title: RAMPAGE from A375 (ENCLB162IBE)

description:
https://www.encodeproject.org/experiments/ENCSR080XAB/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line A375. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR080XAB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR504VXC
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB162IBE
size range: >200

source_name: Homo sapiens A375 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/1fade950-1a84-45aa-b940-c89d686f3ed5/@@download/attachment/289924.pdf

value: Epithelial cells, malignant melanoma

value: 54 year

value: adult

value: female

value: malignant melanoma

value: Bradley Bernstein, Broad

value: ENCBS607AAA at ENCODE; https://www.encodeproject.org/ENCBS607AAA/

value: Derived from ENCODE donor ENCDO348AAA; https://www.encodeproject.org/ENCDO348AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0132; http://web.expasy.org/cellosaurus/CVCL_0132

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1619.aspx


title: shRNA RNA-seq from HepG2 (ENCLB862DHU)

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/ENCSR082YGI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPLP0 in HepG2 cells followed by RNA-seq. (RPLP0_BGHLV18)
experiment encode accession: ENCSR082YGI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB862DHU
size range: >200
spikeins used: /references/ENCSR449DXG/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RPLP0

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c7f1ec69-fa8b-4f3f-b6af-0491d4d6ed13/@@download/attachment/L-RPLP0_BGHLV18_53.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPLP0. (RPLP0_BGHLV18_53)

tag: biosample encode accession

tag: dev stage

value: child

tag: Sex

value: male

tag: age

value: 15 year

tag: health state

value: hepatocellular carcinoma

tag: lab

value: Brenton Graveley, UConn

tag: link

value: ENCBS877GRH at ENCODE; https://www.encodeproject.org/ENCBS877GRH/

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 A375 (ENCLB653CMB)

description:
https://www.encodeproject.org/experiments/ENCSR080XAB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line A375. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR080XAB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR504VXC
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB653CMB
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/8705cb76-5148-481d-a242-f943e2e7a220/@@download/attachment/289923.pdf

value: Epithelial cells, malignant melanoma

value: 54 year

value: adult

tag: passage number

value: female

value: ENCBS606AAA at ENCODE; https://www.encodeproject.org/ENCBS606AAA/


title: RAMPAGE from thyroid gland (ENCLB821XZO)

description:
https://www.encodeproject.org/experiments/ENCSR069LRO/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's thyroid gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR069LRO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR023ZXN
encode release date: 2016-03-16
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB821XZO
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cdffb4cc-3bf6-4d74-8811-b60cc570a4f8/@@download/attachment/295993.pdf

value: thyroid gland

value: tissue

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

value: Thomas Gingeras, CSHL

value: ENCBS624WYQ at ENCODE; https://www.encodeproject.org/ENCBS624WYQ/

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


title: shRNA RNA-seq from K562 (ENCLB792VKI)

description:
https://www.encodeproject.org/experiments/ENCSR079LMZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC21. (DNAJC21_BGKLV24)
experiment encode accession: ENCSR079LMZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB792VKI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DNAJC21

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fb27a90f-e820-49d1-903d-85207a9bb566/@@download/attachment/L-DNAJC21_BGKLV24_20_17612.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC21. (DNAJC21_BGKLV24_20_17612)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS244ZUD at ENCODE; https://www.encodeproject.org/ENCBS244ZUD/

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 (ENCLB878LWY)

description:
https://www.encodeproject.org/experiments/ENCSR070LJO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX1 in HepG2 cells followed by RNA-seq. (DDX1-BGHLV20)
experiment encode accession: ENCSR070LJO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB878LWY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7c1430e1-adcc-489d-9d8d-10a78d8e4618/@@download/attachment/L-DDX1-BGHLV20-12_17713.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX1. (DDX1-BGHLV20-12_17713)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS524YUI at ENCODE; https://www.encodeproject.org/ENCBS524YUI/

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: SGE_219

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. PMID 25319552) 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 that cell type.
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: peripheral blood mononuclear cells

growth_protocol: we drew 12-20 mL of blood from each female, purified the PBMC fraction using density gradient centrifugation, and performed fluorescent activated cell sortingto purify 5 PBMC populations. We sorted cell types as follows: classical monocytes (CD3-/CD20-/HLA-DR+/CD14+), natural killer cells (CD3-/CD20-/HLA-DR-/CD16+), B cells (CD3-/CD20+/HLA-DR+), helper T cells (CD3+/CD8-/CD4+), cytotoxic T cells (CD3+/CD8+/CD4-)

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction 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.

tag: cell type

tag: sample date

tag: study phase

value: phase 1

tag: study group


title: shRNA RNA-seq from HepG2 (ENCLB769ZMR)

description:
https://www.encodeproject.org/experiments/ENCSR070LJO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX1 in HepG2 cells followed by RNA-seq. (DDX1-BGHLV20)
experiment encode accession: ENCSR070LJO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB769ZMR
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/80f3134c-c777-49e8-8aa7-531158843fa2/@@download/attachment/L-DDX1-BGHLV20-11_17712.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX1. (DDX1-BGHLV20-11_17712)

value: ENCBS520MGH at ENCODE; https://www.encodeproject.org/ENCBS520MGH/


title: shRNA RNA-seq from HepG2 (ENCLB347AZD)

description:
https://www.encodeproject.org/experiments/ENCSR067AUG/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX59 in HepG2 cells followed by RNA-seq. (DDX59_BGHLV18)
experiment encode accession: ENCSR067AUG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB347AZD
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c0d49aaa-86cb-4107-a528-bc304a9c2896/@@download/attachment/L-DDX59_BGHLV18_4.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX59. (DDX59_BGHLV18_4)

value: ENCBS157CAN at ENCODE; https://www.encodeproject.org/ENCBS157CAN/


title: SGE_217

value: cytotoxic T (CD3+/CD4-/CD8+)


title: shRNA RNA-seq from HepG2 (ENCLB641COQ)

description:
https://www.encodeproject.org/experiments/ENCSR067AUG/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX59 in HepG2 cells followed by RNA-seq. (DDX59_BGHLV18)
experiment encode accession: ENCSR067AUG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB641COQ
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/bc6e15f5-e6f5-46ce-9ba6-a7b0c959bbf8/@@download/attachment/L-DDX59_BGHLV18_3.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX59. (DDX59_BGHLV18_3)

value: ENCBS542DRS at ENCODE; https://www.encodeproject.org/ENCBS542DRS/


title: SGE_218

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: siRNA RNA-seq from K562 (ENCLB371UHP)

description:
https://www.encodeproject.org/experiments/ENCSR067CAG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting CTCF.
experiment encode accession: ENCSR067CAG
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR756JGE, ENCSR443QFD
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB371UHP
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: CTCF

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

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS741ESC at ENCODE; https://www.encodeproject.org/ENCBS741ESC/

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


title: total RNA-seq from HepG2 (ENCLB765JDM)

description:
https://www.encodeproject.org/experiments/ENCSR061SFU/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial nucleus fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR061SFU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB765JDM
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line nuclear fraction

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

value: immortalized cell line

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

tag: subcellular fraction term name

value: nucleus

value: Eric Lécuyer, IRCM

value: ENCBS300GHC at ENCODE; https://www.encodeproject.org/ENCBS300GHC/

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: polyA mRNA RNA-seq from HepG2 (ENCLB941KGI)

description:
https://www.encodeproject.org/experiments/ENCSR058OSL/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial nucleus fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR058OSL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB941KGI
size range: >200
spikeins used: /references/ENCSR422PLF/

value: ENCBS296VMM at ENCODE; https://www.encodeproject.org/ENCBS296VMM/


title: SGE_216

value: helper T (CD3+/CD4+/CD8-)

value: phase 1


title: total RNA-seq from HepG2 (ENCLB476LNH)

description:
https://www.encodeproject.org/experiments/ENCSR061SFU/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial nucleus fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR061SFU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB476LNH
size range: >200
spikeins used: /references/ENCSR422PLF/

value: ENCBS077CZP at ENCODE; https://www.encodeproject.org/ENCBS077CZP/


title: SGE_212

value: cytotoxic T (CD3+/CD4-/CD8+)


title: polyA mRNA RNA-seq from HepG2 (ENCLB581UDH)

description:
https://www.encodeproject.org/experiments/ENCSR058OSL/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial nucleus fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR058OSL
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB581UDH
size range: >200
spikeins used: /references/ENCSR422PLF/

value: ENCBS055KDL at ENCODE; https://www.encodeproject.org/ENCBS055KDL/


title: SGE_213

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: SGE_214


title: SGE_220


title: SGE_211


title: SGE_215


title: RAMPAGE from SK-MEL-5 (ENCLB923HGA)

description:
https://www.encodeproject.org/experiments/ENCSR054RIR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SK-MEL-5, a metastatic malignant melanoma from 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: ENCSR054RIR
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR669KQU
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB923HGA
size range: >200

source_name: Homo sapiens SK-MEL-5 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/6c20259c-1893-4068-9ee3-c2a1955879cb/@@download/attachment/289910.pdf

value: immortalized cell line

value: 24 year

value: adult

value: female

value: John Stamatoyannopoulos, UW

value: ENCBS519AAA at ENCODE; https://www.encodeproject.org/ENCBS519AAA/

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

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


title: SGE_209


title: siRNA RNA-seq from K562 (ENCLB954ZOY)

description:
https://www.encodeproject.org/experiments/ENCSR051NHG/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting RAD21.
experiment encode accession: ENCSR051NHG
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR443QFD, ENCSR756JGE
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB954ZOY
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting RAD21

value: K562 cells treated with a siRNA knockdown against RAD21, used in RNA-seq experiments.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS155ZZZ at ENCODE; https://www.encodeproject.org/ENCBS155ZZZ/

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


title: siRNA RNA-seq from K562 (ENCLB003PWK)

description:
https://www.encodeproject.org/experiments/ENCSR051NHG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting RAD21.
experiment encode accession: ENCSR051NHG
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR443QFD, ENCSR756JGE
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB003PWK
size range: >200
spikeins used: /references/ENCSR866KGS/

value: ENCBS378WNR at ENCODE; https://www.encodeproject.org/ENCBS378WNR/

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


title: siRNA RNA-seq from K562 (ENCLB076JAC)

description:
https://www.encodeproject.org/experiments/ENCSR051NHG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting RAD21.
experiment encode accession: ENCSR051NHG
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR443QFD, ENCSR756JGE
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB076JAC
size range: >200
spikeins used: /references/ENCSR866KGS/

value: ENCBS019CUH at ENCODE; https://www.encodeproject.org/ENCBS019CUH/


title: SGE_207

value: cytotoxic T (CD3+/CD4-/CD8+)

value: phase 1


title: SGE_208

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: RAMPAGE from SK-MEL-5 (ENCLB019GZG)

description:
https://www.encodeproject.org/experiments/ENCSR054RIR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SK-MEL-5, a metastatic malignant melanoma from 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: ENCSR054RIR
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR669KQU
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB019GZG
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/194b997c-0354-451a-9875-3041b0fa93bb/@@download/attachment/289909.pdf

value: immortalized cell line

value: 24 year

value: adult

value: female

value: ENCBS518AAA at ENCODE; https://www.encodeproject.org/ENCBS518AAA/


title: SGE_206

value: helper T (CD3+/CD4+/CD8-)


title: shRNA RNA-seq from HepG2 (ENCLB493FYI)

description:
https://www.encodeproject.org/experiments/ENCSR052IYH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against HNRNPC in HepG2 cells followed by RNA-seq. (HNRNPC-BGHLV20)
experiment encode accession: ENCSR052IYH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB493FYI
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/36b90bd0-57c7-4a3c-a648-8b8cc76a077f/@@download/attachment/L-HNRNPC-BGHLV20-33_17722.pdf

value: HNRNPC

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPC. (HNRNPC-BGHLV20-33_17722)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS433TIQ at ENCODE; https://www.encodeproject.org/ENCBS433TIQ/

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 (ENCLB874PSY)

description:
https://www.encodeproject.org/experiments/ENCSR052IYH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against HNRNPC in HepG2 cells followed by RNA-seq. (HNRNPC-BGHLV20)
experiment encode accession: ENCSR052IYH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB874PSY
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/17a09563-5ffa-44ca-af5a-fbe9797fd3a0/@@download/attachment/L-HNRNPC-BGHLV20-34_17723.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPC. (HNRNPC-BGHLV20-34_17723)

value: ENCBS210TEK at ENCODE; https://www.encodeproject.org/ENCBS210TEK/


title: shRNA RNA-seq from HepG2 (ENCLB285WVR)

description:
https://www.encodeproject.org/experiments/ENCSR047VPW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FAM120A in HepG2 cells followed by RNA-seq. (FAM120A_BGHLV16)
experiment encode accession: ENCSR047VPW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB285WVR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/b32131ff-7add-41c9-b383-a54d9b3fc539/@@download/attachment/L-FAM120A_BGHLV16_25.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FAM120A. (FAM120A_BGHLV16_25)

value: ENCBS504IUW at ENCODE; https://www.encodeproject.org/ENCBS504IUW/


title: SGE_205

value: phase 1


title: SGE_204


title: shRNA RNA-seq from HepG2 (ENCLB121PMY)

description:
https://www.encodeproject.org/experiments/ENCSR047VPW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FAM120A in HepG2 cells followed by RNA-seq. (FAM120A_BGHLV16)
experiment encode accession: ENCSR047VPW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB121PMY
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/ef2058aa-3395-4d3c-836c-537ba7427527/@@download/attachment/L-FAM120A_BGHLV16_26.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against FAM120A. (FAM120A_BGHLV16_26)

value: ENCBS840QTY at ENCODE; https://www.encodeproject.org/ENCBS840QTY/


title: shRNA RNA-seq from K562 (ENCLB790EVQ)

description:
https://www.encodeproject.org/experiments/ENCSR047AJA/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SUB1 in K562 cells followed by RNA-seq. (SUB1 BGKLV13)
experiment encode accession: ENCSR047AJA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB790EVQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SUB1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6ad56cdb-9a3e-4d42-9b7a-43f817288c59/@@download/attachment/L-SUB1_BGKLV13_42.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUB1.(SUB1_BGKLV13_42)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS776WTE at ENCODE; https://www.encodeproject.org/ENCBS776WTE/

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: SGE_210


title: siRNA RNA-seq from K562 (ENCLB025BXE)

description:
https://www.encodeproject.org/experiments/ENCSR045TQN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ATF3.
experiment encode accession: ENCSR045TQN
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR128HAQ, ENCSR109YDL
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB025BXE
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting ATF3

value: K562 cells treated with a siRNA knockdown against ATF3, used in RNA-seq experiments.

value: Sherman Weissman, Yale

value: ENCBS903YXD at ENCODE; https://www.encodeproject.org/ENCBS903YXD/


title: SGE_203

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: shRNA RNA-seq from K562 (ENCLB410OUB)

description:
https://www.encodeproject.org/experiments/ENCSR047AJA/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SUB1 in K562 cells followed by RNA-seq. (SUB1 BGKLV13)
experiment encode accession: ENCSR047AJA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB410OUB
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/9fef9b3f-ad36-4c13-9bb1-c97d1af32fde/@@download/attachment/L-SUB1_BGKLV13_41.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUB1.(SUB1_BGKLV13_41)

value: Brenton Graveley, UConn

value: ENCBS285VBM at ENCODE; https://www.encodeproject.org/ENCBS285VBM/


title: SGE_200

value: phase 1


title: SGE_201

value: helper T (CD3+/CD4+/CD8-)


title: SGE_198


title: SGE_202

value: cytotoxic T (CD3+/CD4-/CD8+)


title: SGE_199


title: SGE_195


title: SGE_194


title: total RNA-seq from K562 (ENCLB645CDM)

description:
https://www.encodeproject.org/experiments/ENCSR040YBR/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial nucleus fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR040YBR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB645CDM
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line nuclear fraction

value: 53 year

value: adult

value: nucleus

value: Eric Lécuyer, IRCM

value: ENCBS371NDR at ENCODE; https://www.encodeproject.org/ENCBS371NDR/


title: siRNA RNA-seq from K562 (ENCLB407VFN)

description:
https://www.encodeproject.org/experiments/ENCSR041KOX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA (1x Buffer, 3x siRNA) against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR041KOX
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB407VFN
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: Control

value: K562 cells treated with siRNA knockdown using a human non-targeting control.

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS435USI at ENCODE; https://www.encodeproject.org/ENCBS435USI/

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


title: SGE_196


title: SGE_193

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: total RNA-seq from K562 (ENCLB754WAC)

description:
https://www.encodeproject.org/experiments/ENCSR038WEK/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial membrane fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR038WEK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB754WAC
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line membrane fraction

value: immortalized cell line

value: membrane

value: ENCBS751WKI at ENCODE; https://www.encodeproject.org/ENCBS751WKI/

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


title: shRNA RNA-seq from K562 (ENCLB291BKX)

description:
https://www.encodeproject.org/experiments/ENCSR040FSN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2_BGKLV25)
experiment encode accession: ENCSR040FSN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB291BKX
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF4G2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/71f790e5-0adc-4b19-8d01-33136675f741/@@download/attachment/L-EIF4G2_BGKLV25-17.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2_BGKLV25-17)

value: Brenton Graveley, UConn

value: ENCBS180BMC at ENCODE; https://www.encodeproject.org/ENCBS180BMC/


title: shRNA RNA-seq from HepG2 (ENCLB758GJZ)

description:
https://www.encodeproject.org/experiments/ENCSR042QTH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV23)
experiment encode accession: ENCSR042QTH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB758GJZ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/289d371d-88f0-4444-be61-a353a4fa519d/@@download/attachment/L-non-target-BGHLV23-1.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (non-target-BGHLV23-1)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS745UGC at ENCODE; https://www.encodeproject.org/ENCBS745UGC/

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 (ENCLB029PGL)

description:
https://www.encodeproject.org/experiments/ENCSR040FSN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2_BGKLV25)
experiment encode accession: ENCSR040FSN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB029PGL
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/d170346a-dcf8-4467-b363-4752c3b53fc8/@@download/attachment/L-EIF4G2_BGKLV25-18.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2_BGKLV25-18)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS099HZF at ENCODE; https://www.encodeproject.org/ENCBS099HZF/

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


title: total RNA-seq from K562 (ENCLB873LMQ)

description:
https://www.encodeproject.org/experiments/ENCSR040YBR/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial nucleus fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR040YBR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB873LMQ
size range: >200
spikeins used: /references/ENCSR866KGS/

value: immortalized cell line

value: nucleus

value: Eric Lécuyer, IRCM

value: ENCBS175LZM at ENCODE; https://www.encodeproject.org/ENCBS175LZM/

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


title: shRNA RNA-seq from HepG2 (ENCLB967MGK)

description:
https://www.encodeproject.org/experiments/ENCSR042QTH/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV23)
experiment encode accession: ENCSR042QTH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB967MGK
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/5afd7fb4-989b-4005-846b-f06a0e71d3e1/@@download/attachment/L-non-target-BGHLV23-2.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (non-target-BGHLV23-2)

value: 15 year

value: child

value: male

value: Brenton Graveley, UConn

value: ENCBS074PUV at ENCODE; https://www.encodeproject.org/ENCBS074PUV/


title: SGE_191

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction 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.

value: helper T (CD3+/CD4+/CD8-)

value: phase 1


title: siRNA RNA-seq from K562 (ENCLB097GVT)

description:
https://www.encodeproject.org/experiments/ENCSR045TQN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ATF3.
experiment encode accession: ENCSR045TQN
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR128HAQ, ENCSR109YDL
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB097GVT
size range: >200
spikeins used: /references/ENCSR866KGS/

value: K562 cells treated with a siRNA knockdown against ATF3, used in RNA-seq experiments.

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS596KIC at ENCODE; https://www.encodeproject.org/ENCBS596KIC/


title: total RNA-seq from K562 (ENCLB116UNI)

description:
https://www.encodeproject.org/experiments/ENCSR038WEK/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial membrane fractions on K562 Long Total from Lecuyer
experiment encode accession: ENCSR038WEK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB116UNI
size range: >200
spikeins used: /references/ENCSR866KGS/

value: immortalized cell line

value: membrane

value: Eric Lécuyer, IRCM

value: ENCBS614RYV at ENCODE; https://www.encodeproject.org/ENCBS614RYV/

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: SGE_189


title: SGE_190


title: SGE_188

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: SGE_187

value: cytotoxic T (CD3+/CD4-/CD8+)


title: shRNA RNA-seq from K562 (ENCLB109SBD)

description:
https://www.encodeproject.org/experiments/ENCSR031RZS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TAF1168. (K-TAF1168-30B)
experiment encode accession: ENCSR031RZS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR942UNX
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB109SBD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TAF15

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/2f5ebd32-51f9-48d0-848f-e1d1f958c101/@@download/attachment/L-K-TAF1168-30B-2.pdf

value: K562 cells treated with an shRNA knockdown against TAF1168, used in RNA-seq experiments. (K-TAF1168-30B-2)

value: Brenton Graveley, UConn

value: ENCBS771FYZ at ENCODE; https://www.encodeproject.org/ENCBS771FYZ/


title: SGE_197

value: phase 1


title: shRNA RNA-seq from K562 (ENCLB277TIJ)

description:
https://www.encodeproject.org/experiments/ENCSR029LGJ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX51 in K562 cells followed by RNA-seq. (DDX51_BGKLV19)
experiment encode accession: ENCSR029LGJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB277TIJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX51

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5215f0c6-f8b0-42e6-b0c8-49c6db25aaf7/@@download/attachment/L-DDX51_BGKLV19_16B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX51. (DDX51_BGKLV19_16B)

value: 53 year

value: adult

value: ENCBS820QHU at ENCODE; https://www.encodeproject.org/ENCBS820QHU/


title: shRNA RNA-seq from K562 (ENCLB338UHN)

description:
https://www.encodeproject.org/experiments/ENCSR031RZS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TAF1168. (K-TAF1168-30B)
experiment encode accession: ENCSR031RZS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR942UNX
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB338UHN
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/a079e89d-5915-4d25-a82e-e831ae565025/@@download/attachment/L-K-TAF1168-30B-1.pdf

value: K562 cells treated with an shRNA knockdown against TAF1168, used in RNA-seq experiments. (K-TAF1168-30B-1)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS552LNH at ENCODE; https://www.encodeproject.org/ENCBS552LNH/


title: SGE_185

source_name: peripheral blood mononuclear cells


title: SGE_186

value: helper T (CD3+/CD4+/CD8-)


title: SGE_192


title: shRNA RNA-seq from K562 (ENCLB019EVU)

description:
https://www.encodeproject.org/experiments/ENCSR029LGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX51 in K562 cells followed by RNA-seq. (DDX51_BGKLV19)
experiment encode accession: ENCSR029LGJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB019EVU
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/60cbaf49-080e-4f1c-89c8-a8747fdf2aec/@@download/attachment/L-DDX51_BGKLV19_15B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX51. (DDX51_BGKLV19_15B)

value: ENCBS079AJY at ENCODE; https://www.encodeproject.org/ENCBS079AJY/

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


title: SGE_184


title: SGE_183

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: shRNA RNA-seq from HepG2 (ENCLB415DWE)

description:
https://www.encodeproject.org/experiments/ENCSR028YAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PA2G4 in HepG2 cells followed by RNA-seq. (PA2G4_BGHLV16)
experiment encode accession: ENCSR028YAQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB415DWE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting PA2G4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/da5ec44e-7d10-4c71-808d-0d77336aa21b/@@download/attachment/L-PA2G4_BGHLV16_35.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PA2G4. (PA2G4_BGHLV16_35)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS987BVJ at ENCODE; https://www.encodeproject.org/ENCBS987BVJ/

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

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


title: total RNA-seq from thyroid gland (ENCLB002CRS)

description:
https://www.encodeproject.org/experiments/ENCSR023ZXN/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's thyroid gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR023ZXN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB002CRS
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9781407d-e8dc-4c34-9fce-fc44f3b6618a/@@download/attachment/295799.pdf

value: thyroid gland

value: tissue

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

value: 54 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS624WYQ at ENCODE; https://www.encodeproject.org/ENCBS624WYQ/

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


title: total RNA-seq from thyroid gland (ENCLB976GLA)

description:
https://www.encodeproject.org/experiments/ENCSR023ZXN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's thyroid gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR023ZXN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB976GLA
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7705c415-b42a-4861-a11d-817f9624c19d/@@download/attachment/295798.pdf


title: SGE_180

value: phase 1


title: SGE_182

value: cytotoxic T (CD3+/CD4-/CD8+)


title: SGE_181

value: helper T (CD3+/CD4+/CD8-)


title: RAMPAGE from H7-hESC (ENCLB328DNP)

description:
https://www.encodeproject.org/experiments/ENCSR022VBF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of embryonic stem cell line H7-hESC. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR022VBF
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR490SQH
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB328DNP
size range: >200

source_name: Homo sapiens H7-hESC stem 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/0f567bf0-7f1a-4330-83fc-9b6328a2b720/@@download/attachment/293011.pdf

value: stem cell

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS624XJG at ENCODE; https://www.encodeproject.org/ENCBS624XJG/

value: Derived from ENCODE donor ENCDO221AAA; https://www.encodeproject.org/ENCDO221AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_9772; http://web.expasy.org/cellosaurus/CVCL_9772


title: shRNA RNA-seq from K562 (ENCLB028GBY)

description:
https://www.encodeproject.org/experiments/ENCSR023HWI/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1_BGKLV24)
experiment encode accession: ENCSR023HWI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB028GBY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting KHDRBS1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6955d87a-3b3a-4161-9e2b-001dd5c383e6/@@download/attachment/L-KHDRBS1_BGKLV24_39_17620.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1_BGKLV24_39_17620)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS649DTO at ENCODE; https://www.encodeproject.org/ENCBS649DTO/

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: SGE_179

value: phase 1


title: RAMPAGE from HT1080 (ENCLB493JGS)

description:
https://www.encodeproject.org/experiments/ENCSR022PAU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR022PAU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR166QLP
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB493JGS
size range: >200

source_name: Homo sapiens HT1080 immortalized cell line cytosolic fraction

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2ec4dc50-cbae-45f9-9872-c8b79b7f96d4/@@download/attachment/LID294198.pdf

value: An immortalized fibrosarcoma cell line of the connective tissue from a 35 year old male.

value: 35 year

value: adult

value: male

value: fibrosarcoma

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS816VMN at ENCODE; https://www.encodeproject.org/ENCBS816VMN/

value: Derived from ENCODE donor ENCDO033CRF; https://www.encodeproject.org/ENCDO033CRF/

value: ENCODE dbxrefs Cellosaurus CVCL_0317; http://web.expasy.org/cellosaurus/CVCL_0317

value: ATCC sample source; http://www.atcc.org/products/all/CCL-121.aspx


title: SGE_178

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: RAMPAGE from HT1080 (ENCLB612NNJ)

description:
https://www.encodeproject.org/experiments/ENCSR022PAU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR022PAU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR166QLP
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB612NNJ
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/9e1fea22-14ed-482a-b04c-4036ac1bf977/@@download/attachment/LID294197.pdf

value: immortalized cell line

value: ENCBS688VJF at ENCODE; https://www.encodeproject.org/ENCBS688VJF/


title: polyA mRNA RNA-seq from HepG2 (ENCLB545YAL)

description:
https://www.encodeproject.org/experiments/ENCSR019MXZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial insoluble fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR019MXZ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB545YAL
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line insoluble cytoplasmic fraction

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

value: 15 year

value: child

value: hepatocellular carcinoma

value: insoluble cytoplasmic fraction

value: Eric Lécuyer, IRCM

value: ENCBS132XIH at ENCODE; https://www.encodeproject.org/ENCBS132XIH/

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: SGE_177

value: cytotoxic T (CD3+/CD4-/CD8+)

value: phase 1


title: polyA mRNA RNA-seq from HepG2 (ENCLB475LVF)

description:
https://www.encodeproject.org/experiments/ENCSR019MXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial insoluble fractions on HepG2 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR019MXZ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB475LVF
size range: >200
spikeins used: /references/ENCSR422PLF/

value: male

value: ENCBS638MWB at ENCODE; https://www.encodeproject.org/ENCBS638MWB/


title: SGE_176

value: helper T (CD3+/CD4+/CD8-)


title: SGE_175


title: shRNA RNA-seq from K562 (ENCLB120IOA)

description:
https://www.encodeproject.org/experiments/ENCSR023HWI/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1_BGKLV24)
experiment encode accession: ENCSR023HWI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB120IOA
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/54684aa7-5363-4348-9072-8597e0fb0cf2/@@download/attachment/L-KHDRBS1_BGKLV24_40_17621.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against KHDRBS1. (KHDRBS1_BGKLV24_40_17621)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS946SUX at ENCODE; https://www.encodeproject.org/ENCBS946SUX/

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: SGE_174


title: shRNA RNA-seq from K562 (ENCLB148LJW)

description:
https://www.encodeproject.org/experiments/ENCSR014VQS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RECQ1. (K-RECQ1-30B)
experiment encode accession: ENCSR014VQS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR942UNX
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB148LJW
size range: >200
spikeins used: /references/ENCSR449DXG/

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

value: RECQL

value: immortalized cell line

value: K562 cells treated with an shRNA knockdown against RECQ1, used in RNA-seq experiments. (K-RECQ1-30B-2)

value: ENCBS111BRF at ENCODE; https://www.encodeproject.org/ENCBS111BRF/


title: SGE_171

value: phase 1


title: shRNA RNA-seq from HepG2 (ENCLB227OGF)

description:
https://www.encodeproject.org/experiments/ENCSR012DAF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against APOBEC3C. (APOBE-BGHLV22)
experiment encode accession: ENCSR012DAF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB227OGF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting APOBEC3C

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a9fedda5-3c91-4b7c-8677-036665f3f257/@@download/attachment/L-APOBE-BGHLV22-3_17748.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against APOBEC3C. (APOBE-BGHLV22-3_17748)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS783AYY at ENCODE; https://www.encodeproject.org/ENCBS783AYY/

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 (ENCLB491KGF)

description:
https://www.encodeproject.org/experiments/ENCSR014VQS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RECQ1. (K-RECQ1-30B)
experiment encode accession: ENCSR014VQS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR942UNX
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB491KGF
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/112829f2-bc0b-4cee-b148-a28a10604494/@@download/attachment/L-K-RECQ1-30B-1.pdf

value: K562 cells treated with an shRNA knockdown against RECQ1, used in RNA-seq experiments. (K-RECQ1-30B-1)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS056HKT at ENCODE; https://www.encodeproject.org/ENCBS056HKT/


title: shRNA RNA-seq from HepG2 (ENCLB624ZWG)

description:
https://www.encodeproject.org/experiments/ENCSR028YAQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PA2G4 in HepG2 cells followed by RNA-seq. (PA2G4_BGHLV16)
experiment encode accession: ENCSR028YAQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB624ZWG
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/729a09b6-9280-4cd3-8685-c3e115f98172/@@download/attachment/L-PA2G4_BGHLV16_36.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PA2G4. (PA2G4_BGHLV16_36)

value: ENCBS732KTS at ENCODE; https://www.encodeproject.org/ENCBS732KTS/


title: SGE_172

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction 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.

value: cytotoxic T (CD3+/CD4-/CD8+)

value: phase 1


title: SGE_169


title: shRNA RNA-seq from HepG2 (ENCLB550DZJ)

description:
https://www.encodeproject.org/experiments/ENCSR011BBS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SART3. (SART3-BGHLV22)
experiment encode accession: ENCSR011BBS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB550DZJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SART3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8cc32b60-ca56-4317-85b3-b03426f8aa82/@@download/attachment/L-SART3-BGHLV22-45.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SART3. (SART3-BGHLV22-45)

value: child

value: male

value: 15 year

value: ENCBS937BJO at ENCODE; https://www.encodeproject.org/ENCBS937BJO/


title: SGE_168

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: shRNA RNA-seq from HepG2 (ENCLB460VRK)

description:
https://www.encodeproject.org/experiments/ENCSR011BBS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SART3. (SART3-BGHLV22)
experiment encode accession: ENCSR011BBS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB460VRK
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/ae7b7dbc-904f-473b-baf6-56a70051dd28/@@download/attachment/L-SART3-BGHLV22-46.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SART3. (SART3-BGHLV22-46)

value: hepatocellular carcinoma

value: ENCBS777UEV at ENCODE; https://www.encodeproject.org/ENCBS777UEV/

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 (ENCLB120KJG)

description:
https://www.encodeproject.org/experiments/ENCSR007XKL/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against NFX1 in K562 cells followed by RNA-seq. (NFX1 BGKLV13)
experiment encode accession: ENCSR007XKL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB120KJG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting NFX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9998bda7-0753-43d5-a23b-3a909e5d00f9/@@download/attachment/L-NFX1_BGKLV13_26.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NFX1.(NFX1_BGKLV13_26)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS654OPT at ENCODE; https://www.encodeproject.org/ENCBS654OPT/

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: SGE_167

value: cytotoxic T (CD3+/CD4-/CD8+)

value: phase 1


title: shRNA RNA-seq from K562 (ENCLB180VMG)

description:
https://www.encodeproject.org/experiments/ENCSR007XKL/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against NFX1 in K562 cells followed by RNA-seq. (NFX1 BGKLV13)
experiment encode accession: ENCSR007XKL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB180VMG
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/051a4771-f999-4513-ab9b-314c813c2060/@@download/attachment/L-NFX1_BGKLV13_25.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against NFX1.(NFX1_BGKLV13_25)

value: ENCBS143LJI at ENCODE; https://www.encodeproject.org/ENCBS143LJI/


title: SGE_166

value: helper T (CD3+/CD4+/CD8-)


title: RAMPAGE from SK-MEL-5 (ENCLB193FIG)

description:
https://www.encodeproject.org/experiments/ENCSR007RIV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic 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: ENCSR007RIV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR291DJH
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB193FIG
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f9b162e4-8b77-4e7d-9e67-202f000bbcb7/@@download/attachment/LID294487.pdf

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

value: 24 year

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS697RNA at ENCODE; https://www.encodeproject.org/ENCBS697RNA/

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 HepG2 (ENCLB915COF)

description:
https://www.encodeproject.org/experiments/ENCSR012DAF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against APOBEC3C. (APOBE-BGHLV22)
experiment encode accession: ENCSR012DAF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB915COF
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/7fd5ce8d-458d-4b63-b645-1cd6117f923a/@@download/attachment/L-APOBE-BGHLV22-4_17749.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against APOBEC3C. (APOBE-BGHLV22-4_17749)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS636ANV at ENCODE; https://www.encodeproject.org/ENCBS636ANV/

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: SGE_165

value: phase 1


title: shRNA RNA-seq from K562 (ENCLB629JYK)

description:
https://www.encodeproject.org/experiments/ENCSR004RGI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPS10 in K562 cells followed by RNA-seq. (RPS10 BGKLV13)
experiment encode accession: ENCSR004RGI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB629JYK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RPS10

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/590760f8-2e1c-4976-930a-53a5ec1a317f/@@download/attachment/L-RPS10_BGKLV13_63.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS10.(RPS10_BGKLV13_63)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS417FMB at ENCODE; https://www.encodeproject.org/ENCBS417FMB/

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: SGE_164


title: SGE_163

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: SGE_173


title: shRNA RNA-seq from K562 (ENCLB801ECF)

description:
https://www.encodeproject.org/experiments/ENCSR004RGI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RPS10 in K562 cells followed by RNA-seq. (RPS10 BGKLV13)
experiment encode accession: ENCSR004RGI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB801ECF
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/583042f2-0e65-49df-94ea-6a2f6da3ddc0/@@download/attachment/L-RPS10_BGKLV13_64.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS10.(RPS10_BGKLV13_64)

value: ENCBS691GWJ at ENCODE; https://www.encodeproject.org/ENCBS691GWJ/


title: SGE_162

value: cytotoxic T (CD3+/CD4-/CD8+)


title: shRNA RNA-seq from HepG2 (ENCLB559QMK)

description:
https://www.encodeproject.org/experiments/ENCSR004OSI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DNAJC2 in HepG2 cells followed by RNA-seq. (DNAJC2-57-BGHLV20)
experiment encode accession: ENCSR004OSI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB559QMK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/bfc317da-453c-4af6-a384-da3c2b0e3bb7/@@download/attachment/L-DNAJC2-57-BGHLV20-22_17717.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown againstDNAJC2. (DNAJC2-57-BGHLV20-22_17717)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS767KUR at ENCODE; https://www.encodeproject.org/ENCBS767KUR/


title: SGE_170

value: phase 1


title: RAMPAGE from LHCN-M2 (ENCLB592AEE)

description:
https://www.encodeproject.org/experiments/ENCSR002MPN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line LHCN-M2, skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR002MPN
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR332DBS
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB592AEE
size range: >200

source_name: Homo sapiens LHCN-M2 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/ef9647a3-da14-486f-ab24-b1e1c7022a14/@@download/attachment/293015.pdf

value: immortalized cell line

value: skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT (LH), and Cdk4-neo (CN), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2:not in 2011 analysis.

value: 41 year

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS233AAA at ENCODE; https://www.encodeproject.org/ENCBS233AAA/

value: Derived from ENCODE donor ENCDO000ACW; https://www.encodeproject.org/ENCDO000ACW/

value: ENCODE dbxrefs Cellosaurus CVCL_8890; http://web.expasy.org/cellosaurus/CVCL_8890

value: ENCODE dbxrefs LHCN-M2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=LHCN-M2


title: shRNA RNA-seq from HepG2 (ENCLB457CWR)

description:
https://www.encodeproject.org/experiments/ENCSR004OSI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DNAJC2 in HepG2 cells followed by RNA-seq. (DNAJC2-57-BGHLV20)
experiment encode accession: ENCSR004OSI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB457CWR
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/9cf27887-1cbf-494b-ae06-c969fc034a48/@@download/attachment/L-DNAJC2-57-BGHLV20-21_17716.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown againstDNAJC2. (DNAJC2-57-BGHLV20-21_17716)

value: ENCBS991MPK at ENCODE; https://www.encodeproject.org/ENCBS991MPK/

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: SGE_161

value: helper T (CD3+/CD4+/CD8-)


title: single cell RNA-seq from GM12878 (ENCLB550GYC)

description:
https://www.encodeproject.org/experiments/ENCSR000AJG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a GM12878 10-11 cell pool
experiment encode accession: ENCSR000AJG
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB550GYC
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: cells

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/e3110414-4013-425e-94f6-72c549702bde/@@download/attachment/Supplemental_Material.pdf
extraction method: None

value: Control

value: GM12878 10 cell pool

value: female

value: unknown

value: Barbara Wold, Caltech

value: ENCBS934CYZ at ENCODE; https://www.encodeproject.org/ENCBS934CYZ/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: single cell RNA-seq from GM12878 (ENCLB576ZGP)

description:
https://www.encodeproject.org/experiments/ENCSR000AJG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq of a GM12878 10-11 cell pool
experiment encode accession: ENCSR000AJG
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB576ZGP
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 11
nucleic acid starting quantity units: cells

value: immortalized cell line

value: GM12878 11 cell pool

value: adult

value: ENCBS236ZAD at ENCODE; https://www.encodeproject.org/ENCBS236ZAD/


title: SGE_160

value: phase 1


title: SGE_159


title: single cell RNA-seq from GM12878 (ENCLB482LEX)

description:
https://www.encodeproject.org/experiments/ENCSR000AIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a GM12878 30 cell pool
experiment encode accession: ENCSR000AIZ
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB482LEX
size range: >200
spikeins used: /references/ENCSR193ZXE/
nucleic acid starting quantity: 30
nucleic acid starting quantity units: cells

value: GM12878 30 cell pool

value: ENCBS791FEH at ENCODE; https://www.encodeproject.org/ENCBS791FEH/


title: single cell RNA-seq from GM12878 (ENCLB898RJN)

description:
https://www.encodeproject.org/experiments/ENCSR000AIZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq of a GM12878 30 cell pool
experiment encode accession: ENCSR000AIZ
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB898RJN
size range: >200
spikeins used: /references/ENCSR193ZXE/
nucleic acid starting quantity: 30
nucleic acid starting quantity units: cells

value: ENCBS839NNF at ENCODE; https://www.encodeproject.org/ENCBS839NNF/


title: SGE_158

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: SGE_156

value: helper T (CD3+/CD4+/CD8-)


title: SGE_154


title: total RNA-seq from heart (ENCLB172ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHH/
***************
biological replicate number: 1
technical replicate number: 1
description: CSHL Long RNA-seq Human heart from Snyder Lab 097WC
experiment encode accession: ENCSR000AHH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB172ZZZ
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens heart tissue male adult (34 years)

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bc505a2d-4afb-48f0-b8dd-77af9006c675/@@download/attachment/LID48879.pdf

value: heart

value: tissue

value: Human heart Tissue obtained from a healthy, 34 year old Caucasian male donor

value: 34 year

value: male

value: healthy with polysubstance abuse

value: Thomas Gingeras, CSHL

value: ENCBS044RNA at ENCODE; https://www.encodeproject.org/ENCBS044RNA/

value: Derived from ENCODE donor ENCDO058AAA; https://www.encodeproject.org/ENCDO058AAA/

value: ENCODE dbxrefs Heart_STL003; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Heart_STL003


title: RAMPAGE from camera-type eye (ENCLB293ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal whole eye tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AHC
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFO
encode release date: 2014-09-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB293ZZZ
size range: >200

source_name: Homo sapiens camera-type eye tissue female fetal (24 weeks)

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/26d396c6-0dbb-4df8-abc1-490e9da829d7/@@download/attachment/SID78278.pdf

value: camera-type eye

value: Human fetal whole eye

value: 24 week

value: fetal

value: female

value: ENCBS085RNA at ENCODE; https://www.encodeproject.org/ENCBS085RNA/

value: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244108-10


title: RAMPAGE from SK-MEL-5 (ENCLB449RXZ)

description:
https://www.encodeproject.org/experiments/ENCSR007RIV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic 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: ENCSR007RIV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR291DJH
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB449RXZ
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/5736501c-ef77-4bd3-b094-50582af76a9f/@@download/attachment/LID294486.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: cytosol

value: ENCBS324XRL at ENCODE; https://www.encodeproject.org/ENCBS324XRL/

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: SGE_155

source_name: peripheral blood mononuclear cells

value: phase 1


title: SGE_153

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: RAMPAGE from uterus (ENCLB291ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal uterus tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AHB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFN
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB291ZZZ
size range: >200

source_name: Homo sapiens uterus tissue female fetal (24 weeks)

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/7fd4a366-4340-41af-a0a5-436842586df8/@@download/attachment/SID78276.pdf

value: uterus

value: tissue

value: Human fetal uterus

value: 24 week

value: Thomas Gingeras, CSHL

value: ENCBS083RNA at ENCODE; https://www.encodeproject.org/ENCBS083RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244274-10


title: RAMPAGE from umbilical cord (ENCLB289ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal umbilical cord tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AHA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFM
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB289ZZZ
size range: >200

source_name: Homo sapiens umbilical cord tissue male fetal (20 weeks)

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/ec255d89-04e9-4776-89a4-45bb9c51e8a8/@@download/attachment/SID78004.pdf

value: umbilical cord

value: Human fetal umbilical cord

value: 20 week

value: fetal

value: male

value: ENCBS081RNA at ENCODE; https://www.encodeproject.org/ENCBS081RNA/

value: Derived from ENCODE donor ENCDO068AAA; https://www.encodeproject.org/ENCDO068AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244272-10


title: SGE_151

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction 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.

value: helper T (CD3+/CD4+/CD8-)

value: phase 1


title: RAMPAGE from uterus (ENCLB292ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHB/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal uterus tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AHB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFN
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB292ZZZ
size range: >200

source_name: Homo sapiens uterus tissue female fetal (28 weeks)

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/0113d02e-583d-42e2-a4e1-28f886345844/@@download/attachment/SID78277.pdf

value: uterus

value: 28 week

value: female

value: ENCBS084RNA at ENCODE; https://www.encodeproject.org/ENCBS084RNA/

value: Derived from ENCODE donor ENCDO062AAA; https://www.encodeproject.org/ENCDO062AAA/


title: RAMPAGE from umbilical cord (ENCLB290ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AHA/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal umbilical cord tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AHA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFM
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB290ZZZ
size range: >200

source_name: Homo sapiens umbilical cord tissue male fetal (31 week)

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/2f96c947-3423-4c35-9a5d-699b0645b40a/@@download/attachment/SID78005.pdf

value: tissue

value: 31 week

value: Thomas Gingeras, CSHL

value: ENCBS082RNA at ENCODE; https://www.encodeproject.org/ENCBS082RNA/

value: Derived from ENCODE donor ENCDO061AAA; https://www.encodeproject.org/ENCDO061AAA/


title: RAMPAGE from tongue (ENCLB287ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal tongue tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFL
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB287ZZZ
size range: >200

source_name: Homo sapiens tongue tissue female fetal (20 weeks)

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/1661b96d-94c0-454f-98da-fed0df234b7a/@@download/attachment/SID78258.pdf

value: tongue

value: Human fetal tongue

value: 20 week

value: fetal

value: ENCBS079RNA at ENCODE; https://www.encodeproject.org/ENCBS079RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244267-50


title: SGE_148

value: monocyte (CD3-/CD20-/HLADR+/CD14+)

value: phase 1


title: RAMPAGE from tongue (ENCLB288ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal tongue tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFL
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB288ZZZ
size range: >200

source_name: Homo sapiens tongue tissue female fetal (24 weeks)

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/c800bc4f-8a86-45d6-afdc-fb28907fea9e/@@download/attachment/SID78259.pdf

value: 24 week

value: female

value: ENCBS080RNA at ENCODE; https://www.encodeproject.org/ENCBS080RNA/

value: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/


title: SGE_149


title: SGE_157

value: cytotoxic T (CD3+/CD4-/CD8+)


title: RAMPAGE from thyroid gland (ENCLB285ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal thyroid gland tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGY
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFK
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB285ZZZ
size range: >200

source_name: Homo sapiens thyroid gland tissue female fetal (37 weeks)

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/3d87ef47-a101-4bb6-9202-81e122ba74d9/@@download/attachment/SID78256.pdf

value: thyroid gland

value: tissue

value: Human fetal thyroid gland

value: 37 week

value: Thomas Gingeras, CSHL

value: ENCBS077RNA at ENCODE; https://www.encodeproject.org/ENCBS077RNA/

value: Derived from ENCODE donor ENCDO063AAA; https://www.encodeproject.org/ENCDO063AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244265-10


title: SGE_146

value: helper T (CD3+/CD4+/CD8-)


title: SGE_147


title: RAMPAGE from temporal lobe (ENCLB283ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal temporal lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFJ
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB283ZZZ
size range: >200

source_name: Homo sapiens temporal lobe tissue female fetal (20 weeks)

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/d5a58af4-9608-480f-bcc3-4ce6d74108f4/@@download/attachment/SID78254.pdf

value: temporal lobe

value: Human fetal temporal lobe

value: 20 week

value: fetal

value: ENCBS075RNA at ENCODE; https://www.encodeproject.org/ENCBS075RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244078-50


title: SGE_144

value: phase 1


title: SGE_152

value: cytotoxic T (CD3+/CD4-/CD8+)