title: siRNA RNA-seq from K562 (ENCLB277JAF)

description:
https://www.encodeproject.org/experiments/ENCSR256NQT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR256NQT
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB277JAF
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: Sherman Weissman, Yale

value: ENCBS680VHW at ENCODE; https://www.encodeproject.org/ENCBS680VHW/


title: shRNA RNA-seq from HepG2 (ENCLB857NYS)

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/ENCSR274KWA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against CNOT7. (CNOT7-BGHLV22)
experiment encode accession: ENCSR274KWA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB857NYS
size range: >200
spikeins used: /references/ENCSR449DXG/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CNOT7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/a7c08812-ad11-49f5-a9ca-a91175c8763f/@@download/attachment/L-CNOT7-BGHLV22-6_17751.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CNOT7. (CNOT7-BGHLV22-6_17751)

tag: biosample encode accession

tag: age

value: 15 year

tag: dev stage

value: child

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

tag: lab

value: Brenton Graveley, UConn

tag: link

value: ENCBS118LZR at ENCODE; https://www.encodeproject.org/ENCBS118LZR/

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

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


title: shRNA RNA-seq from K562 (ENCLB299GQS)

description:
https://www.encodeproject.org/experiments/ENCSR258VGD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF3A. (EIF3A_BGKLV24)
experiment encode accession: ENCSR258VGD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB299GQS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting EIF3A

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4a9985e4-87a9-4ec8-bf6d-f4e4ed7df5d8/@@download/attachment/L-EIF3A_BGKLV24_21_17613.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF3A. (EIF3A_BGKLV24_21_17613)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS162UQR at ENCODE; https://www.encodeproject.org/ENCBS162UQR/

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_444

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 K562 (ENCLB608NIV)

description:
https://www.encodeproject.org/experiments/ENCSR258VGD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF3A. (EIF3A_BGKLV24)
experiment encode accession: ENCSR258VGD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB608NIV
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/ba5b318a-4a81-4041-bbd6-8ac59bf4122b/@@download/attachment/L-EIF3A_BGKLV24_22_17614.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF3A. (EIF3A_BGKLV24_22_17614)

value: ENCBS010SYB at ENCODE; https://www.encodeproject.org/ENCBS010SYB/


title: shRNA RNA-seq from K562 (ENCLB111QIC)

description:
https://www.encodeproject.org/experiments/ENCSR245BNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-A)
experiment encode accession: ENCSR245BNJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB111QIC
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/c9ba3004-d193-4c11-8460-6dbb457d2e70/@@download/attachment/L-NT_BGKLV19_1A.pdf

value: Control

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (NT_BGKLV19_1)

value: ENCBS661YYO at ENCODE; https://www.encodeproject.org/ENCBS661YYO/


title: SGE_443

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


title: microRNA-seq from uterus (ENCLB005PPB)

description:
https://www.encodeproject.org/experiments/ENCSR240RLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human uterus
experiment encode accession: ENCSR240RLZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB005PPB
size range: <30

source_name: Homo sapiens uterus tissue female adult (53 years)

value: uterus

value: tissue

value: Uterus

value: Barbara Wold, Caltech

value: ENCBS084QBB at ENCODE; https://www.encodeproject.org/ENCBS084QBB/

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


title: total RNA-seq from adrenal gland (ENCLB879WXT)

description:
https://www.encodeproject.org/experiments/ENCSR276MMH/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR276MMH
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB879WXT
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0628cb09-fe7e-49f6-ad24-016fb38f5900/@@download/attachment/295772.pdf

value: adrenal gland

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

value: 37 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS227VDO at ENCODE; https://www.encodeproject.org/ENCBS227VDO/

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


title: SGE_441

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

value: phase 2


title: SGE_440


title: microRNA-seq from uterus (ENCLB684TOH)

description:
https://www.encodeproject.org/experiments/ENCSR240RLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human uterus
experiment encode accession: ENCSR240RLZ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB684TOH
size range: <30

value: 53 year

value: female

value: ENCBS057LPE at ENCODE; https://www.encodeproject.org/ENCBS057LPE/


title: SGE_439


title: shRNA RNA-seq from K562 (ENCLB775RZU)

description:
https://www.encodeproject.org/experiments/ENCSR245BNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (NT_BGKLV19-A)
experiment encode accession: ENCSR245BNJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB775RZU
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/4693a860-9a62-4a28-8490-f74e2f496988/@@download/attachment/L-NT_BGKLV19_2A.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an Control shRNA against no target. (NT_BGKLV19_2)

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS250HLF at ENCODE; https://www.encodeproject.org/ENCBS250HLF/

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

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


title: RAMPAGE from NCI-H460 (ENCLB596DKM)

description:
https://www.encodeproject.org/experiments/ENCSR239ZQA/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR239ZQA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR625QJI
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB596DKM
size range: >200

source_name: Homo sapiens NCI-H460 immortalized cell line nuclear fraction

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7f2b2b68-81f4-4e13-a8b1-3a5f4cced19a/@@download/attachment/LID294674.pdf

value: Epithelial-like large cell lung carcinoma immortalized cells from a 37 year old male.

value: 37 year

value: adult

value: male

tag: subcellular fraction term name

value: nucleus

value: ENCBS641PGO at ENCODE; https://www.encodeproject.org/ENCBS641PGO/

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

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

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


title: SGE_452

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

value: WXC

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB808JXZ)

description:
https://www.encodeproject.org/experiments/ENCSR269HQA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ILF3. (ILF3_BGKLV24)
experiment encode accession: ENCSR269HQA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB808JXZ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting ILF3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/80aa1334-43f9-4bd8-a7e9-b3683f779b9e/@@download/attachment/L-ILF3_BGKLV24_38_17618.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against ILF3. (ILF3_BGKLV24_38_17618)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS348UOE at ENCODE; https://www.encodeproject.org/ENCBS348UOE/


title: shRNA RNA-seq from K562 (ENCLB159PPN)

description:
https://www.encodeproject.org/experiments/ENCSR269HQA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against ILF3. (ILF3_BGKLV24)
experiment encode accession: ENCSR269HQA
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB159PPN
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/80af7b6e-837a-4a15-acab-5fe0e1fdfcec/@@download/attachment/L-ILF3_BGKLV24_37_17617.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against ILF3. (ILF3_BGKLV24_37_17617)

value: Brenton Graveley, UConn

value: ENCBS362YBS at ENCODE; https://www.encodeproject.org/ENCBS362YBS/

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 (ENCLB995SHP)

description:
https://www.encodeproject.org/experiments/ENCSR239BCO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PTBP1 in K562 cells followed by RNA-seq
experiment encode accession: ENCSR239BCO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB995SHP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PTBP1

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/5b63c18d-6c5c-4646-a61f-17b12dad0f76/@@download/attachment/L-K-PTBP1-1.pdf

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. This K562 growth has been treated with an shRNA against PTBP1

value: adult

value: ENCBS947VKK at ENCODE; https://www.encodeproject.org/ENCBS947VKK/

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


title: SGE_438

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


title: SGE_437

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

value: phase 2


title: RAMPAGE from NCI-H460 (ENCLB263PKG)

description:
https://www.encodeproject.org/experiments/ENCSR239ZQA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR239ZQA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR625QJI
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB263PKG
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/752a6e31-7f6e-489e-82df-e425c149651b/@@download/attachment/LID294673.pdf

value: immortalized cell line

value: Epithelial-like large cell lung carcinoma immortalized cells from a 37 year old male.

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS446PPO at ENCODE; https://www.encodeproject.org/ENCBS446PPO/

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

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

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


title: SGE_442


title: SGE_435


title: SGE_434


title: shRNA RNA-seq from K562 (ENCLB452BCP)

description:
https://www.encodeproject.org/experiments/ENCSR268JDD/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EIF2C1 in K562 cells followed by RNA-seq. (EIF2C1 BGKLV13)
experiment encode accession: ENCSR268JDD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB452BCP
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting AGO1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d48e6b4c-cdfa-43e5-a94d-1d8adc687282/@@download/attachment/L-EIF2C1_BGKLV13_70.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2C1.(EIF2C1_BGKLV13_70)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS407GJQ at ENCODE; https://www.encodeproject.org/ENCBS407GJQ/

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_433

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

value: phase 2


title: SGE_436

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


title: shRNA RNA-seq from K562 (ENCLB478LKK)

description:
https://www.encodeproject.org/experiments/ENCSR239BCO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PTBP1 in K562 cells followed by RNA-seq
experiment encode accession: ENCSR239BCO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB478LKK
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/8af77f55-5a64-4039-998b-330fd5541ba8/@@download/attachment/L-K-PTBP1-2.pdf

value: immortalized cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. This K562 growth has been treated with an shRNA against PTBP1

value: adult

value: ENCBS494YUP at ENCODE; https://www.encodeproject.org/ENCBS494YUP/

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


title: shRNA RNA-seq from K562 (ENCLB469LRS)

description:
https://www.encodeproject.org/experiments/ENCSR234YMW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SLTM in K562 cells followed by RNA-seq. (SLTM BGKLV13)
experiment encode accession: ENCSR234YMW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB469LRS
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/93e1cf71-786c-494c-8b3d-a919b86ed3fd/@@download/attachment/L-SLTM_BGKLV13_58.pdf

value: SLTM

value: RNA-seq on K562 cells treated with an shRNA knockdown against SLTM.(SLTM_BGKLV13_58)

value: ENCBS850LWJ at ENCODE; https://www.encodeproject.org/ENCBS850LWJ/


title: SGE_432

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


title: SGE_431


title: shRNA RNA-seq from HepG2 (ENCLB151QWB)

description:
https://www.encodeproject.org/experiments/ENCSR237IWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against KIAA1967 in HepG2 cells followed by RNA-seq. (KIAA1967_BGHLV18)
experiment encode accession: ENCSR237IWZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB151QWB
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting CCAR2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8d2a845e-eb9c-443d-995e-e9b673b85987/@@download/attachment/L-KIAA1967_BGHLV18_15.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against KIAA1967. (KIAA1967_BGHLV18_15)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS530ENF at ENCODE; https://www.encodeproject.org/ENCBS530ENF/

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_430

value: phase 2


title: SGE_428

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


title: shRNA RNA-seq from HepG2 (ENCLB993NMX)

description:
https://www.encodeproject.org/experiments/ENCSR237IWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against KIAA1967 in HepG2 cells followed by RNA-seq. (KIAA1967_BGHLV18)
experiment encode accession: ENCSR237IWZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB993NMX
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/d987ecf3-4933-4e79-9177-3693cab5eee8/@@download/attachment/L-KIAA1967_BGHLV18_16.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against KIAA1967. (KIAA1967_BGHLV18_16)

value: Brenton Graveley, UConn

value: ENCBS173ACT at ENCODE; https://www.encodeproject.org/ENCBS173ACT/


title: SGE_427


title: shRNA RNA-seq from K562 (ENCLB479GXM)

description:
https://www.encodeproject.org/experiments/ENCSR232CPD/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against XRCC6 in K562 cells followed by RNA-seq. (XRCC6 BGKLV13)
experiment encode accession: ENCSR232CPD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB479GXM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting XRCC6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/6233b48d-ffba-4202-ae8c-84f96e4fe586/@@download/attachment/L-XRCC6_BGKLV13_23.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against XRCC6.(XRCC6_BGKLV13_23)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS128UKH at ENCODE; https://www.encodeproject.org/ENCBS128UKH/

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_429


title: shRNA RNA-seq from K562 (ENCLB615XOR)

description:
https://www.encodeproject.org/experiments/ENCSR232CPD/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against XRCC6 in K562 cells followed by RNA-seq. (XRCC6 BGKLV13)
experiment encode accession: ENCSR232CPD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB615XOR
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/ac73134f-324d-4674-bc42-5ab9059e2607/@@download/attachment/L-XRCC6_BGKLV13_24.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against XRCC6.(XRCC6_BGKLV13_24)

value: ENCBS063ROH at ENCODE; https://www.encodeproject.org/ENCBS063ROH/


title: SGE_426

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction kit.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra RNA Library Prep Kit. Briefly, we purified the poly-adenylated mRNA from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then reverse transcribed into cDNA, ligated to Illumina adapters, size-selected for a median size of ~350 bp, and amplified via PCR for 13 cycles. We tagged each sample with a unique molecular barcode and pooled 10-12 samples per Illumina HiSeq 2500 lane of single-end 100 bp sequencing.

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


title: shRNA RNA-seq from K562 (ENCLB690EJY)

description:
https://www.encodeproject.org/experiments/ENCSR234YMW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SLTM in K562 cells followed by RNA-seq. (SLTM BGKLV13)
experiment encode accession: ENCSR234YMW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB690EJY
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/d9bb4b1f-733d-4788-8fa3-6b200276242c/@@download/attachment/L-SLTM_BGKLV13_57.pdf

value: SLTM

value: RNA-seq on K562 cells treated with an shRNA knockdown against SLTM.(SLTM_BGKLV13_57)

value: ENCBS433OVV at ENCODE; https://www.encodeproject.org/ENCBS433OVV/


title: shRNA RNA-seq from HepG2 (ENCLB679PHQ)

description:
https://www.encodeproject.org/experiments/ENCSR222SMI/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RBM27 in HepG2 cells followed by RNA-seq. (RBM27_BGHLV18)
experiment encode accession: ENCSR222SMI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB679PHQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RBM27

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/418d0b5f-1993-44fd-9250-30534721ec95/@@download/attachment/L-RBM27_BGHLV18_48.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM27. (RBM27_BGHLV18_48)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS851ZNE at ENCODE; https://www.encodeproject.org/ENCBS851ZNE/

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

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


title: shRNA RNA-seq from K562 (ENCLB368QAK)

description:
https://www.encodeproject.org/experiments/ENCSR227AVS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NOL12. (NOL12-BGKLV25)
experiment encode accession: ENCSR227AVS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB368QAK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting NOL12

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0c7694c8-a0ff-4789-90a2-742afe3b280d/@@download/attachment/L-NOL12-BGKLV25-36.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NOL12. (NOL12-BGKLV25-36)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS113YMQ at ENCODE; https://www.encodeproject.org/ENCBS113YMQ/

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


title: shRNA RNA-seq from K562 (ENCLB194TPG)

description:
https://www.encodeproject.org/experiments/ENCSR232XRZ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SND1 in K562 cells followed by RNA-seq. (SND1 BGKLV13)
experiment encode accession: ENCSR232XRZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB194TPG
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SND1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/34a0d430-ce91-4d07-ad57-fd3908164582/@@download/attachment/L-SND1_BGKLV13_59.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SND1.(SND1_BGKLV13_59)

value: ENCBS146WJY at ENCODE; https://www.encodeproject.org/ENCBS146WJY/

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


title: SGE_422

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

value: phase 2


title: SGE_424


title: SGE_423

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


title: shRNA RNA-seq from HepG2 (ENCLB195HJB)

description:
https://www.encodeproject.org/experiments/ENCSR222SMI/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RBM27 in HepG2 cells followed by RNA-seq. (RBM27_BGHLV18)
experiment encode accession: ENCSR222SMI
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB195HJB
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/c815133c-1063-4292-bdeb-56777f39308f/@@download/attachment/L-RBM27_BGHLV18_47.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM27. (RBM27_BGHLV18_47)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS646RDV at ENCODE; https://www.encodeproject.org/ENCBS646RDV/

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


title: shRNA RNA-seq from K562 (ENCLB792UOL)

description:
https://www.encodeproject.org/experiments/ENCSR227AVS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NOL12. (NOL12-BGKLV25)
experiment encode accession: ENCSR227AVS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB792UOL
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/5c0d80bd-326a-4726-8560-ad66058a96d0/@@download/attachment/L-NOL12-BGKLV25-35.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NOL12. (NOL12-BGKLV25-35)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS798HJU at ENCODE; https://www.encodeproject.org/ENCBS798HJU/


title: SGE_420


title: SGE_421

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


title: shRNA RNA-seq from K562 (ENCLB194RPE)

description:
https://www.encodeproject.org/experiments/ENCSR232XRZ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SND1 in K562 cells followed by RNA-seq. (SND1 BGKLV13)
experiment encode accession: ENCSR232XRZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB194RPE
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/ecf77f28-4ec9-4e56-87eb-4d8ff6457da3/@@download/attachment/L-SND1_BGKLV13_60.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SND1.(SND1_BGKLV13_60)

value: ENCBS478TXQ at ENCODE; https://www.encodeproject.org/ENCBS478TXQ/

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_419

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB293SMR)

description:
https://www.encodeproject.org/experiments/ENCSR222LRL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGKLV24)
experiment encode accession: ENCSR222LRL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB293SMR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CPSF7

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2d8206a0-68e7-4a16-9cae-0ba9455f3a6b/@@download/attachment/L-CPSF7_BGKLV24_10_17601.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGKLV24_10_17601)

value: ENCBS270OAE at ENCODE; https://www.encodeproject.org/ENCBS270OAE/


title: shRNA RNA-seq from K562 (ENCLB043KLA)

description:
https://www.encodeproject.org/experiments/ENCSR222LRL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGKLV24)
experiment encode accession: ENCSR222LRL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB043KLA
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/a29367e5-95e0-484e-bd2b-a44942b01b91/@@download/attachment/L-CPSF7_BGKLV24_9_17600.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CPSF7. (CPSF7_BGKLV24_9_17600)

value: ENCBS870VQI at ENCODE; https://www.encodeproject.org/ENCBS870VQI/


title: shRNA RNA-seq from HepG2 (ENCLB947BPM)

description:
https://www.encodeproject.org/experiments/ENCSR220TBR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DAZAP1. (DAZAP1-BGHLV23)
experiment encode accession: ENCSR220TBR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB947BPM
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DAZAP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/7cb3b57e-109f-4e0a-a5a0-4d9c53818da3/@@download/attachment/L-DAZAP1-BGHLV23-11.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DAZAP1. (DAZAP1-BGHLV23-11)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS581BGT at ENCODE; https://www.encodeproject.org/ENCBS581BGT/

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 (ENCLB798NMN)

description:
https://www.encodeproject.org/experiments/ENCSR222CSF/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX28 in HepG2 cells followed by RNA-seq. (DDX28_BGHLV17)
experiment encode accession: ENCSR222CSF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB798NMN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX28

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c903b149-a4cc-4422-8c54-b647b60dfb63/@@download/attachment/L-DDX28_BGHLV17_56.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX28. (DDX28_BGHLV17_56)

value: Brenton Graveley, UConn

value: ENCBS380ZOW at ENCODE; https://www.encodeproject.org/ENCBS380ZOW/


title: microRNA-seq from lower leg skin (ENCLB093OXX)

description:
https://www.encodeproject.org/experiments/ENCSR219YHR/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human lower leg skin
experiment encode accession: ENCSR219YHR
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB093OXX
size range: <30

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

value: lower leg skin

value: tissue

value: Skin - Sun Exposed (Lower leg)

value: 54 year

value: adult

value: Barbara Wold, Caltech

value: ENCBS602BLH at ENCODE; https://www.encodeproject.org/ENCBS602BLH/

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


title: shRNA RNA-seq from HepG2 (ENCLB570ODX)

description:
https://www.encodeproject.org/experiments/ENCSR222CSF/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX28 in HepG2 cells followed by RNA-seq. (DDX28_BGHLV17)
experiment encode accession: ENCSR222CSF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB570ODX
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/ab95973a-00ac-4dd2-94d3-ba76f144b0c4/@@download/attachment/L-DDX28_BGHLV17_55.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX28. (DDX28_BGHLV17_55)

value: 15 year

value: child

value: male

value: ENCBS289IAE at ENCODE; https://www.encodeproject.org/ENCBS289IAE/


title: SGE_418

source_name: peripheral blood mononuclear cells

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

value: phase 2


title: SGE_425


title: SGE_417

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


title: SGE_416

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


title: SGE_415


title: shRNA RNA-seq from HepG2 (ENCLB175OHP)

description:
https://www.encodeproject.org/experiments/ENCSR220TBR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against DAZAP1. (DAZAP1-BGHLV23)
experiment encode accession: ENCSR220TBR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB175OHP
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/17e5678a-0908-4bdd-8d22-84008c7202da/@@download/attachment/L-DAZAP1-BGHLV23-12.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DAZAP1. (DAZAP1-BGHLV23-12)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS019XED at ENCODE; https://www.encodeproject.org/ENCBS019XED/

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_414


title: shRNA RNA-seq from K562 (ENCLB663EPR)

description:
https://www.encodeproject.org/experiments/ENCSR219DXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SBDS. (SBDS_BGKLV24_B)
experiment encode accession: ENCSR219DXZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB663EPR
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2db7b8c4-bd72-4a34-9322-7942d2a69f40/@@download/attachment/L-SBDS_BGKLV24_55B.pdf

value: SBDS

value: RNA-seq on K562 cells treated with an shRNA knockdown against SBDS. (SBDS_BGKLV24_55B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS225YVR at ENCODE; https://www.encodeproject.org/ENCBS225YVR/

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_413

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB993XMR)

description:
https://www.encodeproject.org/experiments/ENCSR219DXZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against SBDS. (SBDS_BGKLV24_B)
experiment encode accession: ENCSR219DXZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB993XMR
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/7cf3a23d-5a1b-4f0a-8690-fb6b4eaa8e97/@@download/attachment/L-SBDS_BGKLV24_56B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SBDS. (SBDS_BGKLV24_56B)

value: ENCBS566AKW at ENCODE; https://www.encodeproject.org/ENCBS566AKW/


title: shRNA RNA-seq from HepG2 (ENCLB839SYF)

description:
https://www.encodeproject.org/experiments/ENCSR210RWL/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX27 in HepG2 cells followed by RNA-seq. (DDX27_BGHLV17)
experiment encode accession: ENCSR210RWL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB839SYF
size range: >200
spikeins used: /references/ENCSR449DXG/
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DDX27

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/72b709f4-ed2e-434a-91f8-f0c9f6c90017/@@download/attachment/L-DDX27_BGHLV17_54.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX27. (DDX27_BGHLV17_54)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS335TOC at ENCODE; https://www.encodeproject.org/ENCBS335TOC/


title: microRNA-seq from lower leg skin (ENCLB802MIH)

description:
https://www.encodeproject.org/experiments/ENCSR219YHR/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human lower leg skin
experiment encode accession: ENCSR219YHR
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB802MIH
size range: <30

value: lower leg skin

value: tissue

value: Skin - Sun Exposed (Lower leg)

value: 54 year

value: adult

value: Barbara Wold, Caltech

value: ENCBS488XGK at ENCODE; https://www.encodeproject.org/ENCBS488XGK/

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


title: SGE_411

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction kit.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra RNA Library Prep Kit. Briefly, we purified the poly-adenylated mRNA from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then reverse transcribed into cDNA, ligated to Illumina adapters, size-selected for a median size of ~350 bp, and amplified via PCR for 13 cycles. We tagged each sample with a unique molecular barcode and pooled 10-12 samples per Illumina HiSeq 2500 lane of single-end 100 bp sequencing.

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

value: phase 2


title: SGE_410


title: SGE_412

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


title: SGE_409


title: shRNA RNA-seq from K562 (ENCLB050GUS)

description:
https://www.encodeproject.org/experiments/ENCSR210KJB/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RRP9 in K562 cells followed by RNA-seq. (RRP9_BGKLV19)
experiment encode accession: ENCSR210KJB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB050GUS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RRP9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/002e4677-87b4-4475-bb0d-d24089d41ee1/@@download/attachment/L-RRP9_BGKLV19_47B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RRP9. (RRP9_BGKLV19_47B)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS368MWR at ENCODE; https://www.encodeproject.org/ENCBS368MWR/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB806FWN)

description:
https://www.encodeproject.org/experiments/ENCSR210RWL/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX27 in HepG2 cells followed by RNA-seq. (DDX27_BGHLV17)
experiment encode accession: ENCSR210RWL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB806FWN
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/26853f87-4ac8-4271-90c1-f7771acc609d/@@download/attachment/L-DDX27_BGHLV17_53.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DDX27. (DDX27_BGHLV17_53)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS799LNH at ENCODE; https://www.encodeproject.org/ENCBS799LNH/

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_408

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB479NQQ)

description:
https://www.encodeproject.org/experiments/ENCSR210KJB/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RRP9 in K562 cells followed by RNA-seq. (RRP9_BGKLV19)
experiment encode accession: ENCSR210KJB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB479NQQ
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/551b61cf-b6e1-4a88-94ed-131db8d7b37e/@@download/attachment/L-RRP9_BGKLV19_48B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RRP9. (RRP9_BGKLV19_48B)

value: 53 year

value: adult

value: ENCBS657ZYP at ENCODE; https://www.encodeproject.org/ENCBS657ZYP/


title: shRNA RNA-seq from HepG2 (ENCLB461DVA)

description:
https://www.encodeproject.org/experiments/ENCSR210DML/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM2. (PUM2-BGHLV23)
experiment encode accession: ENCSR210DML
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB461DVA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/81df4490-7631-43d6-b989-dbd23cd5c5ca/@@download/attachment/L-PUM2-BGHLV23-35.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM2. (PUM2-BGHLV23-35)

value: ENCBS756FJO at ENCODE; https://www.encodeproject.org/ENCBS756FJO/


title: SGE_405


title: SGE_404


title: SGE_407

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


title: shRNA RNA-seq from K562 (ENCLB318AXI)

description:
https://www.encodeproject.org/experiments/ENCSR208GPE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX1. (DDX1_BGKLV24)
experiment encode accession: ENCSR208GPE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB318AXI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9826dcd4-ef99-4528-8646-60de3fe6e29f/@@download/attachment/L-DDX1_BGKLV24_14_17605.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX1. (DDX1_BGKLV24_14_17605)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS442NXE at ENCODE; https://www.encodeproject.org/ENCBS442NXE/

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_406

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


title: shRNA RNA-seq from K562 (ENCLB873DAI)

description:
https://www.encodeproject.org/experiments/ENCSR208GPE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX1. (DDX1_BGKLV24)
experiment encode accession: ENCSR208GPE
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB873DAI
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/ce1c3fa4-185a-4d0d-bbf9-f88d90a0df3a/@@download/attachment/L-DDX1_BGKLV24_13_17604.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX1. (DDX1_BGKLV24_13_17604)

value: Brenton Graveley, UConn

value: ENCBS962ZXU at ENCODE; https://www.encodeproject.org/ENCBS962ZXU/


title: RAMPAGE from A172 (ENCLB405ENM)

description:
https://www.encodeproject.org/experiments/ENCSR208AWA/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line A172, a glioblastoma cell line derived from a 53 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR208AWA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR580GSX
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB405ENM
size range: >200

source_name: Homo sapiens A172 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/7c3b7fb6-cf2f-4ccc-a4c9-d7c38ad51d39/@@download/attachment/292965.pdf

value: immortalized cell line

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS225AJI at ENCODE; https://www.encodeproject.org/ENCBS225AJI/

value: Derived from ENCODE donor ENCDO934VEN; https://www.encodeproject.org/ENCDO934VEN/

value: ENCODE dbxrefs Cellosaurus CVCL_0131; http://web.expasy.org/cellosaurus/CVCL_0131


title: SGE_403

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB338WUK)

description:
https://www.encodeproject.org/experiments/ENCSR207QGW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2C3. (K-EIF2C3)
experiment encode accession: ENCSR207QGW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB338WUK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting AGO3

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/7b877d6a-04dd-461c-a2bf-c75e369d6856/@@download/attachment/L-K-EIF2C3-1.pdf

value: K562 cells treated with an shRNA knockdown against EIF2C3, used in RNA-seq experiments. (K-EIF2C3-1)

value: 53 year

value: adult

value: female

value: ENCBS833OVZ at ENCODE; https://www.encodeproject.org/ENCBS833OVZ/


title: SGE_401

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


title: shRNA RNA-seq from K562 (ENCLB545JQS)

description:
https://www.encodeproject.org/experiments/ENCSR207QGW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2C3. (K-EIF2C3)
experiment encode accession: ENCSR207QGW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB545JQS
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/c33d8c36-c2bf-417f-bab3-8177457fd073/@@download/attachment/L-K-EIF2C3-2.pdf

value: K562 cells treated with an shRNA knockdown against EIF2C3, used in RNA-seq experiments. (K-EIF2C3-2)

value: chronic myelogenous leukemia (CML)

value: ENCBS324XGY at ENCODE; https://www.encodeproject.org/ENCBS324XGY/

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

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


title: RAMPAGE from A172 (ENCLB204BTL)

description:
https://www.encodeproject.org/experiments/ENCSR208AWA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line A172, a glioblastoma cell line derived from a 53 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR208AWA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR580GSX
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB204BTL
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/258147e2-6058-4788-9445-ebb2f32c8ada/@@download/attachment/292964.pdf

value: immortalized cell line

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS874LTK at ENCODE; https://www.encodeproject.org/ENCBS874LTK/


title: SGE_400


title: SGE_399


title: shRNA RNA-seq from K562 (ENCLB201SRW)

description:
https://www.encodeproject.org/experiments/ENCSR205VSQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX28 in K562 cells followed by RNA-seq. (DDX28_BGKLV19)
experiment encode accession: ENCSR205VSQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB201SRW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX28

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/890abab9-2db2-4700-a76e-0ebd2c24fac6/@@download/attachment/L-DDX28_BGKLV19_14B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX28. (DDX28_BGKLV19_14B)

value: Brenton Graveley, UConn

value: ENCBS676KLB at ENCODE; https://www.encodeproject.org/ENCBS676KLB/


title: shRNA RNA-seq from K562 (ENCLB043KQU)

description:
https://www.encodeproject.org/experiments/ENCSR192GBD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PABPC1. (PABPC1_BGKLV24_B)
experiment encode accession: ENCSR192GBD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB043KQU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PABPC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b72aa780-db3a-4986-b993-94525aae71c6/@@download/attachment/L-PABPC1_BGKLV24_42B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PABPC1. (PABPC1_BGKLV24_42B)

value: 53 year

value: ENCBS016BTC at ENCODE; https://www.encodeproject.org/ENCBS016BTC/


title: SGE_398

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB728TUG)

description:
https://www.encodeproject.org/experiments/ENCSR205VSQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX28 in K562 cells followed by RNA-seq. (DDX28_BGKLV19)
experiment encode accession: ENCSR205VSQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB728TUG
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/bd81db68-dbba-4993-b563-f30b5d55f582/@@download/attachment/L-DDX28_BGKLV19_13B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX28. (DDX28_BGKLV19_13B)

value: adult

value: female

value: ENCBS051ELN at ENCODE; https://www.encodeproject.org/ENCBS051ELN/


title: shRNA RNA-seq from HepG2 (ENCLB776TFZ)

description:
https://www.encodeproject.org/experiments/ENCSR210DML/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM2. (PUM2-BGHLV23)
experiment encode accession: ENCSR210DML
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB776TFZ
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/9f2b7494-206a-4368-9277-4cdb796b4c93/@@download/attachment/L-PUM2-BGHLV23-36.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against PUM2. (PUM2-BGHLV23-36)

value: 15 year

value: child

value: hepatocellular carcinoma

value: ENCBS344JWL at ENCODE; https://www.encodeproject.org/ENCBS344JWL/

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_396

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


title: SGE_397

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


title: SGE_395


title: SGE_402


title: shRNA RNA-seq from K562 (ENCLB121GZA)

description:
https://www.encodeproject.org/experiments/ENCSR191VWK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGKLV25)
experiment encode accession: ENCSR191VWK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB121GZA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PNPT1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c55d53a9-1c94-439f-a24a-8264c8dc1989/@@download/attachment/L-PNPT1-BGKLV25-40.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGKLV25-40)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS380IYL at ENCODE; https://www.encodeproject.org/ENCBS380IYL/

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_393

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

value: phase 2


title: RAMPAGE from myotube (ENCLB150HQL)

description:
https://www.encodeproject.org/experiments/ENCSR187NWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of primary cell line HSMM that has been differentiated into myotubes. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR187NWZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR828TEI
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB150HQL
size range: >200

source_name: Homo sapiens myotube in vitro differentiated cells

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/f2b73eb8-2b25-4924-b8d9-cbe3ffe686d9/@@download/attachment/293012.pdf

value: myotube

value: in vitro differentiated cells

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS140MNV at ENCODE; https://www.encodeproject.org/ENCBS140MNV/

value: Derived from ENCODE donor ENCDO094AAA; https://www.encodeproject.org/ENCDO094AAA/


title: SGE_392

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: microRNA-seq from prostate gland (ENCLB364UKA)

description:
https://www.encodeproject.org/experiments/ENCSR185LOQ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human prostate
experiment encode accession: ENCSR185LOQ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB364UKA
size range: <30

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

value: prostate gland

value: tissue

value: Prostate

value: 37 year

value: adult

value: male

value: Barbara Wold, Caltech

value: ENCBS553XGK at ENCODE; https://www.encodeproject.org/ENCBS553XGK/

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


title: SGE_391

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

value: phase 2


title: SGE_394


title: shRNA RNA-seq from K562 (ENCLB361UST)

description:
https://www.encodeproject.org/experiments/ENCSR188IPO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against GTF2F1 in K562 cells followed by RNA-seq. (GTF2F1 BGKLV13)
experiment encode accession: ENCSR188IPO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB361UST
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting GTF2F1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2133201e-8a0c-40a3-a518-d4894c044173/@@download/attachment/L-GTF2F1_BGKLV13_40.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against GTF2F1.(GTF2F1_BGKLV13_40)

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS904ISV at ENCODE; https://www.encodeproject.org/ENCBS904ISV/

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

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


title: microRNA-seq from prostate gland (ENCLB677CZI)

description:
https://www.encodeproject.org/experiments/ENCSR185LOQ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human prostate
experiment encode accession: ENCSR185LOQ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB677CZI
size range: <30

value: prostate gland

value: tissue

value: Prostate

value: 37 year

value: ENCBS886OHA at ENCODE; https://www.encodeproject.org/ENCBS886OHA/


title: shRNA RNA-seq from K562 (ENCLB806RNW)

description:
https://www.encodeproject.org/experiments/ENCSR188IPO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against GTF2F1 in K562 cells followed by RNA-seq. (GTF2F1 BGKLV13)
experiment encode accession: ENCSR188IPO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB806RNW
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/db8deb13-82af-42ae-a445-22bab6e0f8ba/@@download/attachment/L-GTF2F1_BGKLV13_39.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against GTF2F1.(GTF2F1_BGKLV13_39)

value: adult

value: ENCBS703API at ENCODE; https://www.encodeproject.org/ENCBS703API/


title: SGE_388

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

value: phase 2


title: shRNA RNA-seq from HepG2 (ENCLB276ZKA)

description:
https://www.encodeproject.org/experiments/ENCSR182DAW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against HNRNPA1 in HepG2 cells followed by RNA-seq. (HNRNPA1-BGHLV20)
experiment encode accession: ENCSR182DAW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB276ZKA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting HNRNPA1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d3b57e07-d4ea-48b8-a32e-5cc1f0265623/@@download/attachment/L-HNRNPA1-BGHLV20-31_17720.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown againstHNRNPA1. (HNRNPA1-BGHLV20-31_17720)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS207OWT at ENCODE; https://www.encodeproject.org/ENCBS207OWT/

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_389


title: SGE_387

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


title: SGE_386

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


title: shRNA RNA-seq from K562 (ENCLB600EIL)

description:
https://www.encodeproject.org/experiments/ENCSR192GBD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PABPC1. (PABPC1_BGKLV24_B)
experiment encode accession: ENCSR192GBD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR419JMU
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB600EIL
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/2c714a1a-b587-4ba3-b3f8-5e29a5cc7773/@@download/attachment/L-PABPC1_BGKLV24_41B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PABPC1. (PABPC1_BGKLV24_41B)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS125WRA at ENCODE; https://www.encodeproject.org/ENCBS125WRA/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB551SNN)

description:
https://www.encodeproject.org/experiments/ENCSR182DAW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against HNRNPA1 in HepG2 cells followed by RNA-seq. (HNRNPA1-BGHLV20)
experiment encode accession: ENCSR182DAW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB551SNN
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/a9d37431-ad0f-4695-b2f8-ee2ea1c68bad/@@download/attachment/L-HNRNPA1-BGHLV20-32_17721.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown againstHNRNPA1. (HNRNPA1-BGHLV20-32_17721)

value: 15 year

value: ENCBS072JEO at ENCODE; https://www.encodeproject.org/ENCBS072JEO/


title: SGE_382

value: phase 2


title: SGE_383

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


title: SGE_385


title: shRNA RNA-seq from K562 (ENCLB227PGI)

description:
https://www.encodeproject.org/experiments/ENCSR191VWK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGKLV25)
experiment encode accession: ENCSR191VWK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB227PGI
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/8460217d-eb29-4814-93c5-929464a88ccd/@@download/attachment/L-PNPT1-BGKLV25-39.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PNPT1. (PNPT1-BGKLV25-39)

value: adult

value: ENCBS775HUY at ENCODE; https://www.encodeproject.org/ENCBS775HUY/


title: total RNA-seq from HepG2 (ENCLB707CLT)

description:
https://www.encodeproject.org/experiments/ENCSR181ZGR/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial total fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR181ZGR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB707CLT
size range: >200
spikeins used: /references/ENCSR422PLF/

source_name: Homo sapiens HepG2 immortalized cell line

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

value: child

value: male

value: hepatocellular carcinoma

value: Eric Lécuyer, IRCM

value: ENCBS488HLS at ENCODE; https://www.encodeproject.org/ENCBS488HLS/

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

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


title: siRNA RNA-seq from K562 (ENCLB965KAZ)

description:
https://www.encodeproject.org/experiments/ENCSR181AXM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting CHD1.
experiment encode accession: ENCSR181AXM
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR109YDL
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB965KAZ
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting CHD1

value: K562 cells treated with a siRNA knockdown against CHD1, used in RNA-seq experiments.

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS453CUR at ENCODE; https://www.encodeproject.org/ENCBS453CUR/

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: SGE_381

source_name: peripheral blood mononuclear cells

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

value: phase 2


title: total RNA-seq from HepG2 (ENCLB852SGS)

description:
https://www.encodeproject.org/experiments/ENCSR181ZGR/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial total fractions on HepG2 Long Total from Lecuyer
experiment encode accession: ENCSR181ZGR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB852SGS
size range: >200
spikeins used: /references/ENCSR422PLF/

value: immortalized cell line

value: 15 year

value: child

value: ENCBS204QRM at ENCODE; https://www.encodeproject.org/ENCBS204QRM/


title: shRNA RNA-seq from HepG2 (ENCLB558WAW)

description:
https://www.encodeproject.org/experiments/ENCSR180XTP/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against NUSAP1 in HepG2 cells followed by RNA-seq. (NUSAP1_BGHLV18)
experiment encode accession: ENCSR180XTP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB558WAW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting NUSAP1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/514297f3-b639-404d-855d-9f5b2dfeda4a/@@download/attachment/L-NUSAP1_BGHLV18_37.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGHLV18_37)

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS722LIJ at ENCODE; https://www.encodeproject.org/ENCBS722LIJ/


title: shRNA RNA-seq from K562 (ENCLB499ERT)

description:
https://www.encodeproject.org/experiments/ENCSR181RLB/
***************
biological replicate number: 1
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: ENCLB499ERT
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/481ae6e4-e135-4d9a-a9ec-334b6af1ceb4/@@download/attachment/L-EEF2_BGKLV19_21B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against EEF2. (EEF2_BGKLV19_21B)

value: 53 year

value: adult

value: female

value: ENCBS198UTW at ENCODE; https://www.encodeproject.org/ENCBS198UTW/

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


title: SGE_380


title: siRNA RNA-seq from K562 (ENCLB109CKQ)

description:
https://www.encodeproject.org/experiments/ENCSR181AXM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting CHD1.
experiment encode accession: ENCSR181AXM
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR109YDL
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB109CKQ
size range: >200
spikeins used: /references/ENCSR866KGS/

value: K562 cells treated with a siRNA knockdown against CHD1, used in RNA-seq experiments.

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS397TAP at ENCODE; https://www.encodeproject.org/ENCBS397TAP/

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: SGE_379

value: phase 2


title: SGE_376

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


title: shRNA RNA-seq from HepG2 (ENCLB956UNG)

description:
https://www.encodeproject.org/experiments/ENCSR180XTP/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against NUSAP1 in HepG2 cells followed by RNA-seq. (NUSAP1_BGHLV18)
experiment encode accession: ENCSR180XTP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR674KEK
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB956UNG
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/42fc4885-e716-4268-93f0-330315bb545a/@@download/attachment/L-NUSAP1_BGHLV18_38.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGHLV18_38)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS619OWS at ENCODE; https://www.encodeproject.org/ENCBS619OWS/

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_377

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


title: RAMPAGE from endometrial microvascular endothelial cells (ENCLB370DOO)

description:
https://www.encodeproject.org/experiments/ENCSR171YRA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of endometrial microvascular endothelial primary cell line HEMEC. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR171YRA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR919MZM
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB370DOO
size range: >200

source_name: Homo sapiens endometrial microvascular endothelial cells primary cell female adult (34 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/2c2a7b73-08d8-4830-85bf-a6b2b2d71fe9/@@download/attachment/295341.pdf

value: primary cell

value: Human Endometrial Microvascular Endothelial Cells (HEMEC) from the uterus of a 34 year old caucasian female.  Cells are from ScienCell Research Laboratories and isolated from the inner mucous membrane of the uterus known as the endometrium.

value: 34 year

value: adult

tag: passage number

value: female

value: Thomas Gingeras, CSHL

value: ENCBS635PXV at ENCODE; https://www.encodeproject.org/ENCBS635PXV/

value: Derived from ENCODE donor ENCDO212MHK; https://www.encodeproject.org/ENCDO212MHK/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=7010


title: RAMPAGE from endometrial microvascular endothelial cells (ENCLB256BIF)

description:
https://www.encodeproject.org/experiments/ENCSR171YRA/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of endometrial microvascular endothelial primary cell line HEMEC. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR171YRA
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR919MZM
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB256BIF
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/7c1a783e-faad-4c4f-a807-caf8d00cec94/@@download/attachment/295342.pdf

value: Human Endometrial Microvascular Endothelial Cells (HEMEC) from the uterus of a 34 year old caucasian female.    Cells are from ScienCell Research Laboratories and isolated from the inner mucous membrane of the uterus known as the endometrium

value: ENCBS442ZTY at ENCODE; https://www.encodeproject.org/ENCBS442ZTY/


title: RAMPAGE from cardiac ventricle fibroblast (ENCLB164PDY)

description:
https://www.encodeproject.org/experiments/ENCSR177YJM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cardiac ventricle fibroblast cells (HCF-av). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR177YJM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR369RVN
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB164PDY
size range: >200

source_name: Homo sapiens cardiac ventricle fibroblast primary cell male adult (18 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/45f15fba-78ee-49d2-958c-89af9ba2446a/@@download/attachment/LID295365.pdf

value: cardiac ventricle fibroblast

value: Human Cardiac Fibroblast Cells from the ventrical of an 18 year old male.

value: 18 year

value: male

value: ENCBS143ZKI at ENCODE; https://www.encodeproject.org/ENCBS143ZKI/

value: Derived from ENCODE donor ENCDO831RPK; https://www.encodeproject.org/ENCDO831RPK/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=6315


title: SGE_375

value: phase 2


title: RAMPAGE from cardiac ventricle fibroblast (ENCLB155ZRA)

description:
https://www.encodeproject.org/experiments/ENCSR177YJM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cardiac ventricle fibroblast cells (HCF-av). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR177YJM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR369RVN
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB155ZRA
size range: >200

source_name: Homo sapiens cardiac ventricle fibroblast primary cell

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7f64ce82-08fa-4e41-b89c-3ebfb0432101/@@download/attachment/LID295366.pdf

value: primary cell

value: Human Cardiac Fibroblast Cells

value: unknown

value: not collected

value: ENCBS577BXD at ENCODE; https://www.encodeproject.org/ENCBS577BXD/

value: Derived from ENCODE donor ENCDO690VKB; https://www.encodeproject.org/ENCDO690VKB/


title: SGE_372

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


title: SGE_371

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


title: shRNA RNA-seq from K562 (ENCLB635MPH)

description:
https://www.encodeproject.org/experiments/ENCSR169QQW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MSI2. (MSI2_BGKLV25)
experiment encode accession: ENCSR169QQW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB635MPH
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting MSI2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f917e020-d024-49ab-a83a-bb2bd47dcf84/@@download/attachment/L-MSI2_BGKLV25-34.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against MSI2. (MSI2_BGKLV25-34)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS339WIS at ENCODE; https://www.encodeproject.org/ENCBS339WIS/

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: siRNA RNA-seq from K562 (ENCLB517GTL)

description:
https://www.encodeproject.org/experiments/ENCSR169DSM/
***************
biological replicate number: 3
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: ENCLB517GTL
size range: >200
spikeins used: /references/ENCSR866KGS/

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

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

value: Sherman Weissman, Yale

value: ENCBS407QWZ at ENCODE; https://www.encodeproject.org/ENCBS407QWZ/


title: SGE_368

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB689UJU)

description:
https://www.encodeproject.org/experiments/ENCSR169QQW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against MSI2. (MSI2_BGKLV25)
experiment encode accession: ENCSR169QQW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR620PUP
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB689UJU
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/411e618c-07e0-4bdc-8c47-c4e55054a576/@@download/attachment/L-MSI2_BGKLV25-33.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against MSI2. (MSI2_BGKLV25-33)

value: ENCBS027GJN at ENCODE; https://www.encodeproject.org/ENCBS027GJN/


title: SGE_367

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_378


title: SGE_366

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


title: shRNA RNA-seq from HepG2 (ENCLB601WEK)

description:
https://www.encodeproject.org/experiments/ENCSR167JPY/
***************
biological replicate number: 1
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: ENCLB601WEK
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/d888fb1c-d6f1-4a87-bbce-abddef36ad09/@@download/attachment/L-SRP68_BGHLV17_29.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRP68. (SRP68_BGHLV17_29)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS885ORM at ENCODE; https://www.encodeproject.org/ENCBS885ORM/

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

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