title: RAMPAGE from hair follicular keratinocyte (ENCLB761IVT)

description:
https://www.encodeproject.org/experiments/ENCSR166TEB/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from hair follicular keratinocytes (HHFK). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR166TEB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR680USE
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB761IVT
size range: >200

source_name: Homo sapiens hair follicular keratinocyte primary cell male adult (55 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/0f3e961c-3c2b-44ec-8253-fb8f58d0409b/@@download/attachment/LID295329.pdf

value: hair follicular keratinocyte

value: primary cell

value: Human Hair Follicular Keratinocyte Cells (HHFK).

value: 55 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS473SFT at ENCODE; https://www.encodeproject.org/ENCBS473SFT/

value: Derived from ENCODE donor ENCDO411IHW; https://www.encodeproject.org/ENCDO411IHW/


title: RAMPAGE from hair follicular keratinocyte (ENCLB780IXX)

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/ENCSR166TEB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from hair follicular keratinocytes (HHFK). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR166TEB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR680USE
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB780IXX
size range: >200

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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/a90e1496-3efc-4f39-a670-55f4f74ae274/@@download/attachment/LID295328.pdf

tag: description

value: Human Hair Follicular Keratinocyte Cells (HHFK) from the scalp of a 55 year old male.

tag: biosample encode accession

tag: age

tag: dev stage

tag: passage number

tag: Sex

value: male

tag: lab

tag: link

value: ENCBS534TLF at ENCODE; https://www.encodeproject.org/ENCBS534TLF/

value: Derived from ENCODE donor ENCDO030DJO; https://www.encodeproject.org/ENCDO030DJO/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=2445


title: SGE_364

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 2

tag: study group


title: shRNA RNA-seq from HepG2 (ENCLB935AWZ)

description:
https://www.encodeproject.org/experiments/ENCSR167JPY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRP68 in HepG2 cells followed by RNA-seq. (SRP68_BGHLV17)
experiment encode accession: ENCSR167JPY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB935AWZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SRP68

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e70b37c4-b60a-4054-866d-80ecaac16abd/@@download/attachment/L-SRP68_BGHLV17_30.pdf

tag: antibody

tag: line

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRP68. (SRP68_BGHLV17_30)

value: 15 year

value: child

tag: health state

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS061GZI at ENCODE; https://www.encodeproject.org/ENCBS061GZI/

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_363

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


title: microRNA-seq from smooth muscle cell (ENCLB282TQM)

description:
https://www.encodeproject.org/experiments/ENCSR155LSV/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human smooth muscle cell
experiment encode accession: ENCSR155LSV
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB282TQM
size range: <30

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

value: smooth muscle cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS899TTJ at ENCODE; https://www.encodeproject.org/ENCBS899TTJ/

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


title: SGE_362

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

value: phase 2


title: siRNA RNA-seq from K562 (ENCLB609JLW)

description:
https://www.encodeproject.org/experiments/ENCSR169DSM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ARID3A.
experiment encode accession: ENCSR169DSM
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR109YDL, ENCSR287SHU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB609JLW
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting ARID3A

value: immortalized cell line

value: K562 cells treated with a siRNA knockdown against ARID3A, used in RNA-seq experiments.

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS779WHO at ENCODE; https://www.encodeproject.org/ENCBS779WHO/

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

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


title: microRNA-seq from smooth muscle cell (ENCLB523NXK)

description:
https://www.encodeproject.org/experiments/ENCSR155LSV/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human smooth muscle cell
experiment encode accession: ENCSR155LSV
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB523NXK
size range: <30

value: smooth muscle cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: ENCBS780PCJ at ENCODE; https://www.encodeproject.org/ENCBS780PCJ/


title: SGE_361

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


title: SGE_370

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB989UYO)

description:
https://www.encodeproject.org/experiments/ENCSR164TLB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ADAR. (ADAR_BGKLV24)
experiment encode accession: ENCSR164TLB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB989UYO
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1ee7d949-b256-4758-ab39-ea62bd4597e0/@@download/attachment/L-ADAR_BGKLV24_3_17596.pdf

value: ADAR

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against ADAR. (ADAR_BGKLV24_3_17596)

value: female

value: Brenton Graveley, UConn

value: ENCBS922LYA at ENCODE; https://www.encodeproject.org/ENCBS922LYA/

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


title: SGE_369


title: SGE_360


title: SGE_359


title: siRNA RNA-seq from K562 (ENCLB248RMX)

description:
https://www.encodeproject.org/experiments/ENCSR169DSM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting ARID3A.
experiment encode accession: ENCSR169DSM
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR109YDL, ENCSR287SHU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB248RMX
size range: >200
spikeins used: /references/ENCSR866KGS/

value: K562 cells treated with a siRNA knockdown against ARID3A, used in RNA-seq experiments.

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS664TXM at ENCODE; https://www.encodeproject.org/ENCBS664TXM/

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


title: SGE_358

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


title: shRNA RNA-seq from HepG2 (ENCLB499IUE)

description:
https://www.encodeproject.org/experiments/ENCSR155BMF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL-BGHLV23)
experiment encode accession: ENCSR155BMF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB499IUE
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6a6ea974-34a0-4ad5-b889-d6c3b2c9a846/@@download/attachment/L-HNRNPL-BGHLV23-21.pdf

value: HNRNPL

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL-BGHLV23-21)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS805UZF at ENCODE; https://www.encodeproject.org/ENCBS805UZF/

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 (ENCLB636TOD)

description:
https://www.encodeproject.org/experiments/ENCSR152MON/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2-BGHLV23)
experiment encode accession: ENCSR152MON
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB636TOD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/63df8ace-b780-4fba-9ccf-bf7320552574/@@download/attachment/L-EIF4G2-BGHLV23-16.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2-BGHLV23-16)

value: Brenton Graveley, UConn

value: ENCBS909PJP at ENCODE; https://www.encodeproject.org/ENCBS909PJP/


title: shRNA RNA-seq from HepG2 (ENCLB972RPA)

description:
https://www.encodeproject.org/experiments/ENCSR155BMF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL-BGHLV23)
experiment encode accession: ENCSR155BMF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB972RPA
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/8cc3058d-b5ff-41d4-909f-0b0e81884ed6/@@download/attachment/L-HNRNPL-BGHLV23-22.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPL. (HNRNPL-BGHLV23-22)

value: ENCBS873PJJ at ENCODE; https://www.encodeproject.org/ENCBS873PJJ/


title: shRNA RNA-seq from HepG2 (ENCLB660DHK)

description:
https://www.encodeproject.org/experiments/ENCSR152MON/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2-BGHLV23)
experiment encode accession: ENCSR152MON
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB660DHK
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/c3f257e0-c72f-4cf1-9ab2-8e1196a877e1/@@download/attachment/L-EIF4G2-BGHLV23-15.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EIF4G2. (EIF4G2-BGHLV23-15)

value: ENCBS243GXZ at ENCODE; https://www.encodeproject.org/ENCBS243GXZ/


title: SGE_356

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

value: phase 2


title: SGE_365


title: shRNA RNA-seq from K562 (ENCLB866BIY)

description:
https://www.encodeproject.org/experiments/ENCSR143UET/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EIF3G in K562 cells followed by RNA-seq. (EIF3G BGKLV13)
experiment encode accession: ENCSR143UET
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB866BIY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF3G

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f39a65d0-95ef-4bee-affa-e174b22185c4/@@download/attachment/L-EIF3G_BGKLV13_71.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF3G.(EIF3G_BGKLV13_71)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS330LHC at ENCODE; https://www.encodeproject.org/ENCBS330LHC/

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_355


title: SGE_354


title: shRNA RNA-seq from K562 (ENCLB155EFP)

description:
https://www.encodeproject.org/experiments/ENCSR164TLB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ADAR. (ADAR_BGKLV24)
experiment encode accession: ENCSR164TLB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB155EFP
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/bbe91af2-c898-4c65-96d1-442cee908a90/@@download/attachment/L-ADAR_BGKLV24_4_17597.pdf

value: ADAR

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against ADAR. (ADAR_BGKLV24_4_17597)

value: ENCBS552DXA at ENCODE; https://www.encodeproject.org/ENCBS552DXA/


title: shRNA RNA-seq from K562 (ENCLB770XCJ)

description:
https://www.encodeproject.org/experiments/ENCSR139BIJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FXR2. (K-FXR2-26B)
experiment encode accession: ENCSR139BIJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR081EST
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB770XCJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting FXR2

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/eb417f67-1173-43c2-8f97-42ea86fbfb05/@@download/attachment/L-K-FXR2-26B-2.pdf

value: K562 cells treated with an shRNA knockdown against FXR2, used in RNA-seq experiments. (K-FXR2-26B-2)

value: Brenton Graveley, UConn

value: ENCBS165NPS at ENCODE; https://www.encodeproject.org/ENCBS165NPS/


title: SGE_353

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


title: shRNA RNA-seq from K562 (ENCLB115UGS)

description:
https://www.encodeproject.org/experiments/ENCSR143UET/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF3G in K562 cells followed by RNA-seq. (EIF3G BGKLV13)
experiment encode accession: ENCSR143UET
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB115UGS
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/f5ebe17b-81a2-45fb-b0c5-696305173d69/@@download/attachment/L-EIF3G_BGKLV13_72.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF3G.(EIF3G_BGKLV13_72)

value: ENCBS373HMN at ENCODE; https://www.encodeproject.org/ENCBS373HMN/


title: SGE_351

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

value: phase 2


title: SGE_350


title: SGE_349


title: shRNA RNA-seq from K562 (ENCLB760QTQ)

description:
https://www.encodeproject.org/experiments/ENCSR139BIJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FXR2. (K-FXR2-26B)
experiment encode accession: ENCSR139BIJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR081EST
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB760QTQ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/3ed81a7a-99d0-4175-b9da-e8c8427f09ce/@@download/attachment/L-K-FXR2-26B-1.pdf

value: K562 cells treated with an shRNA knockdown against FXR2, used in RNA-seq experiments. (K-FXR2-26B-1)

value: 53 year

value: adult

value: female

value: ENCBS849TDY at ENCODE; https://www.encodeproject.org/ENCBS849TDY/


title: SGE_347

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


title: siRNA RNA-seq from K562 (ENCLB949HEQ)

description:
https://www.encodeproject.org/experiments/ENCSR136ZPD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAFG.
experiment encode accession: ENCSR136ZPD
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB949HEQ
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: MAFG

value: immortalized cell line

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

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS181BKY at ENCODE; https://www.encodeproject.org/ENCBS181BKY/

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


title: SGE_357


title: siRNA RNA-seq from K562 (ENCLB843QHP)

description:
https://www.encodeproject.org/experiments/ENCSR129WCZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAZ.
experiment encode accession: ENCSR129WCZ
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR109YDL, ENCSR287SHU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB843QHP
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: MAZ

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

value: ENCBS867XVY at ENCODE; https://www.encodeproject.org/ENCBS867XVY/

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


title: SGE_346

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

value: phase 2


title: siRNA RNA-seq from K562 (ENCLB548EKN)

description:
https://www.encodeproject.org/experiments/ENCSR129WCZ/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAZ.
experiment encode accession: ENCSR129WCZ
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR109YDL, ENCSR287SHU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB548EKN
size range: >200
spikeins used: /references/ENCSR866KGS/

value: 53 year

value: adult

value: ENCBS338IDE at ENCODE; https://www.encodeproject.org/ENCBS338IDE/


title: SGE_348

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


title: siRNA RNA-seq from K562 (ENCLB958RKN)

description:
https://www.encodeproject.org/experiments/ENCSR136ZPD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAFG.
experiment encode accession: ENCSR136ZPD
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR608CVU, ENCSR287SHU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB958RKN
size range: >200
spikeins used: /references/ENCSR866KGS/

value: MAFG

value: female

value: ENCBS271ZBI at ENCODE; https://www.encodeproject.org/ENCBS271ZBI/


title: shRNA RNA-seq from K562 (ENCLB015KEA)

description:
https://www.encodeproject.org/experiments/ENCSR137HKS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PRPF8 in K562 cells followed by RNA-seq. (PRPF8_BGKLV19)
experiment encode accession: ENCSR137HKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB015KEA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PRPF8

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/15cbf26a-1a15-40b5-9afc-9360b17c0ef2/@@download/attachment/L-PRPF8_BGKLV19_44B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PRPF8. (PRPF8_BGKLV19_44B)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS530IBU at ENCODE; https://www.encodeproject.org/ENCBS530IBU/

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


title: SGE_343


title: SGE_344


title: siRNA RNA-seq from K562 (ENCLB301MTL)

description:
https://www.encodeproject.org/experiments/ENCSR129WCZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting MAZ.
experiment encode accession: ENCSR129WCZ
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR109YDL, ENCSR287SHU
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB301MTL
size range: >200
spikeins used: /references/ENCSR866KGS/

value: MAZ

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

value: Sherman Weissman, Yale

value: ENCBS796YDW at ENCODE; https://www.encodeproject.org/ENCBS796YDW/

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


title: SGE_352

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

value: phase 2


title: siRNA RNA-seq from K562 (ENCLB177BOE)

description:
https://www.encodeproject.org/experiments/ENCSR126QVF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR126QVF
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB177BOE
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: 53 year

value: adult

value: ENCBS421VJZ at ENCODE; https://www.encodeproject.org/ENCBS421VJZ/


title: SGE_342


title: shRNA RNA-seq from K562 (ENCLB215JUZ)

description:
https://www.encodeproject.org/experiments/ENCSR129ROE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SMN1. (SMN1_BGKLV24_B)
experiment encode accession: ENCSR129ROE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB215JUZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SMN1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4de94605-f256-462e-adc4-12cc7e202921/@@download/attachment/L-SMN1_BGKLV24_59B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SMN1. (SMN1_BGKLV24_59B)

value: female

value: ENCBS049ZAC at ENCODE; https://www.encodeproject.org/ENCBS049ZAC/


title: SGE_280


title: SGE_341

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


title: shRNA RNA-seq from K562 (ENCLB651VCU)

description:
https://www.encodeproject.org/experiments/ENCSR126ARZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ILF2. (ILF2_BGKLV24_B)
experiment encode accession: ENCSR126ARZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB651VCU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting ILF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f6ea8817-b856-447c-acad-bd9a93949702/@@download/attachment/L-ILF2_BGKLV24_36B.pdf

value: RNA-seq on k562 cells treated with an shRNA knockdown against ILF2. (ILF2_BGKLV24_36B)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS753LXR at ENCODE; https://www.encodeproject.org/ENCBS753LXR/

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


title: shRNA RNA-seq from K562 (ENCLB153FAG)

description:
https://www.encodeproject.org/experiments/ENCSR129ROE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SMN1. (SMN1_BGKLV24_B)
experiment encode accession: ENCSR129ROE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB153FAG
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/bfc4541e-e7dd-4571-9e68-6724dd943921/@@download/attachment/L-SMN1_BGKLV24_60B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SMN1. (SMN1_BGKLV24_60B)

value: ENCBS477MKD at ENCODE; https://www.encodeproject.org/ENCBS477MKD/

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


title: SGE_279

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB825VKF)

description:
https://www.encodeproject.org/experiments/ENCSR181RLB/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EEF2 in K562 cells followed by RNA-seq. (EEF2_BGKLV19)
experiment encode accession: ENCSR181RLB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB825VKF
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EEF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/5ac3ad8a-ccfc-4f7d-b5cb-d9438c010305/@@download/attachment/L-EEF2_BGKLV19_22B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EEF2. (EEF2_BGKLV19_22B)

value: 53 year

value: ENCBS715XGH at ENCODE; https://www.encodeproject.org/ENCBS715XGH/


title: shRNA RNA-seq from K562 (ENCLB600JFJ)

description:
https://www.encodeproject.org/experiments/ENCSR126ARZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ILF2. (ILF2_BGKLV24_B)
experiment encode accession: ENCSR126ARZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB600JFJ
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/969f11ea-a4f4-4172-86e4-fd46bab407aa/@@download/attachment/L-ILF2_BGKLV24_35B.pdf

value: immortalized cell line

value: RNA-seq on k562 cells treated with an shRNA knockdown against ILF2. (ILF2_BGKLV24_35B)

value: adult

value: ENCBS254WUV at ENCODE; https://www.encodeproject.org/ENCBS254WUV/


title: SGE_278

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


title: SGE_277

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


title: SGE_276

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


title: shRNA RNA-seq from K562 (ENCLB403XUO)

description:
https://www.encodeproject.org/experiments/ENCSR118XYK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PUM2. (PUM2-BGKLV25)
experiment encode accession: ENCSR118XYK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB403XUO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PUM2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/87a7101e-348d-4177-97de-5846d1f3fee1/@@download/attachment/L-PUM2-BGKLV25-47.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PUM2. (PUM2-BGKLV25-47)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS071UNK at ENCODE; https://www.encodeproject.org/ENCBS071UNK/


title: SGE_274

source_name: peripheral blood mononuclear cells


title: shRNA RNA-seq from K562 (ENCLB161QBJ)

description:
https://www.encodeproject.org/experiments/ENCSR118XYK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PUM2. (PUM2-BGKLV25)
experiment encode accession: ENCSR118XYK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB161QBJ
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/b8374a52-a759-48de-93c0-fa271b10dc2d/@@download/attachment/L-PUM2-BGKLV25-48.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PUM2. (PUM2-BGKLV25-48)

value: ENCBS790JBM at ENCODE; https://www.encodeproject.org/ENCBS790JBM/

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_272

value: phase 2


title: SGE_275


title: SGE_273


title: total RNA-seq from epithelial cell of proximal tubule (ENCLB193IVT)

description:
https://www.encodeproject.org/experiments/ENCSR118TVR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from epithelial cells of proximal tubule (HRPTE piC). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR118TVR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB193IVT
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens epithelial of proximal tubule primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ace1aeaa-3240-4960-9b88-742d3ba78a99/@@download/attachment/295119.pdf

value: epithelial cell of proximal tubule

value: primary cell

value: Human Renal Proximal Tubular Epithelial Cells.

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

value: ENCBS492GGP at ENCODE; https://www.encodeproject.org/ENCBS492GGP/

value: Derived from ENCODE donor ENCDO771VPD; https://www.encodeproject.org/ENCDO771VPD/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=4105


title: SGE_271

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


title: SGE_270


title: shRNA RNA-seq from HepG2 (ENCLB309OJU)

description:
https://www.encodeproject.org/experiments/ENCSR118VQR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS3A. (RPS3A-BGHLV22)
experiment encode accession: ENCSR118VQR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB309OJU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RPS3A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/79d3ff1b-6117-45fe-8830-a631c80526c6/@@download/attachment/L-RPS3A-BGHLV22-43.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS3A. (RPS3A-BGHLV22-43)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS927AKA at ENCODE; https://www.encodeproject.org/ENCBS927AKA/

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 epithelial cell of proximal tubule (ENCLB024PXV)

description:
https://www.encodeproject.org/experiments/ENCSR118TVR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from epithelial cells of proximal tubule (HRPTE piC). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR118TVR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB024PXV
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e10171ba-94da-4709-921b-95b83980fa1e/@@download/attachment/295120.pdf

value: epithelial cell of proximal tubule

value: primary cell

value: Human Renal Proximal Tubular Epithelial Cells.

value: unknown

value: ENCBS175CMC at ENCODE; https://www.encodeproject.org/ENCBS175CMC/

value: Derived from ENCODE donor ENCDO359WZJ; https://www.encodeproject.org/ENCDO359WZJ/


title: shRNA RNA-seq from HepG2 (ENCLB117STV)

description:
https://www.encodeproject.org/experiments/ENCSR118VQR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS3A. (RPS3A-BGHLV22)
experiment encode accession: ENCSR118VQR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB117STV
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/3d1016bf-9917-4bd9-920f-5b813e7696e0/@@download/attachment/L-RPS3A-BGHLV22-44.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPS3A. (RPS3A-BGHLV22-44)

value: ENCBS253SJT at ENCODE; https://www.encodeproject.org/ENCBS253SJT/


title: shRNA RNA-seq from K562 (ENCLB116WII)

description:
https://www.encodeproject.org/experiments/ENCSR137HKS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PRPF8 in K562 cells followed by RNA-seq. (PRPF8_BGKLV19)
experiment encode accession: ENCSR137HKS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB116WII
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/bbe793bb-d0cf-4a6d-87d5-bf3679046bdf/@@download/attachment/L-PRPF8_BGKLV19_43B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PRPF8. (PRPF8_BGKLV19_43B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS474CTB at ENCODE; https://www.encodeproject.org/ENCBS474CTB/

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_269

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB513IJB)

description:
https://www.encodeproject.org/experiments/ENCSR117WLY/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EFTUD2 in K562 cells followed by RNA-seq. (EFTUD2_BGKLV19)
experiment encode accession: ENCSR117WLY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB513IJB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EFTUD2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/bf1eac4e-426b-4dda-87e9-28f9550f7414/@@download/attachment/L-EFTUD2_BGKLV19_23B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EFTUD2. (EFTUD2_BGKLV19_23B)

value: Brenton Graveley, UConn

value: ENCBS943ODH at ENCODE; https://www.encodeproject.org/ENCBS943ODH/


title: shRNA RNA-seq from HepG2 (ENCLB657TMS)

description:
https://www.encodeproject.org/experiments/ENCSR116YMU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against GNB2L1 in HepG2 cells followed by RNA-seq. (GNB2L1_BGHLV18)
experiment encode accession: ENCSR116YMU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB657TMS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting GNB2L1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/75e83382-6aa3-4e5c-a97a-9c6fc7fb307b/@@download/attachment/L-GNB2L1_BGHLV18_11.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GNB2L1. (GNB2L1_BGHLV18_11)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS108PEU at ENCODE; https://www.encodeproject.org/ENCBS108PEU/

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_268

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


title: shRNA RNA-seq from K562 (ENCLB828WOZ)

description:
https://www.encodeproject.org/experiments/ENCSR117WLY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EFTUD2 in K562 cells followed by RNA-seq. (EFTUD2_BGKLV19)
experiment encode accession: ENCSR117WLY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB828WOZ
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/552dc2a0-3c52-4087-9e01-34a29673fc74/@@download/attachment/L-EFTUD2_BGKLV19_24B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against EFTUD2. (EFTUD2_BGKLV19_24B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS174YKM at ENCODE; https://www.encodeproject.org/ENCBS174YKM/


title: SGE_267

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB615XYX)

description:
https://www.encodeproject.org/experiments/ENCSR113PYX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CNOT7. (CNOT7_BGKLV24_B)
experiment encode accession: ENCSR113PYX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB615XYX
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CNOT7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/616dc99c-2a2a-40d7-87c0-31fb4f1cf2dc/@@download/attachment/L-CNOT7_BGKLV24_7B.pdf

value: RNA-seq on k562 cells treated with an shRNA knockdown against CNOT7. (CNOT7_BGKLV24_7B)

value: Brenton Graveley, UConn

value: ENCBS728WBV at ENCODE; https://www.encodeproject.org/ENCBS728WBV/

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

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


title: shRNA RNA-seq from K562 (ENCLB739MQM)

description:
https://www.encodeproject.org/experiments/ENCSR113PYX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CNOT7. (CNOT7_BGKLV24_B)
experiment encode accession: ENCSR113PYX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB739MQM
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/cb39844a-2ae6-4501-a25e-8a8c8282c398/@@download/attachment/L-CNOT7_BGKLV24_8B.pdf

value: RNA-seq on k562 cells treated with an shRNA knockdown against CNOT7. (CNOT7_BGKLV24_8B)

value: ENCBS677GYI at ENCODE; https://www.encodeproject.org/ENCBS677GYI/


title: SGE_264


title: siRNA RNA-seq from K562 (ENCLB402IPG)

description:
https://www.encodeproject.org/experiments/ENCSR109YDL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR109YDL
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB402IPG
size range: >200
spikeins used: /references/ENCSR866KGS/

value: Control

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

value: Sherman Weissman, Yale

value: ENCBS191KOV at ENCODE; https://www.encodeproject.org/ENCBS191KOV/


title: SGE_266

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


title: shRNA RNA-seq from K562 (ENCLB253NJO)

description:
https://www.encodeproject.org/experiments/ENCSR112YTD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SLBP. (SLBP_BGKLV24)
experiment encode accession: ENCSR112YTD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB253NJO
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/23afd371-c38c-432d-bd8c-f625050dd03d/@@download/attachment/L-SLBP_BGKLV24_58_17627.pdf

value: SLBP

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SLBP. (SLBP_BGKLV24_58_17627)

value: 53 year

value: adult

value: female

value: ENCBS517XSM at ENCODE; https://www.encodeproject.org/ENCBS517XSM/


title: shRNA RNA-seq from K562 (ENCLB977HYH)

description:
https://www.encodeproject.org/experiments/ENCSR112YTD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SLBP. (SLBP_BGKLV24)
experiment encode accession: ENCSR112YTD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB977HYH
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/0041cf6f-6aac-4bbc-9390-517e5cf2eeaf/@@download/attachment/L-SLBP_BGKLV24_57_17626.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SLBP. (SLBP_BGKLV24_57_17626)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS579CNZ at ENCODE; https://www.encodeproject.org/ENCBS579CNZ/


title: SGE_262

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

value: phase 2


title: shRNA RNA-seq from HepG2 (ENCLB366GTZ)

description:
https://www.encodeproject.org/experiments/ENCSR116YMU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against GNB2L1 in HepG2 cells followed by RNA-seq. (GNB2L1_BGHLV18)
experiment encode accession: ENCSR116YMU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB366GTZ
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/32c07a9d-e90a-423c-a6ff-e038f5e77e68/@@download/attachment/L-GNB2L1_BGHLV18_12.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against GNB2L1. (GNB2L1_BGHLV18_12)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS739HLB at ENCODE; https://www.encodeproject.org/ENCBS739HLB/

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_263

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


title: shRNA RNA-seq from HepG2 (ENCLB519CPM)

description:
https://www.encodeproject.org/experiments/ENCSR110ZYD/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SAFB2 in HepG2 cells followed by RNA-seq. (SAFB2-57-BGHLV20)
experiment encode accession: ENCSR110ZYD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB519CPM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SAFB2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ed99d580-1c93-4293-a42a-4df4646ae301/@@download/attachment/L-SAFB2-57-BGHLV20-54_17735.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SAFB2. (SAFB2-57-BGHLV20-54_17735)

value: ENCBS611PFD at ENCODE; https://www.encodeproject.org/ENCBS611PFD/


title: shRNA RNA-seq from HepG2 (ENCLB155FKV)

description:
https://www.encodeproject.org/experiments/ENCSR110ZYD/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SAFB2 in HepG2 cells followed by RNA-seq. (SAFB2-57-BGHLV20)
experiment encode accession: ENCSR110ZYD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB155FKV
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/54ff64c4-2dfb-46e8-8eb7-5a5493928a3a/@@download/attachment/L-SAFB2-57-BGHLV20-53_17734.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SAFB2. (SAFB2-57-BGHLV20-53_17734)

value: ENCBS702HBU at ENCODE; https://www.encodeproject.org/ENCBS702HBU/


title: RAMPAGE from SJSA1 (ENCLB818TTW)

description:
https://www.encodeproject.org/experiments/ENCSR108KHH/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SJSA1. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR108KHH
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR880EGO
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB818TTW
size range: >200

source_name: Homo sapiens SJSA1 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/c06ea39f-0497-40a4-bc45-83676ece3f3c/@@download/attachment/292969.pdf

value: 19 year

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS327EZG at ENCODE; https://www.encodeproject.org/ENCBS327EZG/

value: Derived from ENCODE donor ENCDO197NLG; https://www.encodeproject.org/ENCDO197NLG/

value: ENCODE dbxrefs Cellosaurus CVCL_1697; http://web.expasy.org/cellosaurus/CVCL_1697


title: RAMPAGE from SJSA1 (ENCLB028WDE)

description:
https://www.encodeproject.org/experiments/ENCSR108KHH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SJSA1. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR108KHH
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR880EGO
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB028WDE
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/8dc33de7-0380-4bd7-97bd-a578c95e782d/@@download/attachment/292968.pdf

value: male

value: ENCBS489PLT at ENCODE; https://www.encodeproject.org/ENCBS489PLT/


title: SGE_259

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: phase 2


title: SGE_261

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


title: SGE_258


title: SGE_260


title: SGE_265


title: SGE_257

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


title: RAMPAGE from RPMI-7951 (ENCLB148UOQ)

description:
https://www.encodeproject.org/experiments/ENCSR104PJD/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line RPMI-7951 isolated from a metastatic site of a malignant melonoma from an 18 year old caucasian female. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR104PJD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR320BRR
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB148UOQ
size range: >200

source_name: Homo sapiens RPMI-7951 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/54b387bd-1c3e-4630-9017-b22c5e0a8096/@@download/attachment/293017.pdf

value: Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high.

value: 18 year

value: female

value: malignant melanoma

value: ENCBS262AAA at ENCODE; https://www.encodeproject.org/ENCBS262AAA/

value: Derived from ENCODE donor ENCDO000ADL; https://www.encodeproject.org/ENCDO000ADL/

value: ENCODE dbxrefs Cellosaurus CVCL_1666; http://web.expasy.org/cellosaurus/CVCL_1666

value: ENCODE dbxrefs RPMI-7951; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=RPMI-7951


title: shRNA RNA-seq from HepG2 (ENCLB558WMQ)

description:
https://www.encodeproject.org/experiments/ENCSR105OXX/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against MARK2 in HepG2 cells followed by RNA-seq. (MARK2_BGHLV18)
experiment encode accession: ENCSR105OXX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB558WMQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting MARK2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/98a08f34-a350-4d16-9708-c1c16df7fd1a/@@download/attachment/L-MARK2_BGHLV18_28.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MARK2. (MARK2_BGHLV18_28)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS086PXC at ENCODE; https://www.encodeproject.org/ENCBS086PXC/

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_256

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

value: phase 2


title: RAMPAGE from RPMI-7951 (ENCLB999GHL)

description:
https://www.encodeproject.org/experiments/ENCSR104PJD/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line RPMI-7951 isolated from a metastatic site of a malignant melonoma from an 18 year old caucasian female. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR104PJD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR320BRR
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB999GHL
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/460151fc-f8a8-40fb-b508-da508cec6402/@@download/attachment/293018.pdf

value: 18 year

value: adult

value: female

value: John Stamatoyannopoulos, UW

value: ENCBS493TPA at ENCODE; https://www.encodeproject.org/ENCBS493TPA/


title: SGE_254


title: shRNA RNA-seq from HepG2 (ENCLB899IOC)

description:
https://www.encodeproject.org/experiments/ENCSR105OXX/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against MARK2 in HepG2 cells followed by RNA-seq. (MARK2_BGHLV18)
experiment encode accession: ENCSR105OXX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB899IOC
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/b2ebe444-7609-4a60-9885-dc242f427800/@@download/attachment/L-MARK2_BGHLV18_27.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against MARK2. (MARK2_BGHLV18_27)

value: male

value: ENCBS237FEL at ENCODE; https://www.encodeproject.org/ENCBS237FEL/


title: SGE_253

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


title: shRNA RNA-seq from HepG2 (ENCLB918BSZ)

description:
https://www.encodeproject.org/experiments/ENCSR104OLN/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against ADAR in HepG2 cells followed by RNA-seq. (ADAR-BGHLV20)
experiment encode accession: ENCSR104OLN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB918BSZ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4c845167-bf9f-4340-841a-e340236ae705/@@download/attachment/L-ADAR-BGHLV20-3_17708.pdf

value: ADAR

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ADAR. (ADAR-BGHLV20-3_17708)

value: child

value: 15 year

value: ENCBS879GXJ at ENCODE; https://www.encodeproject.org/ENCBS879GXJ/


title: shRNA RNA-seq from K562 (ENCLB418ICS)

description:
https://www.encodeproject.org/experiments/ENCSR101OPF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGKLV25)
experiment encode accession: ENCSR101OPF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB418ICS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SUCLG1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/1dc36a01-467d-452e-a52c-52247f06f61f/@@download/attachment/L-SUCLG1-BGKLV25-57.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGKLV25-57)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS380BDK at ENCODE; https://www.encodeproject.org/ENCBS380BDK/

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_252

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB085PFP)

description:
https://www.encodeproject.org/experiments/ENCSR101OPF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGKLV25)
experiment encode accession: ENCSR101OPF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB085PFP
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/1021348b-494e-4b33-a367-53c3a9c27a90/@@download/attachment/L-SUCLG1-BGKLV25-58.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SUCLG1. (SUCLG1-BGKLV25-58)

value: adult

value: female

value: ENCBS621XIY at ENCODE; https://www.encodeproject.org/ENCBS621XIY/


title: shRNA RNA-seq from HepG2 (ENCLB012QRD)

description:
https://www.encodeproject.org/experiments/ENCSR104OLN/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against ADAR in HepG2 cells followed by RNA-seq. (ADAR-BGHLV20)
experiment encode accession: ENCSR104OLN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB012QRD
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/3ab257f3-a42c-4e16-84d6-21f137b2d513/@@download/attachment/L-ADAR-BGHLV20-4_17709.pdf

value: ADAR

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ADAR. (ADAR-BGHLV20-4_17709)

value: male

value: hepatocellular carcinoma

value: ENCBS863WKZ at ENCODE; https://www.encodeproject.org/ENCBS863WKZ/

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 kidney epithelial cell (ENCLB503LLE)

description:
https://www.encodeproject.org/experiments/ENCSR100NLN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of kidney epithelial primary cell type (HREpiC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR100NLN
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR373BDG
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB503LLE
size range: >200

source_name: Homo sapiens kidney epithelial primary cell male newborn

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/0651efa6-7fd7-4b33-ab11-b05348c9f1c0/@@download/attachment/295491.pdf

value: kidney epithelial cell

value: primary cell

value: Human Renal Epithelial Cells (HREpiC) from the kidney of a neonatal male.

value: unknown

value: newborn

value: Thomas Gingeras, CSHL

value: ENCBS007YZP at ENCODE; https://www.encodeproject.org/ENCBS007YZP/

value: Derived from ENCODE donor ENCDO076GQZ; https://www.encodeproject.org/ENCDO076GQZ/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=4125


title: RAMPAGE from kidney epithelial cell (ENCLB274FMY)

description:
https://www.encodeproject.org/experiments/ENCSR100NLN/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of kidney epithelial primary cell type (HREpiC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR100NLN
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR373BDG
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB274FMY
size range: >200

source_name: Homo sapiens kidney epithelial primary cell male fetal (22 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/af0f5854-74de-4c02-a0a2-e04d179619d4/@@download/attachment/295492.pdf

value: 22 week

value: fetal

value: ENCBS945YXY at ENCODE; https://www.encodeproject.org/ENCBS945YXY/

value: Derived from ENCODE donor ENCDO792EJQ; https://www.encodeproject.org/ENCDO792EJQ/


title: SGE_249

value: phase 2


title: SGE_251

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


title: shRNA RNA-seq from K562 (ENCLB788LQN)

description:
https://www.encodeproject.org/experiments/ENCSR098NHI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPS19_13 in K562 cells followed by RNA-seq. (RPS19_BGKLV19)
experiment encode accession: ENCSR098NHI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB788LQN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RPS19

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2682f0ba-712c-44b2-b2f3-858c34a0238f/@@download/attachment/L-RPS19_BGKLV19_45B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS19_13. (RPS19_BGKLV19_45B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS139SNH at ENCODE; https://www.encodeproject.org/ENCBS139SNH/

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_248

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


title: RAMPAGE from NCI-H460 (ENCLB356JJN)

description:
https://www.encodeproject.org/experiments/ENCSR093UPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line NCI-H460, a male large cell lung carcinoma. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR093UPQ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR164OCT
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB356JJN
size range: >200

source_name: Homo sapiens NCI-H460 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/03db6336-0b60-4c20-98ba-b25628fb57ab/@@download/attachment/288548.pdf

value: 37 year

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS514AAA at ENCODE; https://www.encodeproject.org/ENCBS514AAA/

value: Derived from ENCODE donor ENCDO337AAA; https://www.encodeproject.org/ENCDO337AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0459; http://web.expasy.org/cellosaurus/CVCL_0459


title: SGE_255

source_name: peripheral blood mononuclear cells

value: phase 2


title: RAMPAGE from NCI-H460 (ENCLB199RYI)

description:
https://www.encodeproject.org/experiments/ENCSR093UPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line NCI-H460, a male large cell lung carcinoma. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR093UPQ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR164OCT
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB199RYI
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/31a68e5a-c370-4a73-b670-c4966b675149/@@download/attachment/288549.pdf

value: immortalized cell line

value: ENCBS515AAA at ENCODE; https://www.encodeproject.org/ENCBS515AAA/

value: ATCC sample source; http://www.atcc.org/products/all/HTB-177.aspx


title: siRNA RNA-seq from K562 (ENCLB978VYE)

description:
https://www.encodeproject.org/experiments/ENCSR092LZV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting both CTCF and RAD21 together.
experiment encode accession: ENCSR092LZV
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR443QFD, ENCSR041KOX
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB978VYE
size range: >200
spikeins used: /references/ENCSR866KGS/

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

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

value: 53 year

value: adult

value: female

value: Sherman Weissman, Yale

value: ENCBS206QAM at ENCODE; https://www.encodeproject.org/ENCBS206QAM/


title: SGE_247

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


title: SGE_245


title: SGE_246

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


title: siRNA RNA-seq from K562 (ENCLB811UGH)

description:
https://www.encodeproject.org/experiments/ENCSR092LZV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting both CTCF and RAD21 together.
experiment encode accession: ENCSR092LZV
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR443QFD, ENCSR041KOX
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB811UGH
size range: >200
spikeins used: /references/ENCSR866KGS/

value: chronic myelogenous leukemia (CML)

value: ENCBS155DKW at ENCODE; https://www.encodeproject.org/ENCBS155DKW/

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


title: shRNA RNA-seq from K562 (ENCLB319NAR)

description:
https://www.encodeproject.org/experiments/ENCSR098NHI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RPS19_13 in K562 cells followed by RNA-seq. (RPS19_BGKLV19)
experiment encode accession: ENCSR098NHI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB319NAR
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/119259ea-af53-4877-8691-6c793feff42c/@@download/attachment/L-RPS19_BGKLV19_46B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS19_13. (RPS19_BGKLV19_46B)

value: Brenton Graveley, UConn

value: ENCBS713VDJ at ENCODE; https://www.encodeproject.org/ENCBS713VDJ/

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


title: SGE_243

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

value: phase 2


title: SGE_244


title: microRNA-seq from testis (ENCLB536UZP)

description:
https://www.encodeproject.org/experiments/ENCSR088SDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human testis
experiment encode accession: ENCSR088SDZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB536UZP
size range: <30

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

value: testis

value: tissue

value: Testis 2-2

value: 54 year

value: male

value: Barbara Wold, Caltech

value: ENCBS238DLV at ENCODE; https://www.encodeproject.org/ENCBS238DLV/

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


title: shRNA RNA-seq from HepG2 (ENCLB241ZWH)

description:
https://www.encodeproject.org/experiments/ENCSR090UMI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SMN1 in HepG2 cells followed by RNA-seq. (SMN1-BGHLV20)
experiment encode accession: ENCSR090UMI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB241ZWH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SMN1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/14fe865f-ec6c-4ba4-9a4c-f01a66590079/@@download/attachment/L-SMN1-BGHLV20-56_17737.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SMN1. (SMN1-BGHLV20-56_17737)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS483WGW at ENCODE; https://www.encodeproject.org/ENCBS483WGW/

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_240

value: phase 2


title: microRNA-seq from testis (ENCLB804FNJ)

description:
https://www.encodeproject.org/experiments/ENCSR088SDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human testis
experiment encode accession: ENCSR088SDZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB804FNJ
size range: <30

value: testis

value: Testis 2-1

value: adult

value: ENCBS288YWQ at ENCODE; https://www.encodeproject.org/ENCBS288YWQ/


title: shRNA RNA-seq from HepG2 (ENCLB215KSZ)

description:
https://www.encodeproject.org/experiments/ENCSR090UMI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SMN1 in HepG2 cells followed by RNA-seq. (SMN1-BGHLV20)
experiment encode accession: ENCSR090UMI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB215KSZ
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/56a09c83-6e98-4060-a4cc-f7b410158148/@@download/attachment/L-SMN1-BGHLV20-55_17736.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SMN1. (SMN1-BGHLV20-55_17736)

value: male

value: Brenton Graveley, UConn

value: ENCBS403UGF at ENCODE; https://www.encodeproject.org/ENCBS403UGF/


title: SGE_242

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+)


title: SGE_241

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


title: shRNA RNA-seq from K562 (ENCLB972QAM)

description:
https://www.encodeproject.org/experiments/ENCSR084SCN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target BGKLV13)
experiment encode accession: ENCSR084SCN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB972QAM
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0f6e2883-5bab-48b5-9e97-7cd9790c0a9f/@@download/attachment/L-non-target_BGKLV13_74.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (non-target_BGKLV13_74)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS252OWV at ENCODE; https://www.encodeproject.org/ENCBS252OWV/

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_231

value: phase 2


title: SGE_230

value: phase 1


title: SGE_228

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


title: shRNA RNA-seq from K562 (ENCLB005KIJ)

description:
https://www.encodeproject.org/experiments/ENCSR081EST/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-26B)
experiment encode accession: ENCSR081EST
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB005KIJ
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/467fe79d-8498-45c9-b3df-3b42093167a4/@@download/attachment/L-K-NT-26B-2.pdf

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (K-NT-26B-2)

value: adult

value: ENCBS092VTJ at ENCODE; https://www.encodeproject.org/ENCBS092VTJ/


title: shRNA RNA-seq from K562 (ENCLB627ZHJ)

description:
https://www.encodeproject.org/experiments/ENCSR079LMZ/
***************
biological replicate number: 1
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: ENCLB627ZHJ
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/bf040067-a023-42a3-9307-011fd1c93ccb/@@download/attachment/L-DNAJC21_BGKLV24_19_17611.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC21. (DNAJC21_BGKLV24_19_17611)

value: Brenton Graveley, UConn

value: ENCBS464DIX at ENCODE; https://www.encodeproject.org/ENCBS464DIX/


title: SGE_226

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


title: siRNA RNA-seq from K562 (ENCLB304NND)

description:
https://www.encodeproject.org/experiments/ENCSR074DIJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR074DIJ
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB304NND
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: immortalized cell line

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

value: Sherman Weissman, Yale

value: ENCBS364OFM at ENCODE; https://www.encodeproject.org/ENCBS364OFM/


title: SGE_237

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


title: shRNA RNA-seq from HepG2 (ENCLB674UTW)

description:
https://www.encodeproject.org/experiments/ENCSR082YGI/
***************
biological replicate number: 2
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: ENCLB674UTW
size range: >200
spikeins used: /references/ENCSR449DXG/

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/54aacabf-5a26-4231-9a8e-38552ddd9f00/@@download/attachment/L-RPLP0_BGHLV18_54.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RPLP0. (RPLP0_BGHLV18_54)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS110FVC at ENCODE; https://www.encodeproject.org/ENCBS110FVC/

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_224

value: phase 1


title: SGE_235

value: phase 2


title: SGE_233

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


title: SGE_229


title: SGE_234


title: shRNA RNA-seq from K562 (ENCLB063CVU)

description:
https://www.encodeproject.org/experiments/ENCSR082UWF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against STIP1. (STIP1_BGKLV24_B)
experiment encode accession: ENCSR082UWF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB063CVU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting STIP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7659095b-ee0d-4593-b47a-b892a0f525a7/@@download/attachment/L-STIP1_BGKLV24_61B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against STIP1. (STIP1_BGKLV24_61B)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS877RXF at ENCODE; https://www.encodeproject.org/ENCBS877RXF/

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_232

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


title: SGE_225


title: SGE_227


title: SGE_223


title: RAMPAGE from thyroid gland (ENCLB782TAW)

description:
https://www.encodeproject.org/experiments/ENCSR069LRO/
***************
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 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: ENCLB782TAW
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/89662eb6-865d-4456-80f3-00b687920125/@@download/attachment/295992.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: male

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: SGE_236

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

value: phase 2


title: SGE_222

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

value: phase 1


title: shRNA RNA-seq from K562 (ENCLB136JSZ)

description:
https://www.encodeproject.org/experiments/ENCSR084SCN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target BGKLV13)
experiment encode accession: ENCSR084SCN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB136JSZ
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/df522db9-2bca-46e9-891a-32dff02ed17c/@@download/attachment/L-non-target_BGKLV13_73.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (non-target_BGKLV13_73)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS418OCT at ENCODE; https://www.encodeproject.org/ENCBS418OCT/


title: siRNA RNA-seq from K562 (ENCLB384RCE)

description:
https://www.encodeproject.org/experiments/ENCSR067CAG/
***************
biological replicate number: 2
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: ENCLB384RCE
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: Sherman Weissman, Yale

value: ENCBS467YFZ at ENCODE; https://www.encodeproject.org/ENCBS467YFZ/

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


title: shRNA RNA-seq from K562 (ENCLB385PHF)

description:
https://www.encodeproject.org/experiments/ENCSR081EST/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (K-NT-26B)
experiment encode accession: ENCSR081EST
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB385PHF
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/ce87e489-392b-4289-b606-51d4e041a514/@@download/attachment/L-K-NT-26B-1.pdf

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (K-NT-26B-1)

value: ENCBS184UCR at ENCODE; https://www.encodeproject.org/ENCBS184UCR/

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


title: SGE_239

value: phase 2


title: SGE_221

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

value: phase 1


title: shRNA RNA-seq from K562 (ENCLB298UKR)

description:
https://www.encodeproject.org/experiments/ENCSR082UWF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against STIP1. (STIP1_BGKLV24_B)
experiment encode accession: ENCSR082UWF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB298UKR
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/fc6be632-e31e-41dc-a898-7854d6ca4b88/@@download/attachment/L-STIP1_BGKLV24_62B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against STIP1. (STIP1_BGKLV24_62B)

value: 53 year

value: ENCBS497UCZ at ENCODE; https://www.encodeproject.org/ENCBS497UCZ/