS/

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


title: RAMPAGE from airway epithelial cell (ENCLB228JMH)

description:
https://www.encodeproject.org/experiments/ENCSR582BUX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from airway epithelial cells (HSA EpiC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR582BUX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR822SUG
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB228JMH
size range: >200

source_name: Homo sapiens airway epithelial primary cell

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/79ae9b47-6210-4cca-a9ef-4965712bd0fd/@@download/attachment/LID295327.pdf

value: airway epithelial cell

value: primary cell

value: Human Small Airway Epithelial Cells

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

value: ENCBS050ADW at ENCODE; https://www.encodeproject.org/ENCBS050ADW/

value: Derived from ENCODE donor ENCDO749MBK; https://www.encodeproject.org/ENCDO749MBK/


title: RAMPAGE from airway epithelial cell (ENCLB353HTH)

description:
https://www.encodeproject.org/experiments/ENCSR582BUX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from airway epithelial cells (HSA EpiC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR582BUX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR822SUG
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB353HTH
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/913900de-0e91-4ba6-b160-0ca9d9add6d6/@@download/attachment/LID295326.pdf

value: ENCBS408ZXF at ENCODE; https://www.encodeproject.org/ENCBS408ZXF/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=3235


title: siRNA RNA-seq from K562 (ENCLB570SQZ)

description:
https://www.encodeproject.org/experiments/ENCSR576FFB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting KAT2B.
experiment encode accession: ENCSR576FFB
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR401RKW, ENCSR109YDL
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB570SQZ
size range: >200
spikeins used: /references/ENCSR866KGS/

value: immortalized cell line

value: K562 cells treated with a siRNA knockdown against KAT2B, used in RNA-seq experiments.

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS571FHN at ENCODE; https://www.encodeproject.org/ENCBS571FHN/

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

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: shRNA RNA-seq from K562 (ENCLB370KSD)

description:
https://www.encodeproject.org/experiments/ENCSR577OVP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC2. (DNAJC2_BGKLV24)
experiment encode accession: ENCSR577OVP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB370KSD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DNAJC2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0f674a2a-4977-48b6-9ea1-ffb6a1a432a5/@@download/attachment/L-DNAJC2_BGKLV24_18_17609.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC2. (DNAJC2_BGKLV24_18_17609)

value: 53 year

value: adult

value: female

value: Brenton Graveley, UConn

value: ENCBS723ZIW at ENCODE; https://www.encodeproject.org/ENCBS723ZIW/

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


title: MB231shKAP1_wt

city: Duarte

first: David

middle: Kong

last: Ann

address: 1500 E. Duarte Rd.

institute: City of Hope

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using software Partek
Genome_build: hg19
Supplementary_files_format_and_content: one tab-delimited text file including log2(RPKM) values for each Sample ...

source_name: MDA-MB-231 cell

growth_protocol: Cultured in DMEM supplemented with 10% FBS in 37°C, 5% CO2

extract_protocol:
Total RNA was isolated from cells using the TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: variation

value: wild type


title: MB231shKAP1_S473A


title: MB231shKAP1_S473D


title: shRNA RNA-seq from HepG2 (ENCLB144PBT)

description:
https://www.encodeproject.org/experiments/ENCSR573UBF/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TFIP11 in HepG2 cells followed by RNA-seq. (TFIP11_BGHLV17)
experiment encode accession: ENCSR573UBF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB144PBT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting TFIP11

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fb1a149d-645c-4579-8fa5-1cc2a627feca/@@download/attachment/L-TFIP11_BGHLV17_33.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TFIP11. (TFIP11_BGHLV17_33)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS962POD at ENCODE; https://www.encodeproject.org/ENCBS962POD/

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 (ENCLB024HRW)

description:
https://www.encodeproject.org/experiments/ENCSR577OVP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC2. (DNAJC2_BGKLV24)
experiment encode accession: ENCSR577OVP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB024HRW
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/287bfdc4-7eb6-4cbf-882b-e5c821662b5a/@@download/attachment/L-DNAJC2_BGKLV24_17_17608.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC2. (DNAJC2_BGKLV24_17_17608)

value: chronic myelogenous leukemia (CML)

value: ENCBS025ONJ at ENCODE; https://www.encodeproject.org/ENCBS025ONJ/

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


title: 400nM_5_Rep2


title: microRNA-seq from thyroid gland (ENCLB816BUM)

description:
https://www.encodeproject.org/experiments/ENCSR566RDG/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human thyroid gland
experiment encode accession: ENCSR566RDG
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB816BUM
size range: <30

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

value: thyroid gland

value: tissue

value: Thyroid

value: 54 year

value: adult

value: Barbara Wold, Caltech

value: ENCBS504VQX at ENCODE; https://www.encodeproject.org/ENCBS504VQX/

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


title: microRNA-seq from thyroid gland (ENCLB658GGD)

description:
https://www.encodeproject.org/experiments/ENCSR566RDG/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human thyroid gland
experiment encode accession: ENCSR566RDG
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB658GGD
size range: <30

value: male

value: ENCBS182ITA at ENCODE; https://www.encodeproject.org/ENCBS182ITA/


title: shRNA RNA-seq from HepG2 (ENCLB731PTU)

description:
https://www.encodeproject.org/experiments/ENCSR570CWH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against BCCIP in HepG2 cells followed by RNA-seq. (BCCIP_BGHLV17)
experiment encode accession: ENCSR570CWH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB731PTU
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7b05b702-135b-43e3-a2ce-611374a05fcb/@@download/attachment/L-BCCIP_BGHLV17_46.pdf

value: BCCIP

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against BCCIP. (BCCIP_BGHLV17_46)

value: child

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS928CHW at ENCODE; https://www.encodeproject.org/ENCBS928CHW/

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


title: shRNA RNA-seq from K562 (ENCLB466TXY)

description:
https://www.encodeproject.org/experiments/ENCSR584LDM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX27 in K562 cells followed by RNA-seq. (DDX27_BGKLV19)
experiment encode accession: ENCSR584LDM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR245BNJ
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB466TXY
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/adf2971a-5dfa-4c75-a641-49d8748deede/@@download/attachment/L-DDX27_BGKLV19_12A.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX27. (DDX27_BGKLV19_12A)

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS907QMF at ENCODE; https://www.encodeproject.org/ENCBS907QMF/

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 (ENCLB678MEZ)

description:
https://www.encodeproject.org/experiments/ENCSR570CWH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against BCCIP in HepG2 cells followed by RNA-seq. (BCCIP_BGHLV17)
experiment encode accession: ENCSR570CWH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB678MEZ
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/78bb5fc5-078c-4a89-a6e7-65029c716316/@@download/attachment/L-BCCIP_BGHLV17_45.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against BCCIP. (BCCIP_BGHLV17_45)

value: male

value: ENCBS322SEN at ENCODE; https://www.encodeproject.org/ENCBS322SEN/

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


title: polyA mRNA RNA-seq from HepG2 (ENCLB334PQC)

description:
https://www.encodeproject.org/experiments/ENCSR561FEE/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial total fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR561FEE
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB334PQC
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line

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

value: 15 year

value: child

value: Eric Lécuyer, IRCM

value: ENCBS775RGP at ENCODE; https://www.encodeproject.org/ENCBS775RGP/


title: polyA mRNA RNA-seq from HepG2 (ENCLB806KQR)

description:
https://www.encodeproject.org/experiments/ENCSR561FEE/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial total fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR561FEE
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB806KQR
size range: >200
spikeins used: /references/ENCSR422PLF/

value: hepatocellular carcinoma

value: ENCBS608AFV at ENCODE; https://www.encodeproject.org/ENCBS608AFV/

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


title: shRNA RNA-seq from K562 (ENCLB240QHE)

description:
https://www.encodeproject.org/experiments/ENCSR560RSZ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX52_06 in K562 cells followed by RNA-seq. (DDX52_BGKLV19)
experiment encode accession: ENCSR560RSZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB240QHE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX52

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/32aa12cc-f77a-443b-9377-8881069e4b93/@@download/attachment/L-DDX52_BGKLV19_18B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX52. (DDX52_BGKLV19_18B)

value: adult

value: female

value: Brenton Graveley, UConn

value: ENCBS957NCU at ENCODE; https://www.encodeproject.org/ENCBS957NCU/


title: siRNA RNA-seq from K562 (ENCLB936DMZ)

description:
https://www.encodeproject.org/experiments/ENCSR555CYH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ZNF180.
experiment encode accession: ENCSR555CYH
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR401RKW, ENCSR608CVU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB936DMZ
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting ZNF180

value: K562 cells treated with a siRNA knockdown against ZNF180, used in RNA-seq experiments.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS588EST at ENCODE; https://www.encodeproject.org/ENCBS588EST/

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


title: siRNA RNA-seq from K562 (ENCLB471ZGA)

description:
https://www.encodeproject.org/experiments/ENCSR555CYH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ZNF180.
experiment encode accession: ENCSR555CYH
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR401RKW, ENCSR608CVU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB471ZGA
size range: >200
spikeins used: /references/ENCSR866KGS/

value: ENCBS635YQN at ENCODE; https://www.encodeproject.org/ENCBS635YQN/


title: shRNA RNA-seq from HepG2 (ENCLB483ITG)

description:
https://www.encodeproject.org/experiments/ENCSR573UBF/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TFIP11 in HepG2 cells followed by RNA-seq. (TFIP11_BGHLV17)
experiment encode accession: ENCSR573UBF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB483ITG
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/a65f08f4-baf9-44b6-baca-fc0f0a9b63df/@@download/attachment/L-TFIP11_BGHLV17_34.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TFIP11. (TFIP11_BGHLV17_34)

value: 15 year

value: child

value: male

value: ENCBS137REJ at ENCODE; https://www.encodeproject.org/ENCBS137REJ/

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


title: shRNA RNA-seq from K562 (ENCLB479KQQ)

description:
https://www.encodeproject.org/experiments/ENCSR560RSZ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX52_06 in K562 cells followed by RNA-seq. (DDX52_BGKLV19)
experiment encode accession: ENCSR560RSZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB479KQQ
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/97f0adc2-c55d-4710-a19d-5b0c72ec0212/@@download/attachment/L-DDX52_BGKLV19_17B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX52. (DDX52_BGKLV19_17B)

value: adult

value: ENCBS416ZWV at ENCODE; https://www.encodeproject.org/ENCBS416ZWV/

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


title: shRNA RNA-seq from K562 (ENCLB576CDW)

description:
https://www.encodeproject.org/experiments/ENCSR558XNA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PUF60. (PUF60-BGKLV25)
experiment encode accession: ENCSR558XNA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB576CDW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PUF60

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/869b11ce-cdc1-4b0a-967f-5364d39a0c72/@@download/attachment/L-PUF60-BGKLV25-44.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PUF60. (PUF60-BGKLV25-44)

value: 53 year

value: female

value: Brenton Graveley, UConn

value: ENCBS456TNJ at ENCODE; https://www.encodeproject.org/ENCBS456TNJ/


title: microRNA-seq from uterus (ENCLB310MTK)

description:
https://www.encodeproject.org/experiments/ENCSR550GPA/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human uterus
experiment encode accession: ENCSR550GPA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB310MTK
size range: <30

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

value: uterus

value: tissue

value: Uterus

value: 51 year

value: Barbara Wold, Caltech

value: ENCBS171SNZ at ENCODE; https://www.encodeproject.org/ENCBS171SNZ/

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


title: shRNA RNA-seq from K562 (ENCLB272GWS)

description:
https://www.encodeproject.org/experiments/ENCSR558XNA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PUF60. (PUF60-BGKLV25)
experiment encode accession: ENCSR558XNA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB272GWS
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/7c07fd54-d2b7-4f4c-b6d1-21386c7fc916/@@download/attachment/L-PUF60-BGKLV25-43.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PUF60. (PUF60-BGKLV25-43)

value: chronic myelogenous leukemia (CML)

value: ENCBS948HVW at ENCODE; https://www.encodeproject.org/ENCBS948HVW/

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


title: shRNA RNA-seq from K562 (ENCLB074RMZ)

description:
https://www.encodeproject.org/experiments/ENCSR552NBS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0_BGKLV24_B)
experiment encode accession: ENCSR552NBS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB074RMZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting HNRNPA0

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8a452c96-1fb3-496a-9acd-8d5bbd61e1a2/@@download/attachment/L-HNRNPA0_BGKLV24_30B.pdf

value: RNA-seq on k562 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0_BGKLV24_30B)

value: adult

value: ENCBS409CCX at ENCODE; https://www.encodeproject.org/ENCBS409CCX/

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


title: shRNA RNA-seq from K562 (ENCLB118ECI)

description:
https://www.encodeproject.org/experiments/ENCSR572FFX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV21)
experiment encode accession: ENCSR572FFX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB118ECI
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/143c10ba-59b6-48ac-b0e3-81626215c373/@@download/attachment/L-non-target_BGKLV21_1.pdf

value: Control

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (non-target_BGKLV21_1)

value: 53 year

value: female

value: Brenton Graveley, UConn

value: ENCBS709TUN at ENCODE; https://www.encodeproject.org/ENCBS709TUN/


title: shRNA RNA-seq from K562 (ENCLB663HDM)

description:
https://www.encodeproject.org/experiments/ENCSR552NBS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0_BGKLV24_B)
experiment encode accession: ENCSR552NBS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB663HDM
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/122e9e95-1f00-4fd2-b794-104fe743b6a5/@@download/attachment/L-HNRNPA0_BGKLV24_29B.pdf

value: RNA-seq on k562 cells treated with an shRNA knockdown against HNRNPA0. (HNRNPA0_BGKLV24_29B)

value: ENCBS463ABO at ENCODE; https://www.encodeproject.org/ENCBS463ABO/


title: microRNA-seq from uterus (ENCLB781IOM)

description:
https://www.encodeproject.org/experiments/ENCSR550GPA/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human uterus
experiment encode accession: ENCSR550GPA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB781IOM
size range: <30

value: uterus

value: tissue

value: Uterus

value: 51 year

value: Barbara Wold, Caltech

value: ENCBS133MAA at ENCODE; https://www.encodeproject.org/ENCBS133MAA/

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


title: polyA mRNA RNA-seq from K562 (ENCLB075GEK)

description:
https://www.encodeproject.org/experiments/ENCSR545DKY/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial total fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR545DKY
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB075GEK
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: adult

value: chronic myelogenous leukemia (CML)

value: Eric Lécuyer, IRCM

value: ENCBS741VGS at ENCODE; https://www.encodeproject.org/ENCBS741VGS/

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


title: shRNA RNA-seq from K562 (ENCLB504RCK)

description:
https://www.encodeproject.org/experiments/ENCSR556FNN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PPIL4. (PPIL4_BGKLV24_B)
experiment encode accession: ENCSR556FNN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB504RCK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PPIL4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b5c7a9a2-97c1-4f31-b6a7-33f0c1e5ac44/@@download/attachment/L-PPIL4_BGKLV24_46B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PPIL4. (PPIL4_BGKLV24_46B)

value: 53 year

value: female

value: Brenton Graveley, UConn

value: ENCBS001TOZ at ENCODE; https://www.encodeproject.org/ENCBS001TOZ/

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


title: polyA mRNA RNA-seq from HepG2 (ENCLB788HAS)

description:
https://www.encodeproject.org/experiments/ENCSR541TIG/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial membrane fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR541TIG
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB788HAS
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line membrane fraction

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: membrane

value: ENCBS346DEZ at ENCODE; https://www.encodeproject.org/ENCBS346DEZ/

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 (ENCLB570OOU)

description:
https://www.encodeproject.org/experiments/ENCSR547NWD/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against AARS in HepG2 cells followed by RNA-seq. (AARS_BGHLV17)
experiment encode accession: ENCSR547NWD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB570OOU
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8a0b679b-3d4a-455d-b1ef-6ba51432e367/@@download/attachment/L-AARS_BGHLV17_1.pdf

value: AARS

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against AARS. (AARS_BGHLV17_1)

value: ENCBS453TYZ at ENCODE; https://www.encodeproject.org/ENCBS453TYZ/


title: shRNA RNA-seq from HepG2 (ENCLB812DMC)

description:
https://www.encodeproject.org/experiments/ENCSR547NWD/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against AARS in HepG2 cells followed by RNA-seq. (AARS_BGHLV17)
experiment encode accession: ENCSR547NWD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB812DMC
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/206a1c20-320e-4a9a-8894-f16f18c99b66/@@download/attachment/L-AARS_BGHLV17_2.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TROVE2. (AARS_BGHLV17_2)

value: ENCBS096XGH at ENCODE; https://www.encodeproject.org/ENCBS096XGH/


title: polyA mRNA RNA-seq from K562 (ENCLB365AUY)

description:
https://www.encodeproject.org/experiments/ENCSR545DKY/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial total fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR545DKY
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB365AUY
size range: >200
spikeins used: /references/ENCSR866KGS/

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Eric Lécuyer, IRCM

value: ENCBS016SXN at ENCODE; https://www.encodeproject.org/ENCBS016SXN/

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


title: RAMPAGE from bronchus fibroblast of lung (ENCLB851QFJ)

description:
https://www.encodeproject.org/experiments/ENCSR540CRO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from primary bronchial fibroblast cells (HBF). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR540CRO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR620NSN
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB851QFJ
size range: >200

source_name: Homo sapiens bronchus fibroblast of lung primary cell

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1a943515-5c18-465c-ac09-62792c91b3ed/@@download/attachment/LID295176.pdf

value: bronchus fibroblast of lung

value: primary cell

value: Bronchial primary cell fibroblasts (HBF) from an unknown donor (no metadata associated with the donor).

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

value: ENCBS302ZPK at ENCODE; https://www.encodeproject.org/ENCBS302ZPK/

value: Derived from ENCODE donor ENCDO108OFX; https://www.encodeproject.org/ENCDO108OFX/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=3425


title: RAMPAGE from SJCRH30 (ENCLB825GXT)

description:
https://www.encodeproject.org/experiments/ENCSR540YVD/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SJCRH30, a metastatic rhabdomyosarcoma from a 17 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR540YVD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR568YRP
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB825GXT
size range: >200

source_name: Homo sapiens SJCRH30 immortalized cell line

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/af57a915-4def-4125-b070-39e0734bb230/@@download/attachment/288551.pdf

value: immortalized cell line

value: This immortalized cell line was established from cells from the metastatic site of the bone marrow of a child with rhabdomyosarcoma.

value: 17 year

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS517AAA at ENCODE; https://www.encodeproject.org/ENCBS517AAA/

value: Derived from ENCODE donor ENCDO339AAA; https://www.encodeproject.org/ENCDO339AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0041; http://web.expasy.org/cellosaurus/CVCL_0041


title: total RNA-seq from thyroid gland (ENCLB637GXV)

description:
https://www.encodeproject.org/experiments/ENCSR532LJV/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's thyroid tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR532LJV
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB637GXV
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens thyroid gland tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/77923c25-65c2-4770-a52e-d8ac462cd9de/@@download/attachment/295770.pdf

value: thyroid gland

value: tissue

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

value: 37 year

value: adult

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

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


title: shRNA RNA-seq from K562 (ENCLB328NFA)

description:
https://www.encodeproject.org/experiments/ENCSR556FNN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PPIL4. (PPIL4_BGKLV24_B)
experiment encode accession: ENCSR556FNN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB328NFA
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/cf2e1af1-aa24-4d69-900e-5b6e76bd4a97/@@download/attachment/L-PPIL4_BGKLV24_45B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PPIL4. (PPIL4_BGKLV24_45B)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS667PRV at ENCODE; https://www.encodeproject.org/ENCBS667PRV/

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 bronchus fibroblast of lung (ENCLB412CHU)

description:
https://www.encodeproject.org/experiments/ENCSR540CRO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from primary bronchial fibroblast cells (HBF). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR540CRO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR620NSN
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB412CHU
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/79a31be5-64ea-4ff9-8a62-e0941afbd9ca/@@download/attachment/LID295175.pdf

value: bronchus fibroblast of lung

value: primary cell

value: Human Bronchial Fibroblasts (HBF) from ScienCell Research Laboratories are isolated from human bronchus tissue.  They resemble a mesenchymal stem cell phenotype and their principle function is the production of type III collagen, elastin, and proteoglycans of the extracellular matrix.

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

value: ENCBS787BHC at ENCODE; https://www.encodeproject.org/ENCBS787BHC/

value: Derived from ENCODE donor ENCDO108OFX; https://www.encodeproject.org/ENCDO108OFX/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=3425


title: polyA mRNA RNA-seq from K562 (ENCLB538THW)

description:
https://www.encodeproject.org/experiments/ENCSR530NHO/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial nucleus fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR530NHO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB538THW
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line nuclear fraction

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

value: immortalized cell line

value: adult

value: nucleus

value: Eric Lécuyer, IRCM

value: ENCBS746GKH at ENCODE; https://www.encodeproject.org/ENCBS746GKH/


title: polyA mRNA RNA-seq from K562 (ENCLB278NDX)

description:
https://www.encodeproject.org/experiments/ENCSR530NHO/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial nucleus fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR530NHO
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB278NDX
size range: >200
spikeins used: /references/ENCSR866KGS/

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS885ULI at ENCODE; https://www.encodeproject.org/ENCBS885ULI/


title: microRNA-seq from neural progenitor cell (ENCLB803VTA)

description:
https://www.encodeproject.org/experiments/ENCSR511YYU/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human neural progenitor cell
experiment encode accession: ENCSR511YYU
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB803VTA
size range: <30

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

value: neural progenitor cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/

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


title: siRNA RNA-seq from K562 (ENCLB642GCK)

description:
https://www.encodeproject.org/experiments/ENCSR509YMP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ZMIZ1.
experiment encode accession: ENCSR509YMP
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR644GSV
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB642GCK
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting ZMIZ1

value: immortalized cell line

value: K562 cells treated with a siRNA knockdown against ZMIZ1, used in RNA-seq experiments.

value: adult

value: Sherman Weissman, Yale

value: ENCBS631FGT at ENCODE; https://www.encodeproject.org/ENCBS631FGT/

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

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: microRNA-seq from neural progenitor cell (ENCLB698QQX)

description:
https://www.encodeproject.org/experiments/ENCSR511YYU/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human neural progenitor cell
experiment encode accession: ENCSR511YYU
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB698QQX
size range: <30

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: female

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/


title: siRNA RNA-seq from K562 (ENCLB513FVQ)

description:
https://www.encodeproject.org/experiments/ENCSR509YMP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ZMIZ1.
experiment encode accession: ENCSR509YMP
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR644GSV
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB513FVQ
size range: >200
spikeins used: /references/ENCSR866KGS/

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS975PJY at ENCODE; https://www.encodeproject.org/ENCBS975PJY/


title: polyA mRNA RNA-seq from HepG2 (ENCLB045OPB)

description:
https://www.encodeproject.org/experiments/ENCSR541TIG/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial membrane fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR541TIG
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB045OPB
size range: >200
spikeins used: /references/ENCSR422PLF/

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Eric Lécuyer, IRCM

value: membrane

value: ENCBS910PZQ at ENCODE; https://www.encodeproject.org/ENCBS910PZQ/

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 (ENCLB237RBW)

description:
https://www.encodeproject.org/experiments/ENCSR519KXM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SLBP. (SLBP-BGHLV23)
experiment encode accession: ENCSR519KXM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB237RBW
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/54721809-cc4c-48f0-9df8-d4b845c6f53a/@@download/attachment/L-SLBP-BGHLV23-41.pdf

value: SLBP

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SLBP. (SLBP-BGHLV23-41)

value: Brenton Graveley, UConn

value: ENCBS720SBS at ENCODE; https://www.encodeproject.org/ENCBS720SBS/


title: shRNA RNA-seq from K562 (ENCLB998LYB)

description:
https://www.encodeproject.org/experiments/ENCSR528ASX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against GRWD1. (GRWD1_BGKLV21)
experiment encode accession: ENCSR528ASX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB998LYB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting GRWD1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/595c57ef-1502-4b46-a216-5b7105ce6afe/@@download/attachment/L-GRWD1_BGKLV21_16_17565.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against GRWD1. (GRWD1_BGKLV21_16_17565)

value: adult

value: female

value: 53 year

value: ENCBS861PFY at ENCODE; https://www.encodeproject.org/ENCBS861PFY/

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 (ENCLB311FRB)

description:
https://www.encodeproject.org/experiments/ENCSR528ASX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against GRWD1. (GRWD1_BGKLV21)
experiment encode accession: ENCSR528ASX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB311FRB
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/26642e79-f1c8-4f74-baeb-b01935015cc9/@@download/attachment/L-GRWD1_BGKLV21_15_17564.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against GRWD1. (GRWD1_BGKLV21_15_17564)

value: chronic myelogenous leukemia (CML)

value: ENCBS654PMT at ENCODE; https://www.encodeproject.org/ENCBS654PMT/


title: shRNA RNA-seq from HepG2 (ENCLB210TCP)

description:
https://www.encodeproject.org/experiments/ENCSR519KXM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SLBP. (SLBP-BGHLV23)
experiment encode accession: ENCSR519KXM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB210TCP
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/bc7809e7-798b-4b8a-8a8e-27064231a21e/@@download/attachment/L-SLBP-BGHLV23-42.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SLBP. (SLBP-BGHLV23-42)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS351JCJ at ENCODE; https://www.encodeproject.org/ENCBS351JCJ/

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


title: RAMPAGE from M059J (ENCLB618LRC)

description:
https://www.encodeproject.org/experiments/ENCSR507GYW/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line M059J isolated from a malignant glioblastoma of a 33 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR507GYW
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR696SMK
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB618LRC
size range: >200

source_name: Homo sapiens M059J immortalized cell line

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/016838c5-921d-46bd-8dc4-8d5b74b731a4/@@download/attachment/292971.pdf

value: immortalized cell line

value: 33 year

value: malignant glioblastoma

value: John Stamatoyannopoulos, UW

value: ENCBS304XWS at ENCODE; https://www.encodeproject.org/ENCBS304XWS/

value: Derived from ENCODE donor ENCDO000ACY; https://www.encodeproject.org/ENCDO000ACY/

value: ENCODE dbxrefs Cellosaurus CVCL_0400; http://web.expasy.org/cellosaurus/CVCL_0400


title: shRNA RNA-seq from HepG2 (ENCLB242ZVA)

description:
https://www.encodeproject.org/experiments/ENCSR509LIV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1-BGHLV23)
experiment encode accession: ENCSR509LIV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB242ZVA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EIF4G1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e0f8ea7f-3fc8-4ddb-98e4-8cb12ac5afd4/@@download/attachment/L-EIF4G1-BGHLV23-14.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1-BGHLV23-14)

value: Brenton Graveley, UConn

value: ENCBS610UML at ENCODE; https://www.encodeproject.org/ENCBS610UML/

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


title: RAMPAGE from SJCRH30 (ENCLB941URL)

description:
https://www.encodeproject.org/experiments/ENCSR540YVD/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SJCRH30, a metastatic rhabdomyosarcoma from a 17 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR540YVD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR568YRP
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB941URL
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/5f51bddf-4b94-498a-99aa-ab403f7ef7d8/@@download/attachment/288550.pdf

value: This immortalized cell line was established from cells from the metastatic site of the bone marrow of a child with rhabdomyosarcoma

value: 17 year

value: unknown

value: ENCBS516AAA at ENCODE; https://www.encodeproject.org/ENCBS516AAA/

value: Derived from ENCODE donor ENCDO339AAA; https://www.encodeproject.org/ENCDO339AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0041; http://web.expasy.org/cellosaurus/CVCL_0041


title: RAMPAGE from SK-MEL-5 (ENCLB106JGK)

description:
https://www.encodeproject.org/experiments/ENCSR506WDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR506WDZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR201WVA
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB106JGK
size range: >200

source_name: Homo sapiens SK-MEL-5 immortalized cell line nuclear fraction

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/93c513fe-5ebc-4184-bacf-b7edb9979a2b/@@download/attachment/LID294490.pdf

value: immortalized cell line

value: An immortalized malignant melanoma cell line derived from a metastatic axillary node of a 24 year old female.

value: 24 year

value: adult

value: female

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS029HXQ at ENCODE; https://www.encodeproject.org/ENCBS029HXQ/

value: Derived from ENCODE donor ENCDO338AAA; https://www.encodeproject.org/ENCDO338AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0527; http://web.expasy.org/cellosaurus/CVCL_0527

value: ATCC sample source; http://www.atcc.org/products/all/HTB-70.aspx


title: shRNA RNA-seq from K562 (ENCLB570ESA)

description:
https://www.encodeproject.org/experiments/ENCSR495YSS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2C2. (K-EIF2C2)
experiment encode accession: ENCSR495YSS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB570ESA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting AGO2

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/53494e93-99c5-40f3-b475-3991d4a40989/@@download/attachment/L-K-EIF2C2-1.pdf

value: K562 cells treated with an shRNA knockdown against EIF2C2, used in RNA-seq experiments. (K-EIF2C2-1)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS215KUV at ENCODE; https://www.encodeproject.org/ENCBS215KUV/

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: microRNA-seq from right atrium auricular region (ENCLB892RMT)

description:
https://www.encodeproject.org/experiments/ENCSR493KWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human right cardiac atrium
experiment encode accession: ENCSR493KWZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB892RMT
size range: <30

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

value: right atrium auricular region

value: tissue

value: Heart - Atrial Appendage

value: 51 year

value: Barbara Wold, Caltech

value: ENCBS827YEF at ENCODE; https://www.encodeproject.org/ENCBS827YEF/

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


title: shRNA RNA-seq from HepG2 (ENCLB808KKO)

description:
https://www.encodeproject.org/experiments/ENCSR494VSD/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against CSDA in HepG2 cells followed by RNA-seq. (CSDA-30-BGHLV20)
experiment encode accession: ENCSR494VSD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB808KKO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting YBX3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6cb9a141-1f7e-40a2-963c-01f47d6c3a62/@@download/attachment/L-CSDA-30-BGHLV20-9_17710.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CSDA. (CSDA-30-BGHLV20-9_17710)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS573EMA at ENCODE; https://www.encodeproject.org/ENCBS573EMA/

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

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


title: microRNA-seq from right atrium auricular region (ENCLB309APC)

description:
https://www.encodeproject.org/experiments/ENCSR493KWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human right cardiac atrium
experiment encode accession: ENCSR493KWZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB309APC
size range: <30

value: adult

value: female

value: ENCBS168GTY at ENCODE; https://www.encodeproject.org/ENCBS168GTY/


title: shRNA RNA-seq from HepG2 (ENCLB928XWK)

description:
https://www.encodeproject.org/experiments/ENCSR494VSD/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against CSDA in HepG2 cells followed by RNA-seq. (CSDA-30-BGHLV20)
experiment encode accession: ENCSR494VSD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB928XWK
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/1d5540fb-1972-41c8-80fa-3cd10057607c/@@download/attachment/L-CSDA-30-BGHLV20-10_17711.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CSDA. (CSDA-30-BGHLV20-10_17711)

value: Brenton Graveley, UConn

value: ENCBS433CTJ at ENCODE; https://www.encodeproject.org/ENCBS433CTJ/


title: shRNA RNA-seq from K562 (ENCLB771CGO)

description:
https://www.encodeproject.org/experiments/ENCSR495YSS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2C2. (K-EIF2C2)
experiment encode accession: ENCSR495YSS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB771CGO
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/270b5df4-4fbd-4a93-826b-a2ebf8bd2666/@@download/attachment/L-K-EIF2C2-2.pdf

value: K562 cells treated with an shRNA knockdown against EIF2C2, used in RNA-seq experiments. (K-EIF2C2-2)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS963QYF at ENCODE; https://www.encodeproject.org/ENCBS963QYF/

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 (ENCLB169PEO)

description:
https://www.encodeproject.org/experiments/ENCSR492BKM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FAM120A in K562 cells followed by RNA-seq. (FAM120A_BGKLV19)
experiment encode accession: ENCSR492BKM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB169PEO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting FAM120A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6547e71d-0b62-4d5f-81cf-fc237c014a01/@@download/attachment/L-FAM120A_BGKLV19_27B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against FAM120A. (FAM120A_BGKLV19_27B)

value: ENCBS897PRR at ENCODE; https://www.encodeproject.org/ENCBS897PRR/


title: shRNA RNA-seq from K562 (ENCLB360SAP)

description:
https://www.encodeproject.org/experiments/ENCSR492BKM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FAM120A in K562 cells followed by RNA-seq. (FAM120A_BGKLV19)
experiment encode accession: ENCSR492BKM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB360SAP
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/87c87d01-a243-4ecb-b191-63f6a82ae43a/@@download/attachment/L-FAM120A_BGKLV19_28B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FAM120A. (FAM120A_BGKLV19_28B)

value: ENCBS173WPT at ENCODE; https://www.encodeproject.org/ENCBS173WPT/


title: microRNA-seq from gastrocnemius medialis (ENCLB092GNA)

description:
https://www.encodeproject.org/experiments/ENCSR491VSN/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human skeletal muscle tissue
experiment encode accession: ENCSR491VSN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB092GNA
size range: <30

source_name: Homo sapiens gastrocnemius medialis tissue male adult (54 years)

value: gastrocnemius medialis

value: tissue

value: Muscle - Skeletal

value: 54 year

value: adult

value: male

value: Barbara Wold, Caltech

value: ENCBS178APY at ENCODE; https://www.encodeproject.org/ENCBS178APY/

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


title: microRNA-seq from gastrocnemius medialis (ENCLB979ZDU)

description:
https://www.encodeproject.org/experiments/ENCSR491VSN/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human skeletal muscle tissue
experiment encode accession: ENCSR491VSN
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB979ZDU
size range: <30

value: ENCBS689LIY at ENCODE; https://www.encodeproject.org/ENCBS689LIY/


title: AR (MFZ-treated)

city: Cerdanyola del Vallés

last: Manzano

state: Barcelona

address: Edifici CRAG

department: PLANT METABOLISM AND METABOLIC ENGINEERING

country: Spain

institute: Centre for Research in Agricultural Genomics (CRAG)

data_processing:
Quality of the reads obtained by HiSeq2000 sequencing was checked with FastQC software (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/). Preprocessing of the reads was performed with fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and aScidea specific perl scripts property of aScidea (http://www.ascidea.com) in order to filter regions of low quality. Adaptors and low quality bases at the ends of sequences and reads with undetermined bases or with 80% of their bases with less than 20% quality score were trimmed and raw reads that passed the quality filter threshold were mapped using Tophat 2.0.7 (Trapnell et al., 2009) and Bowtie 2 2.0.6 (Langmead et al., 2009; Langmead and Salzberg, 2012) to generate read alignments for each sample. The reference genome used was the Arabidopsis thaliana genome TAIR10 and genomic annotations were obtained from TAIR database (http://www.arabidopsis.org) in general feature format 3 (GFF3). The inner distance between mate pairs used was 50 bp and the rest of the parameters were used with the default values.
The transcript isoform level and gene level counts were calculated and FPKM normalized using Cufflinks 2.0.2 software (Trapnell et al., 2010).
Differential transcript expression was then computed using Cuffdiff (Trapnell et al., 2013). The resulting lists of differentially expressed genes were filtered by log2 (fold_change) >2 and < -2 and a q-value of 0.05.
Genome_build: The reference genome used was the Arabidopsis thaliana genome TAIR10 and genomic annotations were obtained from TAIR database (http://www.arabidopsis.org) in general feature format 3 (GFF3).
Supplementary_files_format_and_content: "amiFPSa_gene_exp.diff" is an excel file containing  the transcript isoform level and gene level counts (FPKM normalized) using Cufflinks 2.0.2 software (Trapnell et al., 2010)

organism: Arabidopsis thaliana

growth_protocol: amiFPSa plants were first grown for 3 days on MS and then transferred to MS (control) or to MS supplemented with MFZ (treatment)and grown for 5 days more.

extract_protocol:
Seedlings were ground to a fine powder using TissueLyser equipment and used for extraction of RNA using NucleoSpin® RNA Plant (Macherey‐Nagel) according to the manufacturer’s instructions, including the DNase step. The quality and quantity of total RNA samples were assessed using a Bionalyzer Expert 2100 Instrument (Agilent Technologies) and an equimolar mixture of RNA samples from each treatment was prepared.
The RNA samples (3 μg) were fragmented and ligated with adaptors prior to cDNA synthesis and PCR amplification. The cDNA libraries were prepared according to the Illumina protocols and sequenced using an Illumina HiSeq2000 machine to perform 2x100 paired-end sequencing.

tag: ecotype

tag: genotype

value: amiFPSa

tag: tissue

value: whole seedling


title: shRNA RNA-seq from HepG2 (ENCLB273CWD)

description:
https://www.encodeproject.org/experiments/ENCSR486AIO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RPS19 in HepG2 cells followed by RNA-seq. (RPS19_BGHLV16)
experiment encode accession: ENCSR486AIO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB273CWD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RPS19

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/42bac0e2-3087-4373-b2e1-470cd8d0c144/@@download/attachment/L-RPS19_BGHLV16_46.pdf

tag: antibody

tag: line

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS19. (RPS19_BGHLV16_46)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS551CUU at ENCODE; https://www.encodeproject.org/ENCBS551CUU/

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 M059J (ENCLB276RHN)

description:
https://www.encodeproject.org/experiments/ENCSR507GYW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line M059J isolated from a malignant glioblastoma of a 33 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR507GYW
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR696SMK
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB276RHN
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/266a52aa-afda-4371-bbd4-d3474e7d7ac7/@@download/attachment/292970.pdf

tag: biosample encode accession

value: 33 year

value: adult

value: malignant glioblastoma

value: John Stamatoyannopoulos, UW

value: ENCBS062ILC at ENCODE; https://www.encodeproject.org/ENCBS062ILC/

value: Derived from ENCODE donor ENCDO000ACY; https://www.encodeproject.org/ENCDO000ACY/

value: ENCODE dbxrefs Cellosaurus CVCL_0400; http://web.expasy.org/cellosaurus/CVCL_0400


title: shRNA RNA-seq from HepG2 (ENCLB315NEG)

description:
https://www.encodeproject.org/experiments/ENCSR509LIV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1-BGHLV23)
experiment encode accession: ENCSR509LIV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB315NEG
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/cfc8d4a0-9abf-4110-a734-d189de141d61/@@download/attachment/L-EIF4G1-BGHLV23-13.pdf

tag: description

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G1. (EIF4G1-BGHLV23-13)

tag: age

value: male

value: ENCBS258IBQ at ENCODE; https://www.encodeproject.org/ENCBS258IBQ/


title: shRNA RNA-seq from HepG2 (ENCLB901PBR)

description:
https://www.encodeproject.org/experiments/ENCSR486AIO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPS19 in HepG2 cells followed by RNA-seq. (RPS19_BGHLV16)
experiment encode accession: ENCSR486AIO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB901PBR
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/2927eb7b-5b6c-45c4-9b5e-7ca0b31a89e8/@@download/attachment/L-RPS19_BGHLV16_45.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS19. (RPS19_BGHLV16_45)

value: 15 year

tag: dev stage

tag: Sex

value: ENCBS250EAA at ENCODE; https://www.encodeproject.org/ENCBS250EAA/


title: shRNA RNA-seq from K562 (ENCLB041HWE)

description:
https://www.encodeproject.org/experiments/ENCSR481YXD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP3. (K-IGF2BP3-25B)
experiment encode accession: ENCSR481YXD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR771ZZL
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB041HWE
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/93552ab1-a459-46d3-b00a-86ed91b27d1f/@@download/attachment/L-K-IGF2BP3-25B-2.pdf

value: K562 cells treated with an shRNA knockdown against IGF2BP3, used in RNA-seq experiments. (K-IGF2BP3-25B-2)

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: lab

value: Brenton Graveley, UConn

value: ENCBS630OAS at ENCODE; https://www.encodeproject.org/ENCBS630OAS/

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: AM (control)

value: amiFPSa

value: whole seedling


title: VBB_NC

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

data_processing:
Following sequencing, we trimmed Illumina adapter sequence from the ends of the reads using Trim Galore! (v0.2.7), mapped trimmed reads to the rhesus macaque genome (MacaM v7; Zimin et al.) using the STAR 2-pass method, and collated the number of reads that mapped uniquely to each annotated MacaM gene (v7.6.8) using HTSeq-count (v0.6.1) with the option “intersection-nonempty”.
We first filtered out genes that were very lowly or not detectably expressed in our samples by removing any gene with a median RPKM ≤ 2 in all 83 samples.
We normalized the resulting read count matrix using the function voom from the R package limma. We then modeled the normalized expression values as a function of the sample donor’s social group membership. Controlling for the identity of the group removes biological variation related to differences in group dynamics, and most technical batch effects related to sample collection and processing. The residuals of the model relating normalized expression to social group identity as our primary outcome measure in all subsequent analyses.
Genome_build: MacaM
Supplementary_files_format_and_content: [.txt] abundance measurements

molecule: polyA RNA

organism: Macaca mulatta

source_name: whole blood

extract_protocol:
We lysed and discarded the red cells from the remaining cell pellet by applying red blood cell lysis buffer (RBC lysis solution, 5 Prime Inc.) for 10 minutes followed by centrifugation. We lysed the remaining white blood cells in Qiazol for storage at -80°C, and extracted total RNA from each sample using the Qiagen miRNAEASY kit.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra RNA Library Prep Kit. Briefly, we purified the poly-adenylated mRNA from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then reverse transcribed into cDNA, ligated to Illumina adapters, size-selected for a median size of ~350 bp, and amplified via PCR for 13 cycles. We tagged each sample with a unique molecular barcode and pooled 10-12 samples per Illumina HiSeq 2500 lane of single-end 100 bp sequencing.

treatment_protocol: We drew 1 mL of whole blood from each female (in Phase 2 only) directly into a TruCulture tube (Myriad RBM) that contained cell culture media plus 1 μg/mL ultra pure lipopolysaccharide (LPS) from the E. coli 0111:B4 strain (“LPS+”), and another 1 mL of blood from the same draw into a TruCulture tube that contained cell culture media only (“control”). Samples were incubated in parallel for 4 hours at 37°C.

tag: cell type

value: white blood cells

value: VBB

tag: sample date

tag: study phase

value: phase 2

tag: study group

value: NC