title: RAMPAGE from SK-MEL-5 (ENCLB002LHM)

description:
https://www.encodeproject.org/experiments/ENCSR506WDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR506WDZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR201WVA
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB002LHM
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/4cd3c9e1-4a07-42c4-8e04-84d99bfba3b4/@@download/attachment/LID294489.pdf

value: immortalized cell line

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

value: 24 year

value: adult

value: Thomas Gingeras, CSHL

tag: subcellular fraction term name

value: nucleus

tag: link

value: ENCBS524EJL at ENCODE; https://www.encodeproject.org/ENCBS524EJL/

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

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

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


title: WXC_NC

status: Public on Nov 08 2016

type: SRA

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

country: USA

institute: Arizona State University

library_source: transcriptomic

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

molecule: polyA RNA

organism: Macaca mulatta

source_name: whole blood

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

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

tag: cell type

value: white blood cells

value: WXC

tag: sample date

tag: study phase

value: phase 2

tag: study group

tag: treatment

value: NC


title: shRNA RNA-seq from HepG2 (ENCLB493CND)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR481AYC/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against BCLAF1 in HepG2 cells followed by RNA-seq. (BCLAF1_BGHLV17)
experiment encode accession: ENCSR481AYC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB493CND
size range: >200
spikeins used: /references/ENCSR449DXG/

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting BCLAF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/38674844-45a2-4dba-8f74-6f6f955a8732/@@download/attachment/L-BCLAF1_BGHLV17_6.pdf

tag: antibody

tag: line

tag: description

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against BCLAF1. (BCLAF1_BGHLV17_6)

tag: biosample encode accession

tag: age

value: 15 year

tag: dev stage

value: child

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

tag: lab

value: Brenton Graveley, UConn

value: ENCBS033QJG at ENCODE; https://www.encodeproject.org/ENCBS033QJG/

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 (ENCLB432NCU)

description:
https://www.encodeproject.org/experiments/ENCSR481AYC/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against BCLAF1 in HepG2 cells followed by RNA-seq. (BCLAF1_BGHLV17)
experiment encode accession: ENCSR481AYC
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB432NCU
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/8422b6fd-5ce7-49d8-867c-023a572c2ad9/@@download/attachment/L-BCLAF1_BGHLV17_5.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against BCLAF1. (BCLAF1_BGHLV17_5)

value: ENCBS002KIX at ENCODE; https://www.encodeproject.org/ENCBS002KIX/


title: shRNA RNA-seq from K562 (ENCLB297UKH)

description:
https://www.encodeproject.org/experiments/ENCSR481YXD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against IGF2BP3. (K-IGF2BP3-25B)
experiment encode accession: ENCSR481YXD
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR771ZZL
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB297UKH
size range: >200
spikeins used: /references/ENCSR449DXG/

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

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

value: K562 cells treated with an shRNA knockdown against IGF2BP3, used in RNA-seq experiments. (K-IGF2BP3-25B-1)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS159KYP at ENCODE; https://www.encodeproject.org/ENCBS159KYP/

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: VBB_LPS

value: white blood cells

value: VBB

value: phase 2

value: LPS


title: shRNA RNA-seq from HepG2 (ENCLB498CYW)

description:
https://www.encodeproject.org/experiments/ENCSR477TRX/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against EEF2 in HepG2 cells followed by RNA-seq. (EEF2_BGHLV16)
experiment encode accession: ENCSR477TRX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB498CYW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting EEF2

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/96801618-5e02-4d81-8da1-d2414b8550f7/@@download/attachment/L-EEF2_BGHLV16_19.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EEF2. (EEF2_BGHLV16_19)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS850PLY at ENCODE; https://www.encodeproject.org/ENCBS850PLY/

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


title: Rzq10_NC

value: NC


title: siRNA RNA-seq from K562 (ENCLB624NIX)

description:
https://www.encodeproject.org/experiments/ENCSR472UFW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting CDAN1.
experiment encode accession: ENCSR472UFW
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR287SHU, ENCSR608CVU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB624NIX
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting CDAN1

value: immortalized cell line

value: K562 cells treated with a siRNA knockdown against CDAN1, used in RNA-seq experiments.

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS348PYV at ENCODE; https://www.encodeproject.org/ENCBS348PYV/


title: RZe12_NC

value: white blood cells

value: phase 2


title: RZq10_LPS

value: LPS


title: shRNA RNA-seq from HepG2 (ENCLB546IRT)

description:
https://www.encodeproject.org/experiments/ENCSR477TRX/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against EEF2 in HepG2 cells followed by RNA-seq. (EEF2_BGHLV16)
experiment encode accession: ENCSR477TRX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR689PHN
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB546IRT
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/af1bb5d1-f8a6-41d2-a60e-f9b7cd5509c9/@@download/attachment/L-EEF2_BGHLV16_20.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against EEF2. (EEF2_BGHLV16_20)

value: 15 year

value: child

value: male

value: ENCBS199ZPD at ENCODE; https://www.encodeproject.org/ENCBS199ZPD/

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


title: RZe12_LPS


title: RWu12_LPS


title: shRNA RNA-seq from HepG2 (ENCLB232AMR)

description:
https://www.encodeproject.org/experiments/ENCSR471GIS/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RRP9 in HepG2 cells followed by RNA-seq. (RRP9_BGHLV17)
experiment encode accession: ENCSR471GIS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB232AMR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting RRP9

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/272718ef-39f2-4cc9-ab09-a57a799efdf7/@@download/attachment/L-RRP9_BGHLV17_25.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RRP9. (RRP9_BGHLV17_25)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS611LWG at ENCODE; https://www.encodeproject.org/ENCBS611LWG/

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


title: RAMPAGE from SK-N-DZ (ENCLB089DWL)

description:
https://www.encodeproject.org/experiments/ENCSR479BMI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR479BMI
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR255NYQ
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB089DWL
size range: >200

source_name: Homo sapiens SK-N-DZ 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/83ab3369-4dad-43f2-82ba-6646eca6f075/@@download/attachment/LID294659.pdf

value: SK-N-DZ

value: An immortalized neuroblastoma (brain) cell line derived from a metastatic site in the bone marrow of a 2 year old female.

value: 2 year

value: female

value: Thomas Gingeras, CSHL

value: nucleus

value: ENCBS707BMT at ENCODE; https://www.encodeproject.org/ENCBS707BMT/

value: Derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2149.aspx


title: RVw12_NC

value: white blood cells

value: phase 2

value: NC


title: RWu12_NC


title: shRNA RNA-seq from HepG2 (ENCLB567ZLC)

description:
https://www.encodeproject.org/experiments/ENCSR471GIS/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RRP9 in HepG2 cells followed by RNA-seq. (RRP9_BGHLV17)
experiment encode accession: ENCSR471GIS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR856ZRV
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB567ZLC
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/24207225-6725-4e21-ac2b-90299d925c89/@@download/attachment/L-RRP9_BGHLV17_26.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against RRP9. (RRP9_BGHLV17_26)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS692BSS at ENCODE; https://www.encodeproject.org/ENCBS692BSS/

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


title: RVw12_LPS

value: LPS


title: shRNA RNA-seq from K562 (ENCLB247QXU)

description:
https://www.encodeproject.org/experiments/ENCSR470PRV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPC. (K-HNRNPC-25B)
experiment encode accession: ENCSR470PRV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR771ZZL
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB247QXU
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/ae514eda-223c-4679-adb8-f287fd141a6a/@@download/attachment/L-K-HNRNPC-25B-2.pdf

value: HNRNPC

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

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS522JIE at ENCODE; https://www.encodeproject.org/ENCBS522JIE/

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

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


title: RAMPAGE from glomerular endothelial cell (ENCLB500SAN)

description:
https://www.encodeproject.org/experiments/ENCSR469ZUS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of primary renal glomerular endothelial cells (HGC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR469ZUS
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR878EUT
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB500SAN
size range: >200

source_name: Homo sapiens glomerular endothelial primary cell male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/69934ede-55d4-4776-82e6-ef60ebfc443e/@@download/attachment/LID295363.pdf

value: glomerular endothelial cell

value: primary cell

value: Human Renal Glomerular Endothelial Cell (HGC) from a fetal male kidney at 22 weeks gestation.

value: 22 week

value: fetal

tag: passage number

value: Thomas Gingeras, CSHL

value: ENCBS574ALN at ENCODE; https://www.encodeproject.org/ENCBS574ALN/

value: Derived from ENCODE donor ENCDO611INZ; https://www.encodeproject.org/ENCDO611INZ/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=4005


title: RVq13_NC

value: white blood cells

value: phase 2

value: NC


title: shRNA RNA-seq from K562 (ENCLB276FKI)

description:
https://www.encodeproject.org/experiments/ENCSR470PRV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPC. (K-HNRNPC-25B)
experiment encode accession: ENCSR470PRV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR771ZZL
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB276FKI
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/a53e3dfc-4ff9-40e2-8e67-cd81f1e75126/@@download/attachment/L-K-HNRNPC-25B-1.pdf

value: HNRNPC

value: immortalized cell line

value: K562 cells treated with an shRNA knockdown against HNRNPC, used in RNA-seq experiments. (K-HNRNPC-25B-1)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS831RAD at ENCODE; https://www.encodeproject.org/ENCBS831RAD/


title: RVq13_LPS

value: LPS


title: RVe12_LPS


title: total RNA-seq from thyroid gland (ENCLB109UZW)

description:
https://www.encodeproject.org/experiments/ENCSR532LJV/
***************
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 thyroid tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR532LJV
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB109UZW
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f2dde810-92b9-4765-b323-4d440cb63597/@@download/attachment/295769.pdf

value: thyroid gland

value: tissue

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

value: 37 year

value: male

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

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


title: siRNA RNA-seq from K562 (ENCLB291SHL)

description:
https://www.encodeproject.org/experiments/ENCSR472UFW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting CDAN1.
experiment encode accession: ENCSR472UFW
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR287SHU, ENCSR608CVU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB291SHL
size range: >200
spikeins used: /references/ENCSR866KGS/

value: K562 cells treated with a siRNA knockdown against CDAN1, used in RNA-seq experiments.

value: Sherman Weissman, Yale

value: ENCBS566ZHZ at ENCODE; https://www.encodeproject.org/ENCBS566ZHZ/

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


title: shRNA RNA-seq from K562 (ENCLB411ECA)

description:
https://www.encodeproject.org/experiments/ENCSR572FFX/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV21)
experiment encode accession: ENCSR572FFX
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB411ECA
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol: extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (non-target_BGKLV21_2)

value: 53 year

value: Brenton Graveley, UConn

value: ENCBS023EVI at ENCODE; https://www.encodeproject.org/ENCBS023EVI/

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


title: RAMPAGE from gastrocnemius medialis (ENCLB525YUI)

description:
https://www.encodeproject.org/experiments/ENCSR458JVO/
***************
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 aorta tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR458JVO
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR853BNH
encode release date: 2016-05-09
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB525YUI
size range: >200

source_name: Homo sapiens gastrocnemius medialis tissue male adult (37 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/514e6ed8-0699-4daa-9bd8-7edeee32a628/@@download/attachment/296008.pdf

value: gastrocnemius medialis

value: tissue

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

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS543SZC at ENCODE; https://www.encodeproject.org/ENCBS543SZC/


title: shRNA RNA-seq from HepG2 (ENCLB157GSI)

description:
https://www.encodeproject.org/experiments/ENCSR459EMR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against TUFM. (TUFM-BGHLV23)
experiment encode accession: ENCSR459EMR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB157GSI
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/9e06361d-4d6d-4665-81b9-96d1773f48d3/@@download/attachment/L-TUFM-BGHLV23-53.pdf

value: TUFM

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TUFM. (TUFM-BGHLV23-53)

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS994TMS at ENCODE; https://www.encodeproject.org/ENCBS994TMS/

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 (ENCLB634EEZ)

description:
https://www.encodeproject.org/experiments/ENCSR459EMR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against TUFM. (TUFM-BGHLV23)
experiment encode accession: ENCSR459EMR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB634EEZ
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/251ffb61-219e-499f-8cc0-24375281fbc3/@@download/attachment/L-TUFM-BGHLV23-54.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TUFM. (TUFM-BGHLV23-54)

value: Brenton Graveley, UConn

value: ENCBS694IAG at ENCODE; https://www.encodeproject.org/ENCBS694IAG/


title: RAMPAGE from gastrocnemius medialis (ENCLB379XQS)

description:
https://www.encodeproject.org/experiments/ENCSR458JVO/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's aorta tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR458JVO
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR853BNH
encode release date: 2016-05-09
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB379XQS
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/b2306c9b-17f0-4b9e-984b-5d18b97bf0c0/@@download/attachment/296009.pdf

value: gastrocnemius medialis

value: tissue

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

value: 37 year

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


title: total RNA-seq from lower leg skin (ENCLB544ISA)

description:
https://www.encodeproject.org/experiments/ENCSR460YCS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's 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: ENCSR460YCS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB544ISA
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4236b272-087b-4f99-82c4-fcff68623ff2/@@download/attachment/295919.pdf

value: lower leg skin

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

value: 54 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS302SIZ at ENCODE; https://www.encodeproject.org/ENCBS302SIZ/

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


title: RVb12_LPS

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.

value: white blood cells

value: phase 2

value: LPS


title: RUf11_NC

value: NC


title: RVb12_NC


title: RUf11_LPS


title: RUd14_LPS


title: shRNA RNA-seq from K562 (ENCLB221HFS)

description:
https://www.encodeproject.org/experiments/ENCSR455TNF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TDP-43. (K562-set1b-shTDP43)
experiment encode accession: ENCSR455TNF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR372DZW
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB221HFS
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/33394d9a-2118-4f7b-a6ae-02db698ffe0b/@@download/attachment/L-K562-set-11b-shTDP43-1.pdf

value: TARDBP

value: immortalized cell line

value: K562 cells treated with an shRNA knockdown against TDP-43, used in RNA-seq experiments. (K562-set-11b-shTDP43-1)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS445GUZ at ENCODE; https://www.encodeproject.org/ENCBS445GUZ/

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: RTf12_LPS


title: RSu12_NC


title: RVe12_NC


title: shRNA RNA-seq from HepG2 (ENCLB872OQC)

description:
https://www.encodeproject.org/experiments/ENCSR450VQO/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against TIAL1 in HepG2 cells followed by RNA-seq. (TIAL1-BHLV20)
experiment encode accession: ENCSR450VQO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB872OQC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting TIAL1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/8a45643a-b40e-4f65-b11e-ab36750a47e9/@@download/attachment/L-TIAL1-BHLV20-59_17738.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TIAL1. (TIAL1-BHLV20-59_17738)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS817DXX at ENCODE; https://www.encodeproject.org/ENCBS817DXX/

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: RTf12_NC

value: white blood cells

value: phase 2

value: NC


title: shRNA RNA-seq from K562 (ENCLB734GZR)

description:
https://www.encodeproject.org/experiments/ENCSR455TNF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against TDP-43. (K562-set1b-shTDP43)
experiment encode accession: ENCSR455TNF
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR372DZW
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB734GZR
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/13259e4d-7638-4cf0-ac35-994b77b69d77/@@download/attachment/L-K562-set-11b-shTDP43-2.pdf

value: TARDBP

value: immortalized cell line

value: K562 cells treated with an shRNA knockdown against TDP-43, used in RNA-seq experiments. (K562-set-11b-shTDP43-2)

value: 53 year

value: adult

value: female

value: ENCBS555BYH at ENCODE; https://www.encodeproject.org/ENCBS555BYH/


title: RAMPAGE from glomerular endothelial cell (ENCLB240UGX)

description:
https://www.encodeproject.org/experiments/ENCSR469ZUS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of primary renal glomerular endothelial cells (HGC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR469ZUS
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR878EUT
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB240UGX
size range: >200

source_name: Homo sapiens glomerular endothelial primary cell female fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b1bd7b92-12d4-4a9f-9561-20435c4e60e5/@@download/attachment/LID295364.pdf

value: glomerular endothelial cell

value: primary cell

value: Human Renal Glomerular Endothelial Cell (HGC) from a fetal female kidney at 22 weeks gestation.

value: fetal

value: 22 week

value: Thomas Gingeras, CSHL

value: ENCBS889CYK at ENCODE; https://www.encodeproject.org/ENCBS889CYK/

value: Derived from ENCODE donor ENCDO778HJK; https://www.encodeproject.org/ENCDO778HJK/


title: RSu12_LPS

source_name: whole blood

value: white blood cells

value: phase 2

value: LPS


title: siRNA RNA-seq from K562 (ENCLB338HLX)

description:
https://www.encodeproject.org/experiments/ENCSR443QFD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR443QFD
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB338HLX
size range: >200
spikeins used: /references/ENCSR866KGS/

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

value: Control

value: immortalized cell line

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

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS005SNH at ENCODE; https://www.encodeproject.org/ENCBS005SNH/

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


title: shRNA RNA-seq from HepG2 (ENCLB192VDU)

description:
https://www.encodeproject.org/experiments/ENCSR447UCG/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SRSF5 in HepG2 cells followed by RNA-seq. (SRSF5 BGHLV14)
experiment encode accession: ENCSR447UCG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB192VDU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting SRSF5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e29837d4-b662-43ac-9b3d-e987210b389e/@@download/attachment/Library%20Prep%20protocol%20for%20L-SRSF5_BGHLV14-55.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF5. (SRSF5_BGHLV14-55)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS551QFT at ENCODE; https://www.encodeproject.org/ENCBS551QFT/

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 LHCN-M2 (ENCLB991PNX)

description:
https://www.encodeproject.org/experiments/ENCSR439LGW/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human LHCN-M2 differentiated for 7 days
experiment encode accession: ENCSR439LGW
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB991PNX
size range: <30

source_name: Homo sapiens LHCN-M2 in vitro differentiated cells male adult (41 year)

value: in vitro differentiated cells

value: LHCN diff rep2

value: adult

value: 41 year

value: Barbara Wold, Caltech

value: ENCBS986HXG at ENCODE; https://www.encodeproject.org/ENCBS986HXG/

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


title: RSu10_NC

value: white blood cells

value: phase 2

value: NC


title: RSu10_LPS

value: LPS


title: shRNA RNA-seq from HepG2 (ENCLB828EYU)

description:
https://www.encodeproject.org/experiments/ENCSR447UCG/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SRSF5 in HepG2 cells followed by RNA-seq. (SRSF5 BGHLV14)
experiment encode accession: ENCSR447UCG
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR491FOC
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB828EYU
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/f6a36c04-2407-42e2-b729-f996012ed539/@@download/attachment/L-SRSF5_BGHLV14-56.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against SRSF5. (SRSF5_BGHLV14-56)

value: 15 year

value: child

value: male

value: ENCBS582REX at ENCODE; https://www.encodeproject.org/ENCBS582REX/


title: RSi10_LPS


title: total RNA-seq from thoracic aorta (ENCLB093BKT)

description:
https://www.encodeproject.org/experiments/ENCSR429EWK/
***************
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 aorta 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: ENCSR429EWK
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB093BKT
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens thoracic aorta tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/df564a2f-aacf-4564-986c-ed8b2ecec8db/@@download/attachment/295796.pdf

value: thoracic aorta

value: tissue

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

value: 37 year

value: Thomas Gingeras, CSHL

value: ENCBS636GUU at ENCODE; https://www.encodeproject.org/ENCBS636GUU/

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


title: total RNA-seq from thoracic aorta (ENCLB952YYH)

description:
https://www.encodeproject.org/experiments/ENCSR429EWK/
***************
biological replicate number: 1
technical replicate number: 2
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's aorta 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: ENCSR429EWK
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-03-07
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB952YYH
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0809a429-e5a4-48b2-bbbf-8aeca9c09aa0/@@download/attachment/295797.pdf

value: adult


title: RSh11_NC

value: white blood cells

value: phase 2


title: RSh11_LPS

value: LPS


title: shRNA RNA-seq from HepG2 (ENCLB639LZN)

description:
https://www.encodeproject.org/experiments/ENCSR424JSU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGHLV23)
experiment encode accession: ENCSR424JSU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB639LZN
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting UBE2L3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b9e1c10e-889f-4f24-a571-92f9ba5776f5/@@download/attachment/L-UBE2L3-BGHLV23-58.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGHLV23-58)

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS349HZS at ENCODE; https://www.encodeproject.org/ENCBS349HZS/

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

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


title: RAMPAGE from pericardium fibroblast (ENCLB256ZIG)

description:
https://www.encodeproject.org/experiments/ENCSR419VNG/
***************
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 RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR419VNG
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR362HMX
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB256ZIG
size range: >200

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

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/196c69e8-bf0f-474d-a131-d92aacdbfa15/@@download/attachment/LID295135.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

value: female

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

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


title: RAMPAGE from pericardium fibroblast (ENCLB599XYP)

description:
https://www.encodeproject.org/experiments/ENCSR419VNG/
***************
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 RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR419VNG
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR362HMX
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB599XYP
size range: >200

source_name: Homo sapiens pericardium fibroblast primary cell

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/135c1630-b321-449f-a79e-e9d8d0432d2d/@@download/attachment/LID295136.pdf

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

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

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

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


title: RRr13_NC

value: white blood cells

value: phase 2

value: NC


title: shRNA RNA-seq from HepG2 (ENCLB283XKC)

description:
https://www.encodeproject.org/experiments/ENCSR450VQO/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against TIAL1 in HepG2 cells followed by RNA-seq. (TIAL1-BHLV20)
experiment encode accession: ENCSR450VQO
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB283XKC
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/88760b73-756d-414a-bdcd-5cbaf42854b9/@@download/attachment/L-TIAL1-BHLV20-60_17739.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against TIAL1. (TIAL1-BHLV20-60_17739)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS799SQC at ENCODE; https://www.encodeproject.org/ENCBS799SQC/

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 LHCN-M2 (ENCLB737KBR)

description:
https://www.encodeproject.org/experiments/ENCSR439LGW/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human LHCN-M2 differentiated for 7 days
experiment encode accession: ENCSR439LGW
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB737KBR
size range: <30

value: in vitro differentiated cells

value: LHCN diff rep1

value: 41 year

value: adult

value: Barbara Wold, Caltech

value: ENCBS575BSN at ENCODE; https://www.encodeproject.org/ENCBS575BSN/

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


title: RQp9_LPS

value: white blood cells

value: phase 2

value: LPS


title: RQp9_NC

value: NC


title: RPy12_NC


title: shRNA RNA-seq from K562 (ENCLB663FEM)

description:
https://www.encodeproject.org/experiments/ENCSR419JMU/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV24_B)
experiment encode accession: ENCSR419JMU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB663FEM
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/2e8ad4af-621b-435f-ad65-8f0f4aae161e/@@download/attachment/L-non-target_BGKLV24_2B.pdf

value: Control

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (non-target_BGKLV24_2_17595)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS537KCG at ENCODE; https://www.encodeproject.org/ENCBS537KCG/

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: RPs7_NC


title: RSi10_NC


title: RPy12_LPS


title: RAMPAGE from induced pluripotent stem cell (ENCLB745IVK)

description:
https://www.encodeproject.org/experiments/ENCSR410OSB/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of PGP1 donor induced pluripotent stem cells (iPSC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR410OSB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR938LSP
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB745IVK
size range: >200

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

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/cddde32f-b75a-477c-aeea-f14f8ec10f09/@@download/attachment/290915.pdf

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: RPs7_LPS

value: white blood cells

value: phase 2

value: LPS


title: RPq11_NC

value: NC


title: shRNA RNA-seq from K562 (ENCLB854NIY)

description:
https://www.encodeproject.org/experiments/ENCSR410ZPU/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against BCLAF1 in K562 cells followed by RNA-seq. (BCLAF1_BGKLV19)
experiment encode accession: ENCSR410ZPU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR245BNJ
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB854NIY
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting BCLAF1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/04d2d3d3-72b3-4baf-a8b1-efd3c1036104/@@download/attachment/L-BCLAF1_BGKLV19_7A.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against BCLAF1. (BCLAF1_BGKLV19_7A)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS468YAY at ENCODE; https://www.encodeproject.org/ENCBS468YAY/


title: RPq11_LPS


title: shRNA RNA-seq from K562 (ENCLB306VAE)

description:
https://www.encodeproject.org/experiments/ENCSR419JMU/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in K562 cells followed by RNA-seq. (non-target_BGKLV24_B)
experiment encode accession: ENCSR419JMU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-01-12
lab: Brenton Graveley, UConn
library encode accession: ENCLB306VAE
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/e25d120d-2c5b-4c83-a4c8-0ccc5f33c6de/@@download/attachment/L-non-target_BGKLV24_1B.pdf

value: Control

value: RNA-seq on K562 cells treated with an shRNA knockdown against Nontarget. (non-target_BGKLV24_1_17594)

value: adult

value: ENCBS895KNQ at ENCODE; https://www.encodeproject.org/ENCBS895KNQ/

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 (ENCLB272YKU)

description:
https://www.encodeproject.org/experiments/ENCSR410ZPU/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against BCLAF1 in K562 cells followed by RNA-seq. (BCLAF1_BGKLV19)
experiment encode accession: ENCSR410ZPU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR245BNJ
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB272YKU
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/e5f073bb-a593-4c25-b816-10833477198d/@@download/attachment/L-BCLAF1_BGKLV19_8A.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against BCLAF1. (BCLAF1_BGKLV19_8A)

value: ENCBS417QMS at ENCODE; https://www.encodeproject.org/ENCBS417QMS/


title: shRNA RNA-seq from HepG2 (ENCLB888YZO)

description:
https://www.encodeproject.org/experiments/ENCSR424JSU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGHLV23)
experiment encode accession: ENCSR424JSU
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR042QTH
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB888YZO
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/050b8334-4bbc-4931-8c71-f2348dfc2510/@@download/attachment/L-UBE2L3-BGHLV23-57.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against UBE2L3. (UBE2L3-BGHLV23-57)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS336RRO at ENCODE; https://www.encodeproject.org/ENCBS336RRO/

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

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


title: RAMPAGE from SK-N-DZ (ENCLB230HES)

description:
https://www.encodeproject.org/experiments/ENCSR479BMI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR479BMI
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR255NYQ
encode release date: 2015-04-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB230HES
size range: >200

source_name: Homo sapiens SK-N-DZ 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/090640b9-f894-420c-8b4e-38599b16f024/@@download/attachment/LID294658.pdf

value: SK-N-DZ

value: immortalized cell line

value: An immortalized neuroblastoma (brain) cell line derived from a metastatic site in the bone marrow of a 2 year old female.

value: 2 year

value: female

value: Thomas Gingeras, CSHL

tag: subcellular fraction term name

value: nucleus

value: ENCBS514GVM at ENCODE; https://www.encodeproject.org/ENCBS514GVM/

value: Derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2149.aspx


title: RAMPAGE from induced pluripotent stem cell (ENCLB084PDY)

description:
https://www.encodeproject.org/experiments/ENCSR410OSB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of PGP1 donor induced pluripotent stem cells (iPSC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR410OSB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR938LSP
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB084PDY
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/5b756eb2-7b86-4d94-9b14-700ab323ff0d/@@download/attachment/290914.pdf

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

tag: link

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: RPp10_NC

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.

tag: cell type

value: white blood cells

value: phase 2

value: NC


title: shRNA RNA-seq from K562 (ENCLB837OTJ)

description:
https://www.encodeproject.org/experiments/ENCSR410MIQ/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against RPS3 in K562 cells followed by RNA-seq. (RPS3 BGKLV13)
experiment encode accession: ENCSR410MIQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB837OTJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting RPS3

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/0af9c7bb-9a3e-4761-9106-7c3885fbabdf/@@download/attachment/L-RPS3_BGKLV13_66.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS3.(RPS3_BGKLV13_66)

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS055ZTI at ENCODE; https://www.encodeproject.org/ENCBS055ZTI/

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: RRr13_LPS

tag: sample date

value: LPS


title: siRNA RNA-seq from K562 (ENCLB529TUI)

description:
https://www.encodeproject.org/experiments/ENCSR401RKW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR401RKW
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB529TUI
size range: >200
spikeins used: /references/ENCSR866KGS/

value: Control

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

value: adult

value: 53 year

value: Sherman Weissman, Yale

value: ENCBS974SHD at ENCODE; https://www.encodeproject.org/ENCBS974SHD/


title: shRNA RNA-seq from K562 (ENCLB289QVH)

description:
https://www.encodeproject.org/experiments/ENCSR410MIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against RPS3 in K562 cells followed by RNA-seq. (RPS3 BGKLV13)
experiment encode accession: ENCSR410MIQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR084SCN
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB289QVH
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/5816534d-77af-47fd-91c1-4e5497a111d0/@@download/attachment/L-RPS3_BGKLV13_65.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against RPS3.(RPS3_BGKLV13_65)

value: ENCBS515TJK at ENCODE; https://www.encodeproject.org/ENCBS515TJK/


title: RPp10_LPS

value: white blood cells

tag: study phase

value: phase 2


title: RPm4_NC

tag: study group

value: NC


title: shRNA RNA-seq from K562 (ENCLB738ZDR)

description:
https://www.encodeproject.org/experiments/ENCSR408SDL/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against SMNDC1 in K562 cells followed by RNA-seq. (SMNDC1 BGKLV13)
experiment encode accession: ENCSR408SDL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB738ZDR
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting SMNDC1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f1ede540-98b6-48b8-af7c-88555de57359/@@download/attachment/L-SMNDC1_BGKLV13_16.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SMNDC1.(SMNDC1_BGKLV13_16)

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS492SXA at ENCODE; https://www.encodeproject.org/ENCBS492SXA/


title: microRNA-seq from body of pancreas (ENCLB511DDA)

description:
https://www.encodeproject.org/experiments/ENCSR400OKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human pancreas
experiment encode accession: ENCSR400OKQ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB511DDA
size range: <30

source_name: Homo sapiens body of pancreas tissue male adult (37 years)

value: body of pancreas

value: tissue

value: Pancreas

value: 37 year

value: male

value: Barbara Wold, Caltech

value: ENCBS502WML at ENCODE; https://www.encodeproject.org/ENCBS502WML/

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


title: microRNA-seq from body of pancreas (ENCLB411BPZ)

description:
https://www.encodeproject.org/experiments/ENCSR400OKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human pancreas
experiment encode accession: ENCSR400OKQ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB411BPZ
size range: <30

value: adult

value: ENCBS953BPT at ENCODE; https://www.encodeproject.org/ENCBS953BPT/


title: RPj10_LPS

value: white blood cells

value: phase 2

tag: treatment

value: LPS


title: ROv12_LPS


title: ROv12_NC

value: NC


title: shRNA RNA-seq from K562 (ENCLB887JQB)

description:
https://www.encodeproject.org/experiments/ENCSR408SDL/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against SMNDC1 in K562 cells followed by RNA-seq. (SMNDC1 BGKLV13)
experiment encode accession: ENCSR408SDL
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR815CVQ
encode release date: 2014-11-20
lab: Brenton Graveley, UConn
library encode accession: ENCLB887JQB
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/cb527b2f-c11f-4315-8c36-ee96cd3d8394/@@download/attachment/L-SMNDC1_BGKLV13_15.pdf

tag: antibody

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against SMNDC1.(SMNDC1_BGKLV13_15)

value: 53 year

value: female

value: Brenton Graveley, UConn

value: ENCBS007IVF at ENCODE; https://www.encodeproject.org/ENCBS007IVF/

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: ROn5_NC


title: RNi12_NC


title: shRNA RNA-seq from K562 (ENCLB140DGM)

description:
https://www.encodeproject.org/experiments/ENCSR398HXV/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against NONO in K562 cells followed by RNA-seq. (NONO_BGKLV19)
experiment encode accession: ENCSR398HXV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB140DGM
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/262f2ba3-6c80-4652-b2c5-1b7050bdc13f/@@download/attachment/L-NONO_BGKLV19_35B.pdf

value: NONO

tag: line

value: RNA-seq on K562 cells treated with an shRNA knockdown against NONO. (NONO_BGKLV19_35B)

value: chronic myelogenous leukemia (CML)

value: ENCBS311LNQ at ENCODE; https://www.encodeproject.org/ENCBS311LNQ/


title: siRNA RNA-seq from K562 (ENCLB762TVT)

description:
https://www.encodeproject.org/experiments/ENCSR390GWL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting RCOR1.
experiment encode accession: ENCSR390GWL
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR561NXJ, ENCSR608CVU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB762TVT
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting RCOR1

tag: description

value: K562 cells treated with a siRNA knockdown against RCOR1, used in RNA-seq experiments.

value: adult

value: Sherman Weissman, Yale

value: ENCBS906YOJ at ENCODE; https://www.encodeproject.org/ENCBS906YOJ/


title: shRNA RNA-seq from K562 (ENCLB339CVV)

description:
https://www.encodeproject.org/experiments/ENCSR398GHW/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against GEMIN5 in K562 cells followed by RNA-seq. (GEMIN5_BGKLV19)
experiment encode accession: ENCSR398GHW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB339CVV
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting GEMIN5

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/fcfeb053-a92f-4164-9dca-6fbd8d782ccd/@@download/attachment/L-GEMIN5_BGKLV19_31B.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against GEMIN5. (GEMIN5_BGKLV19_31B)

tag: biosample encode accession

value: ENCBS065RXZ at ENCODE; https://www.encodeproject.org/ENCBS065RXZ/


title: RJs11_NC

source_name: whole blood

value: white blood cells

value: phase 2

value: NC


title: RIa13_NC


title: shRNA RNA-seq from K562 (ENCLB995PEF)

description:
https://www.encodeproject.org/experiments/ENCSR398GHW/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against GEMIN5 in K562 cells followed by RNA-seq. (GEMIN5_BGKLV19)
experiment encode accession: ENCSR398GHW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB995PEF
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/05df4da2-7a92-4b99-b14e-601e59ff09b9/@@download/attachment/L-GEMIN5_BGKLV19_32B.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against GEMIN5. (GEMIN5_BGKLV19_32B)

tag: age

value: 53 year

value: female

value: Brenton Graveley, UConn

value: ENCBS576EJU at ENCODE; https://www.encodeproject.org/ENCBS576EJU/


title: siRNA RNA-seq from K562 (ENCLB873RJG)

description:
https://www.encodeproject.org/experiments/ENCSR390GWL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting RCOR1.
experiment encode accession: ENCSR390GWL
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR561NXJ, ENCSR608CVU
encode release date: 2016-10-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB873RJG
size range: >200
spikeins used: /references/ENCSR866KGS/

tag: dev stage

value: chronic myelogenous leukemia (CML)

value: ENCBS337FHK at ENCODE; https://www.encodeproject.org/ENCBS337FHK/

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


title: shRNA RNA-seq from K562 (ENCLB435NUF)

description:
https://www.encodeproject.org/experiments/ENCSR398HXV/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against NONO in K562 cells followed by RNA-seq. (NONO_BGKLV19)
experiment encode accession: ENCSR398HXV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR661HEL
encode release date: 2014-12-17
lab: Brenton Graveley, UConn
library encode accession: ENCLB435NUF
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/7f3ef974-56ca-44ad-9f22-9e522dca36cc/@@download/attachment/L-NONO_BGKLV19_36B.pdf

value: NONO

value: RNA-seq on K562 cells treated with an shRNA knockdown against NONO. (NONO_BGKLV19_36B)

value: adult

tag: Sex

value: ENCBS714TRH at ENCODE; https://www.encodeproject.org/ENCBS714TRH/

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


title: RJI11_NC

value: white blood cells


title: RJs11_LPS

value: phase 2

value: LPS


title: shRNA RNA-seq from K562 (ENCLB270SGX)

description:
https://www.encodeproject.org/experiments/ENCSR392HSJ/
***************
biological replicate number: 2
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: ENCLB270SGX
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/2f16fa58-343f-4d65-b65a-7e94e04a3c59/@@download/attachment/L-HNRNPF_BGKLV21_22_17570.pdf

value: HNRNPF

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPF. (HNRNPF_BGKLV21_22_17570)

tag: health state

value: ENCBS477JCG at ENCODE; https://www.encodeproject.org/ENCBS477JCG/


title: RJI11_LPS


title: RJj10_NC

value: NC


title: RPj10_NC


title: shRNA RNA-seq from K562 (ENCLB783MNU)

description:
https://www.encodeproject.org/experiments/ENCSR386YEV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGKLV24)
experiment encode accession: ENCSR386YEV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB783MNU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting CCAR1

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ce33ad49-d77a-4420-a6f3-920f980c8b38/@@download/attachment/L-CCAR1_BGKLV24_5_17598.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGKLV24_5_17598)

value: 53 year

value: female

tag: lab

value: Brenton Graveley, UConn

value: ENCBS292NBI at ENCODE; https://www.encodeproject.org/ENCBS292NBI/


title: shRNA RNA-seq from HepG2 (ENCLB245ZVU)

description:
https://www.encodeproject.org/experiments/ENCSR385KOY/
***************
biological replicate number: 1
technical replicate number: 1
description: shRNA knockdown against DNAJC21 in HepG2 cells followed by RNA-seq. (DNAJC21-46-BGHLV20)
experiment encode accession: ENCSR385KOY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB245ZVU
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting DNAJC21

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2f5b45b7-e7b1-4828-bd66-4d68783a3697/@@download/attachment/L-DNAJC21-46-BGHLV20-23_17718.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DNAJC21. (DNAJC21-46-BGHLV20-23_17718)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS741RGH at ENCODE; https://www.encodeproject.org/ENCBS741RGH/

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

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


title: polyA mRNA RNA-seq from K562 (ENCLB014EDA)

description:
https://www.encodeproject.org/experiments/ENCSR384ZXD/
***************
biological replicate number: 1
technical replicate number: 1
description: Initial cytosolic fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR384ZXD
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB014EDA
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line cytosolic fraction

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

value: immortalized cell line

value: adult

value: chronic myelogenous leukemia (CML)

value: cytosol

value: Eric Lécuyer, IRCM

value: ENCBS677HPS at ENCODE; https://www.encodeproject.org/ENCBS677HPS/

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: RJf7_NC

value: white blood cells

value: phase 2

value: NC


title: RJj10_LPS

value: LPS


title: RJf7_LPS


title: shRNA RNA-seq from HepG2 (ENCLB747FAW)

description:
https://www.encodeproject.org/experiments/ENCSR385KOY/
***************
biological replicate number: 2
technical replicate number: 1
description: shRNA knockdown against DNAJC21 in HepG2 cells followed by RNA-seq. (DNAJC21-46-BGHLV20)
experiment encode accession: ENCSR385KOY
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR305XWT
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB747FAW
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/10e8d997-4d39-45c1-abb9-bd1fa0d52ab0/@@download/attachment/L-DNAJC21-46-BGHLV20-24_17719.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against DNAJC21. (DNAJC21-46-BGHLV20-24_17719)

value: 15 year

value: child

value: male

value: Brenton Graveley, UConn

value: ENCBS257TYR at ENCODE; https://www.encodeproject.org/ENCBS257TYR/


title: RIe12_NC


title: RNi12_LPS


title: total RNA-seq from cardiac muscle cell (ENCLB387BDY)

description:
https://www.encodeproject.org/experiments/ENCSR379YAE/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this Experiment come from hESC's that were differentiated into cardiomyocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR379YAE
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-01-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB387BDY
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens cardiac muscle in vitro differentiated cells fetal

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/625427b7-b719-4d0b-812d-f2306417c1f3/@@download/attachment/LID295824.pdf

value: cardiac muscle cell

value: in vitro differentiated cells

value: unknown

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS343AKO at ENCODE; https://www.encodeproject.org/ENCBS343AKO/

value: Derived from ENCODE donor ENCDO924HBJ; https://www.encodeproject.org/ENCDO924HBJ/


title: RIe12_LPS

value: white blood cells

value: phase 2


title: RIb12_NC

value: NC


title: RIb12_LPS

value: LPS


title: shRNA RNA-seq from K562 (ENCLB100BTJ)

description:
https://www.encodeproject.org/experiments/ENCSR379VXW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FKBP4. (FKBP4_BGKLV21)
experiment encode accession: ENCSR379VXW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB100BTJ
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting FKBP4

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/c992e95f-9e2e-4b10-aa3a-07aa04afcbbe/@@download/attachment/L-FKBP4_BGKLV21_11_17562.pdf

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against FKBP4. (FKBP4_BGKLV21_11_17562)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS714PSX at ENCODE; https://www.encodeproject.org/ENCBS714PSX/

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: RFs5_NC


title: RIa13_LPS


title: shRNA RNA-seq from K562 (ENCLB259KTS)

description:
https://www.encodeproject.org/experiments/ENCSR386YEV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGKLV24)
experiment encode accession: ENCSR386YEV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR667PLJ
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB259KTS
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/e4c634f3-b42a-4117-a7ba-a0bef5a8e779/@@download/attachment/L-CCAR1_BGKLV24_6_17599.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGKLV24_6_17599)

value: Brenton Graveley, UConn

value: ENCBS340AMO at ENCODE; https://www.encodeproject.org/ENCBS340AMO/


title: microRNA-seq from prostate gland (ENCLB860ZNA)

description:
https://www.encodeproject.org/experiments/ENCSR373CTA/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human prostate
experiment encode accession: ENCSR373CTA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB860ZNA
size range: <30

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

value: prostate gland

value: tissue

value: Prostate

value: 54 year

value: male

value: Barbara Wold, Caltech

value: ENCBS845PWD at ENCODE; https://www.encodeproject.org/ENCBS845PWD/

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


title: RFq9_LPS

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.

value: white blood cells

value: phase 2

value: LPS


title: RFs5_LPS


title: RAMPAGE from epithelial cell of alveolus of lung (ENCLB970KRS)

description:
https://www.encodeproject.org/experiments/ENCSR376IXU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of epithelial cell of alveolus of lung primary of cell type (HPAE EpiC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR376IXU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR897KTO
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB970KRS
size range: >200

source_name: Homo sapiens epithelial of alveolus lung 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/824b03f2-375b-43ff-a705-d69124431216/@@download/attachment/295377.pdf

value: epithelial cell of alveolus of lung

value: primary cell

value: Human Pulmonary Alveolar Epithelial Cell (HPAEpiC) from a female lung at 21 weeks gestation.

value: 21 week

value: fetal

tag: passage number

value: female

value: Thomas Gingeras, CSHL

value: ENCBS542LAX at ENCODE; https://www.encodeproject.org/ENCBS542LAX/

value: Derived from ENCODE donor ENCDO495RWV; https://www.encodeproject.org/ENCDO495RWV/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=3205


title: shRNA RNA-seq from HepG2 (ENCLB508THB)

description:
https://www.encodeproject.org/experiments/ENCSR376RJN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-a-b)
experiment encode accession: ENCSR376RJN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB508THB
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/be1e41c9-73f2-415f-89a9-ece44f3c25b7/@@download/attachment/L-NT-BGHLV12-a_17742.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target (NT-BGHLV12-01-93)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS623BZF at ENCODE; https://www.encodeproject.org/ENCBS623BZF/

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 (ENCLB277OGZ)

description:
https://www.encodeproject.org/experiments/ENCSR379VXW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against FKBP4. (FKBP4_BGKLV21)
experiment encode accession: ENCSR379VXW
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR572FFX
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB277OGZ
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/0fed5c7d-27c8-44d1-97b7-a5f615a88ec4/@@download/attachment/L-FKBP4_BGKLV21_12_17563.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against FKBP4. (FKBP4_BGKLV21_12_17563)

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS388ZVM at ENCODE; https://www.encodeproject.org/ENCBS388ZVM/

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

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


title: shRNA RNA-seq from HepG2 (ENCLB177RRH)

description:
https://www.encodeproject.org/experiments/ENCSR376RJN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT-BGHLV12-a-b)
experiment encode accession: ENCSR376RJN
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Brenton Graveley, UConn
library encode accession: ENCLB177RRH
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/4e36283c-c1a9-4d34-b022-235aae837ce5/@@download/attachment/L-NT-BGHLV12-b_17743.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an Control shRNA against no target (NT-BGHLV12-02-94)

value: ENCBS638ASL at ENCODE; https://www.encodeproject.org/ENCBS638ASL/


title: RFm12_LPS

value: white blood cells

value: phase 2

value: LPS


title: RFm12_NC

value: NC


title: microRNA-seq from prostate gland (ENCLB612UJL)

description:
https://www.encodeproject.org/experiments/ENCSR373CTA/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human prostate
experiment encode accession: ENCSR373CTA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-07-29
lab: Ali Mortazavi, UCI
library encode accession: ENCLB612UJL
size range: <30

value: prostate gland

value: tissue

value: Prostate

value: male

value: 54 year

value: Barbara Wold, Caltech

value: ENCBS940OCV at ENCODE; https://www.encodeproject.org/ENCBS940OCV/

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


title: RAMPAGE from epithelial cell of alveolus of lung (ENCLB769FHY)

description:
https://www.encodeproject.org/experiments/ENCSR376IXU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of epithelial cell of alveolus of lung primary of cell type (HPAE EpiC). They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR376IXU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR897KTO
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB769FHY
size range: >200

source_name: Homo sapiens epithelial of alveolus lung primary cell

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e11501fb-d805-4342-8cf0-6857c9b24b3a/@@download/attachment/295378.pdf

value: epithelial cell of alveolus of lung

value: primary cell

value: Human Pulmonary Alveolar Epithelial Cells (HPAEpiC).

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

value: ENCBS916BSF at ENCODE; https://www.encodeproject.org/ENCBS916BSF/

value: Derived from ENCODE donor ENCDO357WEO; https://www.encodeproject.org/ENCDO357WEO/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=3205


title: total RNA-seq from cardiac muscle cell (ENCLB426JGB)

description:
https://www.encodeproject.org/experiments/ENCSR379YAE/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from hESC's that were differentiated into cardiomyocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR379YAE
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-01-14
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB426JGB
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8a3cbbba-14ba-4c2e-af52-888587173b2f/@@download/attachment/LID295823.pdf

value: cardiac muscle cell

value: in vitro differentiated cells

value: fetal

value: John Stamatoyannopoulos, UW

value: ENCBS806KLM at ENCODE; https://www.encodeproject.org/ENCBS806KLM/

value: Derived from ENCODE donor ENCDO924HBJ; https://www.encodeproject.org/ENCDO924HBJ/


title: shRNA RNA-seq from K562 (ENCLB957IEQ)

description:
https://www.encodeproject.org/experiments/ENCSR372DZW/
***************
biological replicate number: 1
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: ENCLB957IEQ
size range: >200
spikeins used: /references/ENCSR449DXG/

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

extract_protocol:
extraction method: Trizol (LifeTech cat#: 15596-018)
general protocol: https://www.encodeproject.org/documents/63107a5d-ef48-453e-9638-bceeef3c77a3/@@download/attachment/L-k562-set-11b-shCNTRL-1.pdf

value: Control

value: immortalized cell line

value: K562 cells treated with a control shRNA against no target, used in RNA-seq experiments. (k562-set-11b-shCNTRL-1)

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS211WEE at ENCODE; https://www.encodeproject.org/ENCBS211WEE/

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: polyA mRNA RNA-seq from K562 (ENCLB758HRD)

description:
https://www.encodeproject.org/experiments/ENCSR384ZXD/
***************
biological replicate number: 2
technical replicate number: 1
description: Initial cytosolic fractions on K562 Long Poly-A+ from Lecuyer
experiment encode accession: ENCSR384ZXD
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-04-21
lab: Eric Lécuyer, IRCM
library encode accession: ENCLB758HRD
size range: >200
spikeins used: /references/ENCSR866KGS/

tag: subcellular fraction term name

value: cytosol

value: Eric Lécuyer, IRCM

value: ENCBS148ZBT at ENCODE; https://www.encodeproject.org/ENCBS148ZBT/


title: REg12_NC

value: white blood cells

value: phase 2

value: NC


title: RFd12_NC


title: REg12_LPS

value: LPS


title: RFd12_LPS


title: RFq9_NC


title: RCy13_NC


title: RCy13_LPS


title: shRNA RNA-seq from HepG2 (ENCLB437EFX)

description:
https://www.encodeproject.org/experiments/ENCSR366FFV/
***************
biological replicate number: 1
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: ENCLB437EFX
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/09fee843-d968-482f-99ad-b57c06b96028/@@download/attachment/L-ILF2-BGHLV20-39_17728.pdf

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against ILF2. (ILF2-BGHLV20-39_17728)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

tag: link

value: ENCBS446KHP at ENCODE; https://www.encodeproject.org/ENCBS446KHP/

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

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