title: shRNA RNA-seq from K562 (ENCLB498AZF)

description:
https://www.encodeproject.org/experiments/ENCSR372DZW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with a control shRNA against no target. (k562-set-11b-shCNTRL)
experiment encode accession: ENCSR372DZW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB498AZF
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/52ef5d39-a348-4dee-b6fa-02164ff1068c/@@download/attachment/L-k562-set-11b-shCNTRL-2.pdf

value: Control

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (k562-set-11b-shCNTRL-2)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS023XVB at ENCODE; https://www.encodeproject.org/ENCBS023XVB/

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 (ENCLB709LDK)

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/ENCSR368ZRP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PAPOLA. (K-PAPOLA-30B)
experiment encode accession: ENCSR368ZRP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR942UNX
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB709LDK
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 K562 immortalized cell line transiently expressing shRNA targeting PAPOLA

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/617a4a51-8480-4bb9-8a5c-9d48f5392cdc/@@download/attachment/L-K-PAPOLA-30B-2.pdf

tag: antibody

value: PAPOLA

tag: line

value: immortalized cell line

tag: description

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

tag: biosample encode accession

tag: age

tag: dev stage

tag: Sex

tag: health state

tag: lab

tag: link

value: ENCBS360VVZ at ENCODE; https://www.encodeproject.org/ENCBS360VVZ/


title: total RNA-seq from pericardium fibroblast (ENCLB177URQ)

description:
https://www.encodeproject.org/experiments/ENCSR362HMX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from pericardium fibroblast cells (HPcF). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR362HMX
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB177URQ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens pericardium fibroblast primary cell female fetal (20 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e76821f7-bfdb-40b3-9f7b-98b2667418f2/@@download/attachment/295117.pdf

value: pericardium fibroblast

value: primary cell

value: Human Pericardial Fibroblast Cells (HPcF) from a female at 20 weeks gestation.

value: 20 week

value: fetal

tag: passage number

value: Thomas Gingeras, CSHL

value: ENCBS824CUM at ENCODE; https://www.encodeproject.org/ENCBS824CUM/

value: Derived from ENCODE donor ENCDO603DJW; https://www.encodeproject.org/ENCDO603DJW/


title: RBc8_NC

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

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

molecule: polyA RNA

organism: Macaca mulatta

source_name: whole blood

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

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

tag: cell type

value: white blood cells

tag: sample date

tag: study phase

value: phase 2

tag: study group

tag: treatment

value: NC


title: RCw10_NC


title: RCw10_LPS

value: LPS


title: RAMPAGE from mesangial cell (ENCLB280TZQ)

description:
https://www.encodeproject.org/experiments/ENCSR356VOK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from primary mesangial cells (HRMC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR356VOK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR198TKA
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB280TZQ
size range: >200

source_name: Homo sapiens mesangial primary cell female fetal (21 week)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/36431ef7-67fb-4f29-9a1f-7377a1f60a65/@@download/attachment/LID295177.pdf

value: mesangial cell

value: Human Renal Mesangial Cells (HRMC) from the kidney of a female at 22 weeks gestation.

value: 21 week

value: female

value: ENCBS386PWK at ENCODE; https://www.encodeproject.org/ENCBS386PWK/

value: Derived from ENCODE donor ENCDO008MFT; https://www.encodeproject.org/ENCDO008MFT/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=4205


title: total RNA-seq from pericardium fibroblast (ENCLB922RHX)

description:
https://www.encodeproject.org/experiments/ENCSR362HMX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from pericardium fibroblast cells (HPcF). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR362HMX
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB922RHX
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens pericardium fibroblast primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/051fc15e-6fd1-4e11-9264-cba140d89926/@@download/attachment/295118.pdf

value: pericardium fibroblast

value: primary cell

value: Human Pericardial Fibroblast Cells (HPcF) from an unknown donor (no metadata).

value: unknown

value: not collected

value: ENCBS852RZB at ENCODE; https://www.encodeproject.org/ENCBS852RZB/

value: Derived from ENCODE donor ENCDO806ILG; https://www.encodeproject.org/ENCDO806ILG/


title: RAc8_NC

value: white blood cells

value: phase 2


title: RAc8_LPS

value: LPS


title: shRNA RNA-seq from HepG2 (ENCLB528DAW)

description:
https://www.encodeproject.org/experiments/ENCSR354XQY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB--BGHLV22)
experiment encode accession: ENCSR354XQY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB528DAW
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b1b20738-f6d3-4eac-9a66-3e2f21ac1073/@@download/attachment/L-HNRNPAB--BGHLV22-23_17758.pdf

value: HNRNPAB

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB--BGHLV22-23_17758)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS299YGH at ENCODE; https://www.encodeproject.org/ENCBS299YGH/

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 (ENCLB072MLD)

description:
https://www.encodeproject.org/experiments/ENCSR354XQY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB--BGHLV22)
experiment encode accession: ENCSR354XQY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB072MLD
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/a182d966-d727-46b9-be95-7c9658c598f4/@@download/attachment/L-HNRNPAB--BGHLV22-24_17759.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPAB. (HNRNPAB--BGHLV22-24_17759)

value: ENCBS798HNT at ENCODE; https://www.encodeproject.org/ENCBS798HNT/


title: RAMPAGE from HT1080 (ENCLB330INY)

description:
https://www.encodeproject.org/experiments/ENCSR352ANU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR352ANU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR067UNX
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB330INY
size range: >200

source_name: Homo sapiens HT1080 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/75ca8ecb-883b-4264-be6e-bf04863aeeca/@@download/attachment/LID294200.pdf

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

value: 35 year

value: adult

value: fibrosarcoma

value: Thomas Gingeras, CSHL

tag: subcellular fraction term name

value: nucleus

value: ENCBS798NML at ENCODE; https://www.encodeproject.org/ENCBS798NML/

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

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

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


title: shRNA RNA-seq from K562 (ENCLB658TOL)

description:
https://www.encodeproject.org/experiments/ENCSR368ZRP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PAPOLA. (K-PAPOLA-30B)
experiment encode accession: ENCSR368ZRP
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR942UNX
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB658TOL
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/9640231b-67d9-4f57-9bc2-ebe125f655fe/@@download/attachment/L-K-PAPOLA-30B-1.pdf

tag: antibody

value: PAPOLA

value: immortalized cell line

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

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS643OWK at ENCODE; https://www.encodeproject.org/ENCBS643OWK/

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: 482_NC

value: white blood cells

value: phase 2

value: NC


title: 482_LPS

value: LPS


title: RAMPAGE from HT1080 (ENCLB573FOV)

description:
https://www.encodeproject.org/experiments/ENCSR352ANU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR352ANU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR067UNX
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB573FOV
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/654bf0f4-ed58-4cf7-b8ca-210c3c79da66/@@download/attachment/LID294199.pdf

tag: line

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

value: 35 year

value: adult

value: male

value: fibrosarcoma

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS039VHD at ENCODE; https://www.encodeproject.org/ENCBS039VHD/


title: RAMPAGE from HT1080 (ENCLB088BPI)

description:
https://www.encodeproject.org/experiments/ENCSR348DYP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line HT-1080, a connective tissue fibrosarcoma from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR348DYP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR535VTR
encode release date: 2016-03-16
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB088BPI
size range: >200

source_name: Homo sapiens HT1080 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/27adb9f3-374a-4378-85e0-801fc2afa53c/@@download/attachment/289913.pdf

value: immortalized cell line

tag: description

value: epithelial cell line derived from a fibrosarcoma, (PMID:4132053), pseudo-diploid male with a modal chromosome number of 46, numerous chromosome abnormalities

value: John Stamatoyannopoulos, UW

value: ENCBS512AAA at ENCODE; https://www.encodeproject.org/ENCBS512AAA/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB058RZD)

description:
https://www.encodeproject.org/experiments/ENCSR366FFV/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against ILF2 in HepG2 cells followed by RNA-seq. (ILF2-BGHLV20)
experiment encode accession: ENCSR366FFV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB058RZD
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting ILF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e777daa9-0fed-4795-8b7f-a3cd904dbfc4/@@download/attachment/L-ILF2-BGHLV20-40_17729.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ILF2. (ILF2-BGHLV20-40_17729)

tag: biosample encode accession

value: child

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS913KLP at ENCODE; https://www.encodeproject.org/ENCBS913KLP/

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_515

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

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.

value: phase 2


title: SGE_514


title: shRNA RNA-seq from K562 (ENCLB229STK)

description:
https://www.encodeproject.org/experiments/ENCSR351CNN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CUGBP1. (K-CUGBP1-26B)
experiment encode accession: ENCSR351CNN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR081EST
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB229STK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CELF1

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/dc7b0745-6c74-4970-94aa-0f05c2dc57ec/@@download/attachment/L-K-CUGBP1-26B-2.pdf

value: K562 cells treated with an shRNA knockdown against CUGBP1, used in RNA-seq experiments. (K-CUGBP1-26B-2)

tag: age

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS744CXB at ENCODE; https://www.encodeproject.org/ENCBS744CXB/

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 (ENCLB927VWM)

description:
https://www.encodeproject.org/experiments/ENCSR351CNN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CUGBP1. (K-CUGBP1-26B)
experiment encode accession: ENCSR351CNN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR081EST
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB927VWM
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/ea82a848-bb15-407f-8527-3a0b7e129c62/@@download/attachment/L-K-CUGBP1-26B-1.pdf

value: immortalized cell line

value: K562 cells treated with an shRNA knockdown against CUGBP1, used in RNA-seq experiments. (K-CUGBP1-26B-1)

tag: dev stage

value: ENCBS145IJT at ENCODE; https://www.encodeproject.org/ENCBS145IJT/


title: SGE_508

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


title: SGE_509


title: shRNA RNA-seq from HepG2 (ENCLB572CJA)

description:
https://www.encodeproject.org/experiments/ENCSR347ZHQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against XRN2 in HepG2 cells followed by RNA-seq. (XRN2_BGHLV17)
experiment encode accession: ENCSR347ZHQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB572CJA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting XRN2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/d68721e2-93cd-4e74-bd7c-50cace4a9dc0/@@download/attachment/L-XRN2_BGHLV17_42.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRN2. (XRN2_BGHLV17_42)

value: 15 year

value: child

tag: Sex

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS835UPQ at ENCODE; https://www.encodeproject.org/ENCBS835UPQ/


title: SGE_513

value: phase 2


title: SGE_512

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


title: SGE_511

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


title: SGE_507


title: siRNA RNA-seq from K562 (ENCLB652PKH)

description:
https://www.encodeproject.org/experiments/ENCSR341RCF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR341RCF
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB652PKH
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: Control

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

value: 53 year

value: adult

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS536HDZ at ENCODE; https://www.encodeproject.org/ENCBS536HDZ/


title: RAMPAGE from smooth muscle cell (ENCLB427SJR)

description:
https://www.encodeproject.org/experiments/ENCSR337VPD/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from H9-derived embryonic stem cells that were differentiated down a smooth muscle pathway. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR337VPD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR052FJA
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB427SJR
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/43f41100-7b94-4886-b6c2-ad60c65c1acb/@@download/attachment/294739.pdf

value: smooth muscle cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

tag: lab

value: Richard Myers, HAIB

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

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


title: shRNA RNA-seq from K562 (ENCLB737XVO)

description:
https://www.encodeproject.org/experiments/ENCSR345VVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DHX30. (DHX30_BGKLV24)
experiment encode accession: ENCSR345VVZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB737XVO
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DHX30

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e3e42d63-8307-4eb8-bd99-873f439e2033/@@download/attachment/L-DHX30_BGKLV24_15_17606.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DHX30. (DHX30_BGKLV24_15_17606)

value: Brenton Graveley, UConn

tag: link

value: ENCBS720HYG at ENCODE; https://www.encodeproject.org/ENCBS720HYG/

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_510

value: phase 2


title: SGE_506

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


title: shRNA RNA-seq from HepG2 (ENCLB842PZC)

description:
https://www.encodeproject.org/experiments/ENCSR343DHN/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SBDS. (SBDS-BGHLV22)
experiment encode accession: ENCSR343DHN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB842PZC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 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/502dc66a-66c9-4422-af06-902677be18dc/@@download/attachment/L-SBDS-BGHLV22-48.pdf

value: SBDS

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SBDS. (SBDS-BGHLV22-48)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS116LNU at ENCODE; https://www.encodeproject.org/ENCBS116LNU/

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 (ENCLB305SFI)

description:
https://www.encodeproject.org/experiments/ENCSR345VVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DHX30. (DHX30_BGKLV24)
experiment encode accession: ENCSR345VVZ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB305SFI
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/b68b6e41-8c8b-498d-adc1-1f64e541c86e/@@download/attachment/L-DHX30_BGKLV24_16_17607.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against DHX30. (DHX30_BGKLV24_16_17607)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS827YSZ at ENCODE; https://www.encodeproject.org/ENCBS827YSZ/


title: RAMPAGE from smooth muscle cell (ENCLB758VXA)

description:
https://www.encodeproject.org/experiments/ENCSR337VPD/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from H9-derived embryonic stem cells that were differentiated down a smooth muscle pathway. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR337VPD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR052FJA
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB758VXA
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/5213a0c1-04a6-4034-a8a2-a61f96d6fd74/@@download/attachment/294738.pdf

value: smooth muscle cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

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

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


title: SGE_504

value: phase 2


title: SGE_502

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


title: shRNA RNA-seq from HepG2 (ENCLB770IUM)

description:
https://www.encodeproject.org/experiments/ENCSR343DHN/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against SBDS. (SBDS-BGHLV22)
experiment encode accession: ENCSR343DHN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR279HMU
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB770IUM
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/b2be6a09-1a43-47e1-a554-508bcf873046/@@download/attachment/L-SBDS-BGHLV22-47.pdf

value: SBDS

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SBDS. (SBDS-BGHLV22-47)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS748YQE at ENCODE; https://www.encodeproject.org/ENCBS748YQE/

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_501

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


title: shRNA RNA-seq from HepG2 (ENCLB907FAP)

description:
https://www.encodeproject.org/experiments/ENCSR347ZHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against XRN2 in HepG2 cells followed by RNA-seq. (XRN2_BGHLV17)
experiment encode accession: ENCSR347ZHQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB907FAP
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/e7f21f5c-4647-4d42-8365-e052336856e1/@@download/attachment/L-XRN2_BGHLV17_41.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against XRN2. (XRN2_BGHLV17_41)

value: ENCBS924WYL at ENCODE; https://www.encodeproject.org/ENCBS924WYL/


title: SGE_505


title: shRNA RNA-seq from K562 (ENCLB455AYJ)

description:
https://www.encodeproject.org/experiments/ENCSR336DFS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBFOX2. (RBFOX2_BGKLV24)
experiment encode accession: ENCSR336DFS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB455AYJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RBFOX2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/edaaa367-0663-4020-a786-1ee8ca26e149/@@download/attachment/L-RBFOX2_BGKLV24_48_17625.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBFOX2. (RBFOX2_BGKLV24_48_17625)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS341TAT at ENCODE; https://www.encodeproject.org/ENCBS341TAT/

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_500

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB176NHY)

description:
https://www.encodeproject.org/experiments/ENCSR334HNJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX47. (K-DDX47)
experiment encode accession: ENCSR334HNJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB176NHY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX47

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/8425526f-8860-4e67-bbde-ce879f58eecd/@@download/attachment/L-K-DDX47-2.pdf

value: immortalized cell line

value: K562 cells treated with an shRNA knockdown against DDX47, used in RNA-seq experiments. (K-DDX47-2)

value: ENCBS195ZWQ at ENCODE; https://www.encodeproject.org/ENCBS195ZWQ/


title: SGE_498

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


title: shRNA RNA-seq from K562 (ENCLB814XIY)

description:
https://www.encodeproject.org/experiments/ENCSR334HNJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against DDX47. (K-DDX47)
experiment encode accession: ENCSR334HNJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB814XIY
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/55a31ed3-112f-44da-8782-680509b5459a/@@download/attachment/L-K-DDX47-1.pdf

value: K562 cells treated with an shRNA knockdown against DDX47, used in RNA-seq experiments. (K-DDX47-1)

value: Brenton Graveley, UConn

value: ENCBS841YJV at ENCODE; https://www.encodeproject.org/ENCBS841YJV/


title: shRNA RNA-seq from K562 (ENCLB935HGP)

description:
https://www.encodeproject.org/experiments/ENCSR336DFS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against RBFOX2. (RBFOX2_BGKLV24)
experiment encode accession: ENCSR336DFS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB935HGP
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/adf90cd3-979b-4272-84c5-297b9051661a/@@download/attachment/L-RBFOX2_BGKLV24_47_17624.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RBFOX2. (RBFOX2_BGKLV24_47_17624)

value: ENCBS677KBE at ENCODE; https://www.encodeproject.org/ENCBS677KBE/


title: SGE_496

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


title: SGE_495

value: VBB


title: shRNA RNA-seq from K562 (ENCLB422GXQ)

description:
https://www.encodeproject.org/experiments/ENCSR331DUD/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DDX55 in K562 cells followed by RNA-seq. (DDX55_BGKLV19)
experiment encode accession: ENCSR331DUD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB422GXQ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting DDX55

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/cd9a54b2-5c52-45e6-81f0-2dd1eba5cac1/@@download/attachment/L-DDX55_BGKLV19_20B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX55. (DDX55_BGKLV19_20B)

value: 53 year

value: adult

value: female

value: ENCBS383JPN at ENCODE; https://www.encodeproject.org/ENCBS383JPN/


title: SGE_494

value: phase 2


title: SGE_503


title: shRNA RNA-seq from K562 (ENCLB610VSA)

description:
https://www.encodeproject.org/experiments/ENCSR325OOM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against FUS in K562 cells followed by RNA-seq. (FUS BGKLV13)
experiment encode accession: ENCSR325OOM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB610VSA
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/62d3d455-620f-411e-a3cb-6ff83163b442/@@download/attachment/L-FUS_BGKLV13_52.pdf

value: FUS

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against FUS.(FUS_BGKLV13_52)

value: chronic myelogenous leukemia (CML)

value: ENCBS788CSD at ENCODE; https://www.encodeproject.org/ENCBS788CSD/

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_499

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.


title: total RNA-seq from lower leg skin (ENCLB678SEO)

description:
https://www.encodeproject.org/experiments/ENCSR321PGV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's skin from the lower leg tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR321PGV
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB678SEO
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens lower leg skin tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/31acdf9b-b67e-4497-9508-ad9afcedfe34/@@download/attachment/295917.pdf

value: lower leg skin

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS155WKB at ENCODE; https://www.encodeproject.org/ENCBS155WKB/

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


title: shRNA RNA-seq from K562 (ENCLB474UVS)

description:
https://www.encodeproject.org/experiments/ENCSR322XVS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PHF6. (PHF6_BGKLV21)
experiment encode accession: ENCSR322XVS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB474UVS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PHF6

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/906656f2-a481-40b8-bfeb-3c6e5d4b2a3f/@@download/attachment/L-PHF6_BGKLV21_40_17581.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PHF6. (PHF6_BGKLV21_40_17581)

value: 53 year

value: adult

value: female

value: Brenton Graveley, UConn

value: ENCBS593CFU at ENCODE; https://www.encodeproject.org/ENCBS593CFU/


title: shRNA RNA-seq from K562 (ENCLB220QSV)

description:
https://www.encodeproject.org/experiments/ENCSR325OOM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against FUS in K562 cells followed by RNA-seq. (FUS BGKLV13)
experiment encode accession: ENCSR325OOM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB220QSV
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/36cbd796-98f3-4a88-afac-f430ea3d732d/@@download/attachment/L-FUS_BGKLV13_51.pdf

value: FUS

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against FUS.(FUS_BGKLV13_51)

value: chronic myelogenous leukemia (CML)

value: ENCBS631FGS at ENCODE; https://www.encodeproject.org/ENCBS631FGS/


title: SGE_493

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

value: VBB

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB933JBB)

description:
https://www.encodeproject.org/experiments/ENCSR331DUD/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DDX55 in K562 cells followed by RNA-seq. (DDX55_BGKLV19)
experiment encode accession: ENCSR331DUD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB933JBB
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/d81763d1-b940-4e3a-9cdc-2d6aa5e6da9f/@@download/attachment/L-DDX55_BGKLV19_19B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against DDX55. (DDX55_BGKLV19_19B)

value: ENCBS746KYH at ENCODE; https://www.encodeproject.org/ENCBS746KYH/

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 (ENCLB461PHZ)

description:
https://www.encodeproject.org/experiments/ENCSR322XVS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PHF6. (PHF6_BGKLV21)
experiment encode accession: ENCSR322XVS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB461PHZ
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/1aed70c3-ac40-4894-85b9-98855c91d771/@@download/attachment/L-PHF6_BGKLV21_39_17580.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PHF6. (PHF6_BGKLV21_39_17580)

value: 53 year

value: ENCBS609MYU at ENCODE; https://www.encodeproject.org/ENCBS609MYU/


title: SGE_491

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


title: SGE_490


title: shRNA RNA-seq from HepG2 (ENCLB774ZJK)

description:
https://www.encodeproject.org/experiments/ENCSR318OXM/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against UPF2 in HepG2 cells followed by RNA-seq. (UPF2_BGHLV17)
experiment encode accession: ENCSR318OXM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB774ZJK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting UPF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e6e2f387-abdc-4320-bbe8-16d16e9b624c/@@download/attachment/L-UPF2_BGHLV17_40.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UPF2. (UPF2_BGHLV17_40)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS237TGJ at ENCODE; https://www.encodeproject.org/ENCBS237TGJ/

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

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


title: microRNA-seq from bipolar spindle neuron (ENCLB424ORZ)

description:
https://www.encodeproject.org/experiments/ENCSR312RZV/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human bipolar spindle neuron
experiment encode accession: ENCSR312RZV
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB424ORZ
size range: <30

source_name: Homo sapiens bipolar spindle neuron in vitro differentiated cells male adult (53 years) derived from induced pluripotent stem cell

value: bipolar spindle neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS369AAA at ENCODE; https://www.encodeproject.org/ENCBS369AAA/

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


title: SGE_489

value: phase 2


title: shRNA RNA-seq from HepG2 (ENCLB072LAK)

description:
https://www.encodeproject.org/experiments/ENCSR318OXM/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against UPF2 in HepG2 cells followed by RNA-seq. (UPF2_BGHLV17)
experiment encode accession: ENCSR318OXM
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB072LAK
size range: >200
spikeins used: /references/ENCSR449DXG/
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/54b533bf-06c0-47d2-8ab8-2abe55d43b6b/@@download/attachment/L-UPF2_BGHLV17_39.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UPF2. (UPF2_BGHLV17_39)

value: ENCBS713IGS at ENCODE; https://www.encodeproject.org/ENCBS713IGS/


title: shRNA RNA-seq from K562 (ENCLB029DBR)

description:
https://www.encodeproject.org/experiments/ENCSR312SRB/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRP68 in K562 cells followed by RNA-seq. (SRP68_BGKLV19)
experiment encode accession: ENCSR312SRB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB029DBR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 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/9f9425f4-291d-433c-8dd4-0baf8f11bdad/@@download/attachment/L-SRP68_BGKLV19_51B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRP68. (SRP68_BGKLV19_51B)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS222QCU at ENCODE; https://www.encodeproject.org/ENCBS222QCU/

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_497

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


title: microRNA-seq from bipolar spindle neuron (ENCLB284XFC)

description:
https://www.encodeproject.org/experiments/ENCSR312RZV/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human bipolar spindle neuron
experiment encode accession: ENCSR312RZV
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB284XFC
size range: <30

value: bipolar spindle neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: male

value: ENCBS374AAA at ENCODE; https://www.encodeproject.org/ENCBS374AAA/


title: SGE_488

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB081KPX)

description:
https://www.encodeproject.org/experiments/ENCSR312SRB/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRP68 in K562 cells followed by RNA-seq. (SRP68_BGKLV19)
experiment encode accession: ENCSR312SRB
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB081KPX
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/0a8530cb-37ee-43db-9336-cec71f0a18ce/@@download/attachment/L-SRP68_BGKLV19_52B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SRP68. (SRP68_BGKLV19_52B)

value: adult

value: Brenton Graveley, UConn

value: ENCBS972JLR at ENCODE; https://www.encodeproject.org/ENCBS972JLR/


title: shRNA RNA-seq from K562 (ENCLB530ZME)

description:
https://www.encodeproject.org/experiments/ENCSR392HSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPF. (HNRNPF_BGKLV21)
experiment encode accession: ENCSR392HSJ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB530ZME
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/48573d47-ccf1-452e-a0f0-cab937cb5846/@@download/attachment/L-HNRNPF_BGKLV21_21_17569.pdf

value: HNRNPF

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPF. (HNRNPF_BGKLV21_21_17569)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS704YXA at ENCODE; https://www.encodeproject.org/ENCBS704YXA/


title: SGE_487

source_name: peripheral blood mononuclear cells

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


title: siRNA RNA-seq from K562 (ENCLB571SYR)

description:
https://www.encodeproject.org/experiments/ENCSR312FIT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting UBTF.
experiment encode accession: ENCSR312FIT
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR644GSV
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB571SYR
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: UBTF

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

value: Sherman Weissman, Yale

value: ENCBS499ZMJ at ENCODE; https://www.encodeproject.org/ENCBS499ZMJ/

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

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


title: shRNA RNA-seq from K562 (ENCLB093MJI)

description:
https://www.encodeproject.org/experiments/ENCSR312HJY/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CNOT8. (K-CNOT8)
experiment encode accession: ENCSR312HJY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB093MJI
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CNOT8

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/d72482f9-1836-4f3a-81ca-e090e9b64901/@@download/attachment/L-K-CNOT8-1.pdf

value: immortalized cell line

value: K562 cells treated with an shRNA knockdown against CNOT8, used in RNA-seq experiments. (K-CNOT8-1)

value: ENCBS894CLK at ENCODE; https://www.encodeproject.org/ENCBS894CLK/

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


title: SGE_485

value: phase 2


title: SGE_486

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


title: siRNA RNA-seq from K562 (ENCLB858JDD)

description:
https://www.encodeproject.org/experiments/ENCSR312FIT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting UBTF.
experiment encode accession: ENCSR312FIT
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR126QVF, ENCSR644GSV
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB858JDD
size range: >200
spikeins used: /references/ENCSR866KGS/

value: 53 year

value: adult

value: ENCBS514LUT at ENCODE; https://www.encodeproject.org/ENCBS514LUT/


title: SGE_484


title: shRNA RNA-seq from K562 (ENCLB321TNS)

description:
https://www.encodeproject.org/experiments/ENCSR312HJY/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CNOT8. (K-CNOT8)
experiment encode accession: ENCSR312HJY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR898NWE
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB321TNS
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/ba7dc411-b2d5-4ffa-963b-f41e66582634/@@download/attachment/L-K-CNOT8-2.pdf

value: K562 cells treated with an shRNA knockdown against CNOT8, used in RNA-seq experiments. (K-CNOT8-2)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS374DHY at ENCODE; https://www.encodeproject.org/ENCBS374DHY/


title: SGE_492

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

value: VBB


title: SGE_482


title: SGE_481


title: shRNA RNA-seq from K562 (ENCLB293NOS)

description:
https://www.encodeproject.org/experiments/ENCSR309PPC/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against PA2G4 in K562 cells followed by RNA-seq. (PA2G4_BGKLV19)
experiment encode accession: ENCSR309PPC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB293NOS
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PA2G4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/4de8a45e-55e1-4fb2-8f86-99cd9f380111/@@download/attachment/L-PA2G4_BGKLV19_38B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PA2G4. (PA2G4_BGKLV19_38B)

value: ENCBS400HFL at ENCODE; https://www.encodeproject.org/ENCBS400HFL/

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


title: SGE_479


title: shRNA RNA-seq from HepG2 (ENCLB562QSA)

description:
https://www.encodeproject.org/experiments/ENCSR309HXK/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TRIM56 in HepG2 cells followed by RNA-seq. (TRIM56-BGHLV20)
experiment encode accession: ENCSR309HXK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB562QSA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting TRIM56

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/45f79df6-6eed-4bed-8969-080c3a17d71e/@@download/attachment/L-TRIM56-BGHLV20-62_17741.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TRIM56. (TRIM56-BGHLV20-62_17741)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS571XTM at ENCODE; https://www.encodeproject.org/ENCBS571XTM/

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_478

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

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB101ROM)

description:
https://www.encodeproject.org/experiments/ENCSR309PPC/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against PA2G4 in K562 cells followed by RNA-seq. (PA2G4_BGKLV19)
experiment encode accession: ENCSR309PPC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB101ROM
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/29171831-a593-4f15-be98-4ae386e063bf/@@download/attachment/L-PA2G4_BGKLV19_37B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against PA2G4. (PA2G4_BGKLV19_37B)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS552IDC at ENCODE; https://www.encodeproject.org/ENCBS552IDC/

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


title: shRNA RNA-seq from HepG2 (ENCLB407VWN)

description:
https://www.encodeproject.org/experiments/ENCSR309HXK/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TRIM56 in HepG2 cells followed by RNA-seq. (TRIM56-BGHLV20)
experiment encode accession: ENCSR309HXK
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB407VWN
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/f510b474-2521-41f5-ae07-7a54200fa31c/@@download/attachment/L-TRIM56-BGHLV20-61_17740.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TRIM56. (TRIM56-BGHLV20-61_17740)

value: 15 year

value: ENCBS899ZNE at ENCODE; https://www.encodeproject.org/ENCBS899ZNE/


title: SGE_477

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_476

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


title: SGE_475


title: shRNA RNA-seq from HepG2 (ENCLB311STX)

description:
https://www.encodeproject.org/experiments/ENCSR308IKH/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against HNRNPU in HepG2 cells followed by RNA-seq. (HNRNPU-BGHLV20)
experiment encode accession: ENCSR308IKH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB311STX
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/3ab5244a-2222-4aec-af61-8911167cf305/@@download/attachment/L-HNRNPU-BGHLV20-38_17727.pdf

value: HNRNPU

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPU. (HNRNPU-BGHLV20-38_17727)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS018WXY at ENCODE; https://www.encodeproject.org/ENCBS018WXY/

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 (ENCLB708KJY)

description:
https://www.encodeproject.org/experiments/ENCSR306IOF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PARN. (PARN_BGKLV24)
experiment encode accession: ENCSR306IOF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB708KJY
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/07837dcf-c3d6-45f4-8ca7-5a7bc8e9df1a/@@download/attachment/L-PARN_BGKLV24_43_17622.pdf

value: PARN

value: RNA-seq on K562 cells treated with an shRNA knockdown against PARN. (PARN_BGKLV24_43_17622)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS574JXP at ENCODE; https://www.encodeproject.org/ENCBS574JXP/

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


title: SGE_473

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

value: phase 2


title: SGE_474


title: SGE_483


title: shRNA RNA-seq from HepG2 (ENCLB613DQO)

description:
https://www.encodeproject.org/experiments/ENCSR305XWT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV20)
experiment encode accession: ENCSR305XWT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB613DQO
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b3c67f81-cc27-4841-abfb-6fe2f82edda2/@@download/attachment/L-non-target-BGHLV20-1_17706.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (non-target-BGHLV20-1_17706)

value: 15 year

value: child

value: ENCBS149ZGY at ENCODE; https://www.encodeproject.org/ENCBS149ZGY/


title: SGE_471

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


title: shRNA RNA-seq from K562 (ENCLB926FVW)

description:
https://www.encodeproject.org/experiments/ENCSR306IOF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PARN. (PARN_BGKLV24)
experiment encode accession: ENCSR306IOF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB926FVW
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/09741930-8840-4807-80bc-fee27b0b5ddd/@@download/attachment/L-PARN_BGKLV24_44_17623.pdf

value: PARN

value: RNA-seq on K562 cells treated with an shRNA knockdown against PARN. (PARN_BGKLV24_44_17623)

value: ENCBS783CHO at ENCODE; https://www.encodeproject.org/ENCBS783CHO/

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


title: shRNA RNA-seq from K562 (ENCLB057EUN)

description:
https://www.encodeproject.org/experiments/ENCSR306EIU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CSDA. (CSDA_BGKLV24)
experiment encode accession: ENCSR306EIU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB057EUN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting YBX3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c59bc6cc-84c1-4cc3-a92b-a18dc92f3cbc/@@download/attachment/L-CSDA_BGKLV24_11_17602.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CSDA. (CSDA_BGKLV24_11_17602)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS889HVK at ENCODE; https://www.encodeproject.org/ENCBS889HVK/


title: SGE_480

value: phase 2


title: shRNA RNA-seq from K562 (ENCLB646XGP)

description:
https://www.encodeproject.org/experiments/ENCSR306EIU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CSDA. (CSDA_BGKLV24)
experiment encode accession: ENCSR306EIU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB646XGP
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/efa95074-6a65-46e4-a3fb-258d7f649b04/@@download/attachment/L-CSDA_BGKLV24_12_17603.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against CSDA. (CSDA_BGKLV24_12_17603)

value: Brenton Graveley, UConn

value: ENCBS602RSX at ENCODE; https://www.encodeproject.org/ENCBS602RSX/

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


title: SGE_472

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


title: shRNA RNA-seq from HepG2 (ENCLB241GVD)

description:
https://www.encodeproject.org/experiments/ENCSR305XWT/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV20)
experiment encode accession: ENCSR305XWT
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB241GVD
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/ef5aadb8-5a6d-4880-822a-3f32bf5cd103/@@download/attachment/L-non-target-BGHLV20-2_17707.pdf

value: Control

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (non-target-BGHLV20-2_17707)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS624MLL at ENCODE; https://www.encodeproject.org/ENCBS624MLL/

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_470


title: RAMPAGE from HT-29 (ENCLB056YBJ)

description:
https://www.encodeproject.org/experiments/ENCSR295GUQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line HT-29. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR295GUQ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR971GPJ
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB056YBJ
size range: >200

source_name: Homo sapiens HT-29 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/01d8c09e-3f86-4342-aa8b-1837d17868a6/@@download/attachment/289922.pdf

value: adenocarcinoma colon cells

value: 44 year

value: adult

tag: passage number

value: female

value: colorectal adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS605AAA at ENCODE; https://www.encodeproject.org/ENCBS605AAA/

value: Derived from ENCODE donor ENCDO347AAA; https://www.encodeproject.org/ENCDO347AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0320; http://web.expasy.org/cellosaurus/CVCL_0320

value: ATCC sample source; http://www.atcc.org/products/all/HTB-38.aspx


title: SGE_469

tag: cell type

value: phase 2


title: SGE_468

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

tag: sample date


title: microRNA-seq from gastrocnemius medialis (ENCLB122ZPN)

description:
https://www.encodeproject.org/experiments/ENCSR292QOC/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human skeletal muscle tissue
experiment encode accession: ENCSR292QOC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB122ZPN
size range: <30

source_name: Homo sapiens gastrocnemius medialis tissue male adult (37 years)

value: gastrocnemius medialis

value: tissue

value: Muscle - Skeletal

value: male

value: 37 year

value: Barbara Wold, Caltech

value: ENCBS884FWU at ENCODE; https://www.encodeproject.org/ENCBS884FWU/

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


title: SGE_467

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

tag: study phase


title: shRNA RNA-seq from HepG2 (ENCLB565YIW)

description:
https://www.encodeproject.org/experiments/ENCSR308IKH/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against HNRNPU in HepG2 cells followed by RNA-seq. (HNRNPU-BGHLV20)
experiment encode accession: ENCSR308IKH
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB565YIW
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/14d0e4fd-66b3-41ac-b7a0-8a6d9a81989e/@@download/attachment/L-HNRNPU-BGHLV20-37_17726.pdf

value: HNRNPU

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPU. (HNRNPU-BGHLV20-37_17726)

value: child

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS931SHZ at ENCODE; https://www.encodeproject.org/ENCBS931SHZ/

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_466

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

value: phase 2

tag: study group


title: shRNA RNA-seq from K562 (ENCLB025CAT)

description:
https://www.encodeproject.org/experiments/ENCSR300QFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TRIM56. (TRIM56_BGKLV21)
experiment encode accession: ENCSR300QFQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB025CAT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting TRIM56

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0e4e2a95-e191-4cdc-8220-7b15a9a947f5/@@download/attachment/L-TRIM56_BGKLV21_63_17590.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against TRIM56. (TRIM56_BGKLV21_63_17590)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS190TRO at ENCODE; https://www.encodeproject.org/ENCBS190TRO/

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_464


title: RAMPAGE from HT-29 (ENCLB015MFN)

description:
https://www.encodeproject.org/experiments/ENCSR295GUQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line HT-29. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR295GUQ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR971GPJ
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB015MFN
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/09eaa177-85a4-4568-a61b-0641aeea5741/@@download/attachment/289921.pdf

value: immortalized cell line

value: adenocarcinoma colon cells

value: 44 year

value: colorectal adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS604AAA at ENCODE; https://www.encodeproject.org/ENCBS604AAA/

value: Derived from ENCODE donor ENCDO347AAA; https://www.encodeproject.org/ENCDO347AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0320; http://web.expasy.org/cellosaurus/CVCL_0320

value: ATCC sample source; http://www.atcc.org/products/all/HTB-38.aspx


title: RAMPAGE from myometrial cell (ENCLB879IMF)

description:
https://www.encodeproject.org/experiments/ENCSR290RXI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of myometrial smooth muscle primary cell type (HMSMC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR290RXI
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR371VGV
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB879IMF
size range: >200

source_name: Homo sapiens myometrial 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/c68fe4c6-d558-4cca-99db-0a6327a266f5/@@download/attachment/295375.pdf

value: myometrial cell

value: primary cell

value: Myometrial Smooth Muscle Cell (HMSMC) from the uterus of a 34 year old caucasian female.

value: 34 year

value: Thomas Gingeras, CSHL

value: ENCBS824SZZ at ENCODE; https://www.encodeproject.org/ENCBS824SZZ/

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

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=7020


title: RAMPAGE from myometrial cell (ENCLB445AYQ)

description:
https://www.encodeproject.org/experiments/ENCSR290RXI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of myometrial smooth muscle primary cell type (HMSMC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR290RXI
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR371VGV
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB445AYQ
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/7def149e-f1dc-4d40-9203-5da7a33cbf0c/@@download/attachment/295376.pdf

value: adult

value: female

value: ENCBS485TQI at ENCODE; https://www.encodeproject.org/ENCBS485TQI/


title: SGE_463

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

value: phase 2


title: SGE_462

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


title: shRNA RNA-seq from K562 (ENCLB553UHN)

description:
https://www.encodeproject.org/experiments/ENCSR286OKW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against CSTF2T in K562 cells followed by RNA-seq. (CSTF2T BGKLV13)
experiment encode accession: ENCSR286OKW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB553UHN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CSTF2T

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/62afec6e-1f10-4a43-89c7-918ab1ace9b0/@@download/attachment/L-CSTF2T_BGKLV13_43.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against CSTF2T.(CSTF2T_BGKLV13_43)

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS093NNC at ENCODE; https://www.encodeproject.org/ENCBS093NNC/

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 (ENCLB689PHV)

description:
https://www.encodeproject.org/experiments/ENCSR286OKW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against CSTF2T in K562 cells followed by RNA-seq. (CSTF2T BGKLV13)
experiment encode accession: ENCSR286OKW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB689PHV
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/89834332-7e73-4fbe-919d-a2b8a9f869d4/@@download/attachment/L-CSTF2T_BGKLV13_44.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CSTF2T.(CSTF2T_BGKLV13_44)

value: ENCBS566NIL at ENCODE; https://www.encodeproject.org/ENCBS566NIL/


title: microRNA-seq from gastrocnemius medialis (ENCLB000CEQ)

description:
https://www.encodeproject.org/experiments/ENCSR292QOC/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human skeletal muscle tissue
experiment encode accession: ENCSR292QOC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB000CEQ
size range: <30

value: gastrocnemius medialis

value: tissue

value: Muscle - Skeletal

value: 37 year

value: male

value: Barbara Wold, Caltech

value: ENCBS661PVF at ENCODE; https://www.encodeproject.org/ENCBS661PVF/

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


title: SGE_461

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

value: phase 2


title: SGE_460


title: SGE_459


title: shRNA RNA-seq from K562 (ENCLB318LFK)

description:
https://www.encodeproject.org/experiments/ENCSR300QFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TRIM56. (TRIM56_BGKLV21)
experiment encode accession: ENCSR300QFQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB318LFK
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/f76db80d-41e7-4396-a3c5-52b06583d3bd/@@download/attachment/L-TRIM56_BGKLV21_64_17591.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against TRIM56. (TRIM56_BGKLV21_64_17591)

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS941WQP at ENCODE; https://www.encodeproject.org/ENCBS941WQP/


title: SGE_457

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 thyroid gland (ENCLB057VXY)

description:
https://www.encodeproject.org/experiments/ENCSR281KFH/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human thyroid gland
experiment encode accession: ENCSR281KFH
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB057VXY
size range: <30

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

value: thyroid gland

value: tissue

value: Thyroid

value: ENCBS018WOC at ENCODE; https://www.encodeproject.org/ENCBS018WOC/


title: SGE_465


title: total RNA-seq from adrenal gland (ENCLB033URW)

description:
https://www.encodeproject.org/experiments/ENCSR276MMH/
***************
biological replicate number: 1
technical replicate number: 1
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: ENCLB033URW
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/e6315c28-425d-409c-85ab-2d2407eb68ab/@@download/attachment/295771.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: male

value: Thomas Gingeras, CSHL

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


title: SGE_458

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

value: phase 2


title: RAMPAGE from liver (ENCLB504MJS)

description:
https://www.encodeproject.org/experiments/ENCSR285LDX/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from liver tissue from a 32 year old adult. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR285LDX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEU
encode release date: 2014-09-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB504MJS
size range: >200

source_name: Homo sapiens liver tissue male adult (32 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/9dd1b8bf-abc8-4471-8b46-4dbb03a0043d/@@download/attachment/SID30048.pdf

value: liver

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: adult

value: healthy with non-obstructive CAD (coronary artery disease)

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: SGE_455

source_name: peripheral blood mononuclear cells

value: WXC


title: SGE_456

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


title: shRNA RNA-seq from HepG2 (ENCLB006OEV)

description:
https://www.encodeproject.org/experiments/ENCSR279HMU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV22)
experiment encode accession: ENCSR279HMU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB006OEV
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/eca031b3-d089-49f2-8d70-2940d4e77160/@@download/attachment/L-non-target-BGHLV22-1_17746.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (non-target-BGHLV22-1_17746)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS063KED at ENCODE; https://www.encodeproject.org/ENCBS063KED/

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_454

value: phase 2


title: SGE_453

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


title: shRNA RNA-seq from HepG2 (ENCLB710ODZ)

description:
https://www.encodeproject.org/experiments/ENCSR274KWA/
***************
biological replicate number: 1
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: ENCLB710ODZ
size range: >200
spikeins used: /references/ENCSR449DXG/

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/1b690ca7-0dba-4365-b800-535b9478e95f/@@download/attachment/L-CNOT7-BGHLV22-5_17750.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against CNOT7. (CNOT7-BGHLV22-5_17750)

value: male

value: ENCBS859RAZ at ENCODE; https://www.encodeproject.org/ENCBS859RAZ/


title: SGE_449


title: SGE_451

value: WXC


title: SGE_448


title: shRNA RNA-seq from HepG2 (ENCLB037LAW)

description:
https://www.encodeproject.org/experiments/ENCSR279HMU/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (non-target-BGHLV22)
experiment encode accession: ENCSR279HMU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB037LAW
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/14b08ee3-f236-4633-9853-d1d4a78cba62/@@download/attachment/L-non-target-BGHLV22-2_17747.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against Nontarget. (non-target-BGHLV22-2_17747)

value: ENCBS472BZM at ENCODE; https://www.encodeproject.org/ENCBS472BZM/


title: SGE_450


title: shRNA RNA-seq from K562 (ENCLB437EHZ)

description:
https://www.encodeproject.org/experiments/ENCSR268JDD/
***************
biological replicate number: 1
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: ENCLB437EHZ
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/8675daa4-3515-4119-a51a-7ee882a5fc61/@@download/attachment/L-EIF2C1_BGKLV13_69.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against EIF2C1.(EIF2C1_BGKLV13_69)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS040IKC at ENCODE; https://www.encodeproject.org/ENCBS040IKC/

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_445

value: phase 2