title: polyA mRNA RNA-seq from NCI-H460 (ENCLB763MTY)

description:
https://www.encodeproject.org/experiments/ENCSR586SEE/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR586SEE
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-08-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB763MTY
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9b66c749-320e-4387-9aa8-289718733dd7/@@download/attachment/294143.pdf

value: immortalized cell line

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

value: 37 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS398KLJ at ENCODE; https://www.encodeproject.org/ENCBS398KLJ/

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

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

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


title: Hi-C library HS2

status: Public on Mar 18 2016

type: SRA

city: Atlanta

first: Chun-hui

last: Hou

address: 1510 Clifton Rd NE

country: USA

institute: Emory University

description:
Heat shocked
supplementary file: AllHS_hotint_NB_10000rs_allchr.txt

library_source: genomic

data_processing:
Library strategy: Hi-C+
Hi-C datasets were normalized as described (Yaffe and Tanay, Nature Genetics, 2011)
base-calling was carried out by HudsonAlpha Genomic Service Center
Paired reads were aligned to the Drosophila reference genome (Dm3) using Bowtie 0.12.7 (Langmead et al., 2009)  and filtered to remove any pair with one or two ends aligned to multiple locations.
Genome_build: Dm3
Supplementary_files_format_and_content: Six ChIP-seq wig files of protein binding peaks called by MACS, one ChIP input control. One excel file contains listes of long-range interactions identified before and after heat shock at 10kb resolution.
Supplementary_files_format_and_content: AllHS_hotint_NB_10000rs_allchr.txt: 10kb resolution interactions for heat shocked Hi-C in Kc167 cells
Supplementary_files_format_and_content: All3_hotint_NB_10000rs_allchr.txt: 10kb resolution interactions for normal Hi-C in Kc167 cells
Supplementary_files_format_and_content: hsBEAF_treat.wig: BEAF peaks in heat shocked Kc167 cells
Supplementary_files_format_and_content: hsCP190_treat.wig: CP190 peaks in heat shocked Kc167 cells
Supplementary_files_format_and_content: hsCTCF_treat.wig: CTCF peaks in heat shocked Kc167 cells
Supplementary_files_format_and_content: hsPolII_treat.wig: RNAPII peaks in heat shocked Kc167 cells
Supplementary_files_format_and_content: hsSuHw_treat.wig: SuHw peaks in heat shocked Kc167 cells
Supplementary_files_format_and_content: input.wig: input DNA
Supplementary_files_format_and_content: polII_treat.wig: RNAPII in normal Kc167 cells

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: female embryonic cells

growth_protocol: Fruit fly embryonic Kc167 cells were grown to confluence in CCM3 serum-free insect medium (HyClone SH30065.01) at 25oC and collected for Hi-C experiments.

extract_protocol:
Hi-C experiments were carried out as described (Lieberman-Aiden et al., 2009) with some modifications. Cells were lysed then the nuclei were treated with 0.1% SDS at 65 degree for 10mins and the SDS was quenched by adding Triton X-100 to final 1% concentration. Nuclei was digested in 1XNEB (New England Biolaboratory) with 400U of HindIII. Digested DNA was blunted with dATP, dGTP, dTTP and biotin labeled dCTP.  DNA wan then ligated and puried. biotin-labled ligated DNA was purified with streptavidin beads. Illumina paired-end adaptor linkers were ligated to DNA pulled-down and amplified and size selected for sequencing.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols. Hi-C DNA was ligated with Illumina adaptors and then amplified, purified. ChIP DNAs were ligated with six different Illumina index adaptors and amplified, purified.

treatment_protocol: One hundred million Kc167 cells were suspended in 20ml of CM3 medium at room temperature mixed with equal volume of 48 degree medium and incubated in 37 degree water bath for 20 minutes. Heat shocked cells were then fixed by adding 0.6 volume of 4 degree medium contain 2.7% formaldehyde to a final concentration of 1%, and incubated at room temperature for 10 min. The reaction was stopped by adding 1/10 volumes of 1.25 M glycine solution and incubated for 5 min before centrifugation at 3000 rpm for 10 min.

tag: cell type

value: embryonic (established from 6-12hours embryo)

tag: cell line

tag: hi-c enzyme

value: HindIII

tag: treatment

value: Heat shocked


title: total RNA-seq from PC-3 (ENCLB550IUC)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR420NLC/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line PC-3, a metastatic prostate grade IV adenocarcinoma from a 62 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR420NLC
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB550IUC
size range: >200
spikeins used: /references/ENCSR156CIL/

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens PC-3 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c9f23796-3f3f-4299-ab42-0497e3337807/@@download/attachment/LID287572.pdf

tag: line

tag: description

value: prostate cancer cell line

tag: biosample encode accession

tag: age

value: 62 year

tag: dev stage

tag: passage number

tag: Sex

tag: health state

value: grade IV, adenocarcinoma

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS609AAA at ENCODE; https://www.encodeproject.org/ENCBS609AAA/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: total RNA-seq from myometrial cell (ENCLB785VXK)

description:
https://www.encodeproject.org/experiments/ENCSR371VGV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of myometrial smooth muscle primary cell type (HMSMC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR371VGV
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB785VXK
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens myometrial primary cell female adult (34 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c0d154fc-3fd0-4115-9cdc-3fbfd7e8f6cb/@@download/attachment/294919.pdf

value: myometrial cell

value: primary cell

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

value: 34 year

value: adult

value: female

value: Thomas Gingeras, CSHL

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

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

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


title: total RNA-seq from kidney epithelial cell (ENCLB779RPP)

description:
https://www.encodeproject.org/experiments/ENCSR373BDG/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of kidney epithelial primary cell type (HREpiC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR373BDG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB779RPP
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens kidney epithelial primary cell male fetal (22 weeks)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5f0a6f9e-49c4-425f-9eb5-b89975280467/@@download/attachment/295053.pdf

value: kidney epithelial cell

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

value: 22 week

value: fetal

value: male

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

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

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


title: total RNA-seq from cardiac ventricle fibroblast (ENCLB915CSO)

description:
https://www.encodeproject.org/experiments/ENCSR369RVN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cardiac ventricle fibroblast cells (HCF-av). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR369RVN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB915CSO
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens cardiac ventricle fibroblast primary cell male adult (18 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f8c699b3-9492-405c-a518-20f9b7ce7afc/@@download/attachment/295150.pdf

value: cardiac ventricle fibroblast

value: primary cell

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

value: 18 year

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

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

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


title: total RNA-seq from skeletal muscle myoblast (ENCLB493TSJ)

description:
https://www.encodeproject.org/experiments/ENCSR444WHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of primary cell line HSMM that has been differentiated into myoblasts. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR444WHQ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB493TSJ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens skeletal muscle myoblast primary cell

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/382c7b4d-d3db-41c7-a3bd-09d2aaf4b809/@@download/attachment/291757.pdf

value: skeletal muscle myoblast

value: skeletal muscle myoblasts

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS328AAA at ENCODE; https://www.encodeproject.org/ENCBS328AAA/

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

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

value: Lonza  sample source; http://www.lonza.com/


title: total RNA-seq from myometrial cell (ENCLB479DJM)

description:
https://www.encodeproject.org/experiments/ENCSR371VGV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of myometrial smooth muscle primary cell type (HMSMC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR371VGV
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB479DJM
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8775a31a-b341-4aca-9acd-5c558e85412a/@@download/attachment/294920.pdf

value: myometrial cell

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

value: 34 year

value: adult

value: female

value: Thomas Gingeras, CSHL

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

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

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


title: total RNA-seq from PC-3 (ENCLB978NNR)

description:
https://www.encodeproject.org/experiments/ENCSR420NLC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line PC-3, a metastatic prostate grade IV adenocarcinoma from a 62 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR420NLC
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB978NNR
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/05a6e2e4-4a28-41b0-a1fc-ea09e1b7eb39/@@download/attachment/LID287571.pdf

value: immortalized cell line

value: prostate cancer cell line

value: 62 year

value: male

value: grade IV, adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS608AAA at ENCODE; https://www.encodeproject.org/ENCBS608AAA/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: total RNA-seq from LHCN-M2 (ENCLB921UIV)

description:
https://www.encodeproject.org/experiments/ENCSR332DBS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of immortalized cell line LHCN-M2. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR332DBS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB921UIV
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens LHCN-M2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/14c53a5c-0ddc-4b38-b62f-29e01df33fd7/@@download/attachment/292335.pdf

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

value: 41 year

value: John Stamatoyannopoulos, UW

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

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

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

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


title: total RNA-seq from cardiac ventricle fibroblast (ENCLB594YLU)

description:
https://www.encodeproject.org/experiments/ENCSR369RVN/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cardiac ventricle fibroblast cells (HCF-av). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR369RVN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB594YLU
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens cardiac ventricle fibroblast primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e3df0658-b8b8-47bf-a5af-2301d588221f/@@download/attachment/295151.pdf

value: cardiac ventricle fibroblast

value: primary cell

value: Human Cardiac Fibroblast Cells

value: unknown

value: not collected

value: Thomas Gingeras, CSHL

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

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


title: total RNA-seq from RPMI-7951 (ENCLB596KKZ)

description:
https://www.encodeproject.org/experiments/ENCSR320BRR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line RPMI-7951. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR320BRR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB596KKZ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens RPMI-7951 immortalized cell line

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/79f6ebb1-4562-4534-af50-1e6a8e560813/@@download/attachment/291696.pdf

value: immortalized cell line

value: 18 year

value: adult

value: female

value: malignant melanoma

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

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

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


title: total RNA-seq from HepG2 (ENCLB079COW)

description:
https://www.encodeproject.org/experiments/ENCSR468ION/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HepG2 Long Total from Graveley
experiment encode accession: ENCSR468ION
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB079COW
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line

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

value: RNA Evaluation HepG2 Long Total from Graveley (HepG2-2)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS780BKX at ENCODE; https://www.encodeproject.org/ENCBS780BKX/

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

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


title: total RNA-seq from LHCN-M2 (ENCLB756FRE)

description:
https://www.encodeproject.org/experiments/ENCSR332DBS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of immortalized cell line LHCN-M2. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR332DBS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB756FRE
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/026a3378-fbca-466b-bf3c-56848cd36d89/@@download/attachment/292336.pdf

value: immortalized cell line

value: 41 year

value: John Stamatoyannopoulos, UW

value: ENCBS836YFM at ENCODE; https://www.encodeproject.org/ENCBS836YFM/

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

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


title: total RNA-seq from HT1080 (ENCLB406ORD)

description:
https://www.encodeproject.org/experiments/ENCSR535VTR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line HT-1080, a connective tissue fibrosarcoma from a 35 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR535VTR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB406ORD
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens HT1080 immortalized cell line

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fd3696ae-3bc8-4877-8520-0f19aac328c5/@@download/attachment/LID288369.pdf

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

value: 35 year

value: adult

value: fibrosarcoma

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

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

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


title: total RNA-seq from RPMI-7951 (ENCLB484KMD)

description:
https://www.encodeproject.org/experiments/ENCSR320BRR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line RPMI-7951. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR320BRR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB484KMD
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/80d4c4df-22d0-4400-8458-5c61d43fa04a/@@download/attachment/291695.pdf

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

value: 18 year

value: female

value: malignant melanoma

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

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

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

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


title: total RNA-seq from Karpas-422 (ENCLB127UIZ)

description:
https://www.encodeproject.org/experiments/ENCSR314LXG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line Karpas-422, a B cell from a 73 year old female with non-Hodgkins Lymphoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR314LXG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB127UIZ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens Karpas-422 immortalized cell line

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7a703f03-07c4-4718-a6f0-68430912b196/@@download/attachment/LID288494.pdf

value: immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: human B cell non-Hodgkin's lymphoma

value: Bradley Bernstein, Broad

value: ENCBS869AAA at ENCODE; https://www.encodeproject.org/ENCBS869AAA/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: total RNA-seq from Karpas-422 (ENCLB367FKO)

description:
https://www.encodeproject.org/experiments/ENCSR314LXG/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line Karpas-422, a B cell from a 73 year old female with non-Hodgkins Lymphoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR314LXG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB367FKO
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dbbf0a3b-108b-41a2-8987-f337aa2d5346/@@download/attachment/LID288495.pdf

value: adult

value: ENCBS870AAA at ENCODE; https://www.encodeproject.org/ENCBS870AAA/


title: total RNA-seq from HepG2 (ENCLB267WCY)

description:
https://www.encodeproject.org/experiments/ENCSR468ION/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HepG2 Long Total from Graveley
experiment encode accession: ENCSR468ION
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB267WCY
size range: >200
spikeins used: /references/ENCSR449DXG/

value: RNA Evaluation HepG2 Long Total from Graveley (HepG2-1)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS530VUT at ENCODE; https://www.encodeproject.org/ENCBS530VUT/

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 MCF-7 (ENCLB396WIA)

description:
https://www.encodeproject.org/experiments/ENCSR310FIS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation MCF7 Long Poly-A+ from Graveley
experiment encode accession: ENCSR310FIS
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB396WIA
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: RNA Evaluation MCF7 Long Poly-A+ from Graveley (MCF7-LZ-2)

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: ENCBS867ORK at ENCODE; https://www.encodeproject.org/ENCBS867ORK/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031


title: polyA mRNA RNA-seq from SK-MEL-5 (ENCLB418RTH)

description:
https://www.encodeproject.org/experiments/ENCSR291DJH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR291DJH
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB418RTH
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0851dbcf-eba3-4ee5-a346-655c72edd561/@@download/attachment/294188.pdf

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: cytosol

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

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

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

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


title: polyA mRNA RNA-seq from neural cell (ENCLB476DSJ)

description:
https://www.encodeproject.org/experiments/ENCSR292TAP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq H1-neuron cellular polyadenlated RNA greater than 200 bp
experiment encode accession: ENCSR292TAP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB476DSJ
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens neural in vitro differentiated cells male embryo

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d3b8e0b4-1e52-4df3-8860-128e78bf6f66/@@download/attachment/SID29903.pdf

value: neural cell

value: in vitro differentiated cells

value: neurons derived from H1 embryonic stem cells

value: unknown

value: embryonic

value: male

value: healthy

value: ENCBS512ENC at ENCODE; https://www.encodeproject.org/ENCBS512ENC/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs H1-neurons; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-neurons

value: Cellular Dynamics sample source; http://www.cellulardynamics.com/index.html


title: polyA mRNA RNA-seq from SK-MEL-5 (ENCLB699FRX)

description:
https://www.encodeproject.org/experiments/ENCSR291DJH/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR291DJH
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB699FRX
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/24d1f9e0-ac7b-4251-833a-93f7b8046a00/@@download/attachment/294189.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: female

value: Thomas Gingeras, CSHL

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


title: polyA mRNA RNA-seq from SK-N-DZ (ENCLB714MUL)

description:
https://www.encodeproject.org/experiments/ENCSR255NYQ/
***************
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 RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR255NYQ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB714MUL
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens SK-N-DZ immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/09ae1606-4a2c-4cf2-951e-d14c20846576/@@download/attachment/293602.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: child

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: total RNA-seq from kidney epithelial cell (ENCLB459IUG)

description:
https://www.encodeproject.org/experiments/ENCSR373BDG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of kidney epithelial primary cell type (HREpiC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR373BDG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB459IUG
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens kidney epithelial primary cell male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7cc01d11-7c15-4dbc-b294-5796882e4589/@@download/attachment/295052.pdf

value: kidney epithelial cell

value: primary cell

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

value: unknown

value: newborn

value: male

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

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

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


title: total RNA-seq from neural progenitor cell (ENCLB278PIS)

description:
https://www.encodeproject.org/experiments/ENCSR244ISQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of H9 embryonic stem cells that were differentiated down a neuronal pathway.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR244ISQ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB278PIS
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1304f275-668c-42e9-b354-c0213dcc89ee/@@download/attachment/293968.pdf

value: neural progenitor cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/

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


title: polyA mRNA RNA-seq from MCF-7 (ENCLB265FVD)

description:
https://www.encodeproject.org/experiments/ENCSR310FIS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation MCF7 Long Poly-A+ from Graveley
experiment encode accession: ENCSR310FIS
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB265FVD
size range: >200
spikeins used: /references/ENCSR449DXG/

value: immortalized cell line

value: RNA Evaluation MCF7 Long Poly-A+ from Graveley (MCF7-LZ-1)

value: 69 year

value: adult

value: breast cancer (adenocarcinoma)

value: Brenton Graveley, UConn

value: ENCBS584TFV at ENCODE; https://www.encodeproject.org/ENCBS584TFV/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031


title: polyA mRNA RNA-seq from neural cell (ENCLB577EZF)

description:
https://www.encodeproject.org/experiments/ENCSR292TAP/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq H1-neuron cellular polyadenlated RNA greater than 200 bp
experiment encode accession: ENCSR292TAP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB577EZF
size range: >200
spikeins used: /references/ENCSR470JZL/

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/578454b3-8d14-4d2d-b81f-09641ffd7ffb/@@download/attachment/SID29905.pdf

value: neural cell

value: in vitro differentiated cells

value: neurons derived from H1 embryonic stem cells, newly promoted to tier 2:not in 2011 analysis

value: unknown

value: male

value: Thomas Gingeras, CSHL

value: ENCBS513ENC at ENCODE; https://www.encodeproject.org/ENCBS513ENC/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs H1-neurons; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-neurons

value: Cellular Dynamics sample source; http://www.cellulardynamics.com/index.html


title: total RNA-seq from Daoy (ENCLB751OHY)

description:
https://www.encodeproject.org/experiments/ENCSR254JJM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line Daoy. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR254JJM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB751OHY
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens Daoy immortalized cell line

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/07915fb1-a9f1-4e85-83d8-78a3e821e153/@@download/attachment/291390.pdf

value: Daoy

value: immortalized cell line

value: 4 year

value: child

value: John Stamatoyannopoulos, UW

value: ENCBS055ILX at ENCODE; https://www.encodeproject.org/ENCBS055ILX/

value: Derived from ENCODE donor ENCDO735HIP; https://www.encodeproject.org/ENCDO735HIP/

value: ENCODE dbxrefs Cellosaurus CVCL_1167; http://web.expasy.org/cellosaurus/CVCL_1167


title: total RNA-seq from astrocyte (ENCLB773OBJ)

description:
https://www.encodeproject.org/experiments/ENCSR233IJT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of primary astrocytes.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR233IJT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB773OBJ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens astrocyte primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a7349e4f-c990-4f61-a22e-6889c6ac32c7/@@download/attachment/292339.pdf

value: astrocyte

value: primary cell

value: astrocytes (also called Astrocy)

value: not collected

value: ENCBS021ENC at ENCODE; https://www.encodeproject.org/ENCBS021ENC/

value: Derived from ENCODE donor ENCDO916IIE; https://www.encodeproject.org/ENCDO916IIE/

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

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


title: total RNA-seq from neural progenitor cell (ENCLB160QNF)

description:
https://www.encodeproject.org/experiments/ENCSR244ISQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of H9 embryonic stem cells that were differentiated down a neuronal pathway.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR244ISQ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-01-08
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB160QNF
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2340ec46-7c40-4024-8f64-8f5d08603b42/@@download/attachment/293967.pdf

value: neural progenitor cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/

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


title: polyA mRNA RNA-seq from SK-MEL-5 (ENCLB504WFG)

description:
https://www.encodeproject.org/experiments/ENCSR201WVA/
***************
biological replicate number: 2
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 RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR201WVA
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB504WFG
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9846b3bb-3a2f-4922-9940-832b30007924/@@download/attachment/294191.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

value: nucleus

value: ENCBS029HXQ at ENCODE; https://www.encodeproject.org/ENCBS029HXQ/

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: polyA mRNA RNA-seq from SK-N-DZ (ENCLB059THU)

description:
https://www.encodeproject.org/experiments/ENCSR255NYQ/
***************
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 RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR255NYQ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB059THU
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/73eacea1-0e48-4842-bedc-b8f8db8b2c38/@@download/attachment/293603.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: child

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: total RNA-seq from mesangial cell (ENCLB335CWF)

description:
https://www.encodeproject.org/experiments/ENCSR198TKA/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from primary mesangial cells (HRMC). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR198TKA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB335CWF
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens mesangial primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/27db1238-294d-4c20-8689-f37ce02702e0/@@download/attachment/LID294956.pdf

value: mesangial cell

value: primary cell

value: Human Renal Mesangial Cells (HRMC) from an unknown donor (no metadata for donor).

value: unknown

value: not collected

value: ENCBS995MDT at ENCODE; https://www.encodeproject.org/ENCBS995MDT/

value: Derived from ENCODE donor ENCDO223XJD; https://www.encodeproject.org/ENCDO223XJD/


title: total RNA-seq from mesangial cell (ENCLB862KOP)

description:
https://www.encodeproject.org/experiments/ENCSR198TKA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from primary mesangial cells (HRMC). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR198TKA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB862KOP
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/94f0a9de-64bb-4f5b-8d63-96a578d133e9/@@download/attachment/LID294955.pdf

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

value: 21 week

value: fetal

value: female

value: Thomas Gingeras, CSHL

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

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

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


title: polyA mRNA RNA-seq from HT1080 (ENCLB469VQX)

description:
https://www.encodeproject.org/experiments/ENCSR166QLP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR166QLP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB469VQX
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens HT1080 immortalized cell line cytosolic fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0c9e80dd-ff92-47f7-9ee0-be440bbd3ceb/@@download/attachment/294145.pdf

value: immortalized cell line

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

value: 35 year

value: adult

value: male

value: fibrosarcoma

value: cytosol

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

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

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

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


title: total RNA-seq from NCI-H460 (ENCLB432QAM)

description:
https://www.encodeproject.org/experiments/ENCSR164OCT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line NCI-H460, a male large cell lung carcinoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR164OCT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB432QAM
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens NCI-H460 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/aef8e896-1254-4471-bff4-cec2ae2edde7/@@download/attachment/287487.pdf

value: 37 year

value: John Stamatoyannopoulos, UW

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

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

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


title: total RNA-seq from cardiac atrium fibroblast (ENCLB799ASI)

description:
https://www.encodeproject.org/experiments/ENCSR110BDY/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of cardiac atrium fibroblast primary cell type (HCF-aa).  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR110BDY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB799ASI
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens cardiac atrium fibroblast primary cell male child (2 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/46cceec1-2aaf-4e9a-a440-54186b1084db/@@download/attachment/294917.pdf

value: cardiac atrium fibroblast

value: primary cell

value: Cardiac fibroblast (HCF-aa) from the atrial region of a 2 year old caucasian male.

value: 2 year

value: child

value: Thomas Gingeras, CSHL

value: ENCBS958FEK at ENCODE; https://www.encodeproject.org/ENCBS958FEK/

value: Derived from ENCODE donor ENCDO664YBM; https://www.encodeproject.org/ENCDO664YBM/

value: ScienCell sample source; http://sciencellonline.com/human-cardiac-fibroblast-adult-atrial-total-rna.html


title: total RNA-seq from Daoy (ENCLB921OGZ)

description:
https://www.encodeproject.org/experiments/ENCSR254JJM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line Daoy. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR254JJM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB921OGZ
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f4048c64-d783-4f02-b893-007be4153601/@@download/attachment/291391.pdf

value: Daoy

value: immortalized cell line

value: 4 year

value: male

value: ENCBS812KQP at ENCODE; https://www.encodeproject.org/ENCBS812KQP/

value: Derived from ENCODE donor ENCDO735HIP; https://www.encodeproject.org/ENCDO735HIP/

value: ENCODE dbxrefs Cellosaurus CVCL_1167; http://web.expasy.org/cellosaurus/CVCL_1167


title: total RNA-seq from SK-N-DZ (ENCLB120HZY)

description:
https://www.encodeproject.org/experiments/ENCSR136WGP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SK-N-DZ, a metastatic neuroblastoma from a 2 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR136WGP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB120HZY
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens SK-N-DZ immortalized cell line treated with dimethyl sulfoxide for 72 hours

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f4dce001-e92c-41a2-80a2-61e9261fbda4/@@download/attachment/287680.pdf

value: SK-N-DZ

value: female

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:72; duration_units:hour;

value: John Stamatoyannopoulos, UW

value: ENCBS521AAA at ENCODE; https://www.encodeproject.org/ENCBS521AAA/

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

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


title: total RNA-seq from SK-N-DZ (ENCLB210NQG)

description:
https://www.encodeproject.org/experiments/ENCSR136WGP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SK-N-DZ, a metastatic neuroblastoma from a 2 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR136WGP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB210NQG
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2edf8ad7-cfb5-46ef-bb75-b74164471f27/@@download/attachment/287679.pdf

value: 2 year

value: child

value: ENCBS520AAA at ENCODE; https://www.encodeproject.org/ENCBS520AAA/


title: total RNA-seq from K562 (ENCLB822JYE)

description:
https://www.encodeproject.org/experiments/ENCSR109IQO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation K562 Long Total from Graveley
experiment encode accession: ENCSR109IQO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-10-01
lab: Brenton Graveley, UConn
library encode accession: ENCLB822JYE
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line

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

value: RNA Evaluation K562 Long Total from Graveley (K562-1)

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS538WJZ at ENCODE; https://www.encodeproject.org/ENCBS538WJZ/

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 SK-MEL-5 (ENCLB899IDA)

description:
https://www.encodeproject.org/experiments/ENCSR201WVA/
***************
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 RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR201WVA
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB899IDA
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/803a38a9-d1f1-495d-b0f7-d345ae07fd81/@@download/attachment/294190.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: female

value: Thomas Gingeras, CSHL

value: nucleus

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: total RNA-seq from NCI-H460 (ENCLB549VYC)

description:
https://www.encodeproject.org/experiments/ENCSR164OCT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line NCI-H460, a male large cell lung carcinoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR164OCT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB549VYC
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b3052462-2bca-4acf-ab2c-9b2f5025f900/@@download/attachment/287488.pdf

value: 37 year

value: male

value: John Stamatoyannopoulos, UW

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

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

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

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


title: total RNA-seq from K562 (ENCLB374EGQ)

description:
https://www.encodeproject.org/experiments/ENCSR109IQO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation K562 Long Total from Graveley
experiment encode accession: ENCSR109IQO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-10-01
lab: Brenton Graveley, UConn
library encode accession: ENCLB374EGQ
size range: >200
spikeins used: /references/ENCSR449DXG/

value: immortalized cell line

value: RNA Evaluation K562 Long Total from Graveley (K562-2)

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS864OKZ at ENCODE; https://www.encodeproject.org/ENCBS864OKZ/

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 HT1080 (ENCLB861ZBV)

description:
https://www.encodeproject.org/experiments/ENCSR067UNX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR067UNX
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB861ZBV
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens HT1080 immortalized cell line nuclear fraction

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/22034cbe-bcaa-4b39-b446-d2d0224817e6/@@download/attachment/294147.pdf

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

value: 35 year

value: fibrosarcoma

value: Thomas Gingeras, CSHL

value: nucleus

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

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

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

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


title: total RNA-seq from cardiac atrium fibroblast (ENCLB151QMJ)

description:
https://www.encodeproject.org/experiments/ENCSR110BDY/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of cardiac atrium fibroblast primary cell type (HCF-aa).  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR110BDY
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB151QMJ
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f901c0a9-4a34-4ebb-9ede-8d04ea6469da/@@download/attachment/294918.pdf

value: cardiac atrium fibroblast

value: primary cell

value: Cardiac fibroblast (HCF-aa) from the atrial region of a 2 year old caucasian male.

value: 2 year

value: child

value: male

value: ENCBS488CKE at ENCODE; https://www.encodeproject.org/ENCBS488CKE/

value: Derived from ENCODE donor ENCDO452MAH; https://www.encodeproject.org/ENCDO452MAH/

value: ScienCell sample source; http://sciencellonline.com/human-cardiac-fibroblast-adult-atrial-total-rna.html


title: polyA mRNA RNA-seq from HT1080 (ENCLB612QVN)

description:
https://www.encodeproject.org/experiments/ENCSR067UNX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR067UNX
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB612QVN
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ca99baec-19b5-48ad-ae3a-e4b9fcd718a3/@@download/attachment/294148.pdf

value: immortalized cell line

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

value: 35 year

value: adult

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


title: total RNA-seq from OCI-LY7 (ENCLB938NOF)

description:
https://www.encodeproject.org/experiments/ENCSR001HHK/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line Oci-Ly-7, a peripherial blood sample from a 48 year old male with Non-Hodgkin lymphoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR001HHK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB938NOF
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens OCI-LY7 immortalized cell line

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7c57931a-e990-446d-bbe0-1e2c37b3915e/@@download/attachment/LID288493.pdf

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: 48 year

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS866AAA at ENCODE; https://www.encodeproject.org/ENCBS866AAA/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: total RNA-seq from smooth muscle cell (ENCLB113QPT)

description:
https://www.encodeproject.org/experiments/ENCSR052FJA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from H9-derived embryonic stem cells that were differentiated down a smooth muscle pathway.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR052FJA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB113QPT
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4e8b7ab3-1a80-40e8-bcaa-87c8ff5a12d5/@@download/attachment/293971.pdf

value: smooth muscle cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

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

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


title: total RNA-seq from OCI-LY7 (ENCLB092UNV)

description:
https://www.encodeproject.org/experiments/ENCSR001HHK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line Oci-Ly-7, a peripherial blood sample from a 48 year old male with Non-Hodgkin lymphoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR001HHK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB092UNV
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4b5094bf-4128-470b-8afc-8e90360dc86d/@@download/attachment/LID288492.pdf

value: immortalized cell line

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: adult

value: male

value: ENCBS865AAA at ENCODE; https://www.encodeproject.org/ENCBS865AAA/


title: total RNA-seq from melanocyte of skin (ENCLB555APG)

description:
https://www.encodeproject.org/experiments/ENCSR000CUR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on human skin melanocytes primary whole cells (NHEM-M2) rRNA-depleted Total RNA greater than 200 nucleotides in size. (paired end)
experiment encode accession: ENCSR000CUR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APG
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens melanocyte of skin primary cell female adult (52 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f472b769-f738-415d-81a9-3a1075f2f02a/@@download/attachment/LID47258.pdf

value: melanocyte of skin

value: primary cell

value: Epidermal Melanocytes (NHEM_M2) from the temple of a lightly pigmented 52 year old caucasian female

value: 52 year

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: Thomas Gingeras, CSHL

value: ENCBS478ENC at ENCODE; https://www.encodeproject.org/ENCBS478ENC/

value: Derived from ENCODE donor ENCDO147AAA; https://www.encodeproject.org/ENCDO147AAA/

value: ENCODE dbxrefs NHEM_M2_7012303; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=NHEM_M2_7012303

value: ENCODE dbxrefs NHEM_M2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=NHEM_M2

value: PromoCell sample source; http://www.promocell.com/nc/products/human-primary-cells/melanocytes/?sword_list%5B%5D=NHEM


title: total RNA-seq from astrocyte (ENCLB237FQL)

description:
https://www.encodeproject.org/experiments/ENCSR233IJT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of primary astrocytes.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR233IJT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB237FQL
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b7948f1f-b69f-419e-983a-566b1f34e6c3/@@download/attachment/292340.pdf

value: astrocyte

value: unknown

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS052WQU at ENCODE; https://www.encodeproject.org/ENCBS052WQU/

value: Derived from ENCODE donor ENCDO916IIE; https://www.encodeproject.org/ENCDO916IIE/


title: polyA mRNA RNA-seq from HT1080 (ENCLB308HCW)

description:
https://www.encodeproject.org/experiments/ENCSR166QLP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR166QLP
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB308HCW
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6466b7c5-db4c-4256-8261-4dbc156da3dd/@@download/attachment/294146.pdf

value: immortalized cell line

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

value: 35 year

value: adult

value: male

value: fibrosarcoma

value: cytosol

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

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

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

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


title: total RNA-seq from smooth muscle cell (ENCLB391HFM)

description:
https://www.encodeproject.org/experiments/ENCSR052FJA/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from H9-derived embryonic stem cells that were differentiated down a smooth muscle pathway.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR052FJA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB391HFM
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4d601bd2-03b4-42b3-be64-f80be3a0ca46/@@download/attachment/293972.pdf

value: smooth muscle cell

value: in vitro differentiated cells

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

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

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

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


title: total RNA-seq from melanocyte of skin (ENCLB555AMU)

description:
https://www.encodeproject.org/experiments/ENCSR000CUR/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on human skin melanocytes primary whole cells (NHEM-M2) rRNA-depleted Total RNA greater than 200 nucleotides in size. (paired end)
experiment encode accession: ENCSR000CUR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMU
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens melanocyte of skin primary cell male adult (55 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d7939cc0-3a96-4c9f-98cc-330d11bcacf2/@@download/attachment/LID47259.pdf

value: melanocyte of skin

value: primary cell

value: Epidermal Melanocytes (NHEM_M2) from the cheek of a lightly pigmented 55 year old caucasian male

value: 55 year

value: adult

value: male

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: Thomas Gingeras, CSHL

value: ENCBS477ENC at ENCODE; https://www.encodeproject.org/ENCBS477ENC/

value: Derived from ENCODE donor ENCDO146AAA; https://www.encodeproject.org/ENCDO146AAA/

value: ENCODE dbxrefs NHEM_M2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=NHEM_M2

value: PromoCell sample source; http://www.promocell.com/nc/products/human-primary-cells/melanocytes/?sword_list%5B%5D=NHEM


title: total RNA-seq from placental epithelial cell (ENCLB555AQE)

description:
https://www.encodeproject.org/experiments/ENCSR000CUP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from placental epithelial primary whole cells, HPIEpC isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQE
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens placental epithelial primary cell male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bbede61b-3311-4c3c-bb58-8ab430fafb45/@@download/attachment/LID47105.pdf

value: placental epithelial cell

value: Epithelial Cells (HPIEpC) from amniotic membrane from the placenta of a newborn caucasian male

value: unknown

value: newborn

value: ENCBS466ENC at ENCODE; https://www.encodeproject.org/ENCBS466ENC/

value: Derived from ENCODE donor ENCDO141AAA; https://www.encodeproject.org/ENCDO141AAA/

value: ENCODE dbxrefs HPIEpC_9041503.2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HPIEpC_9041503.2

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


title: total RNA-seq from melanocyte of skin (ENCLB555AVZ)

description:
https://www.encodeproject.org/experiments/ENCSR000CUQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on humn skin melanocytes primary whole cells (NHEM-M2) from rRNA-depleted total RNA greater than 200 nucleotides in size.
experiment encode accession: ENCSR000CUQ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AVZ
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens melanocyte of skin primary cell male child (1 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/779a3bcc-698b-40ff-8eb1-0c5d0a7caf5d/@@download/attachment/LID47256.pdf

value: melanocyte of skin

value: primary cell

value: Epidermal Melanocytes (NHEM.f_M2) from the foreskin of a darkly pigmented 1 year old male

value: 1 year

value: child

value: ENCBS480ENC at ENCODE; https://www.encodeproject.org/ENCBS480ENC/

value: Derived from ENCODE donor ENCDO145AAA; https://www.encodeproject.org/ENCDO145AAA/

value: ENCODE dbxrefs NHEM.f_M2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=NHEM.f_M2


title: total RNA-seq from fibroblast of villous mesenchyme (ENCLB555ALW)

description:
https://www.encodeproject.org/experiments/ENCSR000CUL/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from placental villous mesenchymal fibroblasts primary whole cells, HVMF  isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUL
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALW
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens fibroblast of villous mesenchyme primary cell male newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4312ca2a-f3d6-4ea7-b4e3-6c098c489257/@@download/attachment/LID47249.pdf

value: fibroblast of villous mesenchyme

value: Fibroblasts from the villous placental tissue (HVMF) from the placenta of a newborn caucasian male

value: male

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: Thomas Gingeras, CSHL

value: ENCBS472ENC at ENCODE; https://www.encodeproject.org/ENCBS472ENC/

value: Derived from ENCODE donor ENCDO121AAA; https://www.encodeproject.org/ENCDO121AAA/

value: ENCODE dbxrefs HVMF_6091203.3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HVMF_6091203.3

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


title: total RNA-seq from fibroblast of villous mesenchyme (ENCLB555ANB)

description:
https://www.encodeproject.org/experiments/ENCSR000CUL/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from placental villous mesenchymal fibroblasts primary whole cells, HVMF  isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUL
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ANB
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens fibroblast of villous mesenchyme primary cell female newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9e8ee7cb-382d-4676-928c-19ace04cfba7/@@download/attachment/LID47250.pdf

value: Fibroblasts from the villous placental tissue (HVMF) from the placenta of a newborn caucasian female

value: unknown

value: newborn

value: female

value: ENCBS471ENC at ENCODE; https://www.encodeproject.org/ENCBS471ENC/

value: Derived from ENCODE donor ENCDO122AAA; https://www.encodeproject.org/ENCDO122AAA/

value: ENCODE dbxrefs HVMF_6100401.3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HVMF_6100401.3


title: total RNA-seq from thoracic aorta endothelial cell (ENCLB555ALD)

description:
https://www.encodeproject.org/experiments/ENCSR000CUK/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from aortic endothelial primary whole cells, HAoEC isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALD
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens thoracic aorta endothelial primary cell male adult (55 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3dd8cadf-2f5b-457e-a259-da65848a82c0/@@download/attachment/LID47023.pdf

value: thoracic aorta endothelial cell

value: primary cell

value: Aortic Endothelial (HAoEC) from the thoractic region that were surgically resected from a 55 year old caucasian male.

value: 55 year

value: adult

value: ENCBS489ENC at ENCODE; https://www.encodeproject.org/ENCBS489ENC/

value: Derived from ENCODE donor ENCDO128AAA; https://www.encodeproject.org/ENCDO128AAA/

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

value: ENCODE dbxrefs HAoEC_8061102.1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HAoEC_8061102.1


title: total RNA-seq from fibroblast of the aortic adventitia (ENCLB555AWF)

description:
https://www.encodeproject.org/experiments/ENCSR000CUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from aortic adventital fibroblast primary whole cells, HAoAF isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUJ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AWF
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens fibroblast of the aortic adventitia primary cell female adult (24 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/58d0d61c-f836-4ab2-b00c-b805b15a8453/@@download/attachment/LID47020.pdf

value: fibroblast of the aortic adventitia

value: Aortic Adventitial Fibroblasts (HAoAF) from the tunica adventitia region that were surgically resected from a 24 year old caucasian female.

value: 24 year

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: Thomas Gingeras, CSHL

value: ENCBS487ENC at ENCODE; https://www.encodeproject.org/ENCBS487ENC/

value: Derived from ENCODE donor ENCDO126AAA; https://www.encodeproject.org/ENCDO126AAA/

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

value: ENCODE dbxrefs HAoAF_6111301.9; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HAoAF_6111301.9


title: total RNA-seq from thoracic aorta endothelial cell (ENCLB555AQY)

description:
https://www.encodeproject.org/experiments/ENCSR000CUK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from aortic endothelial primary whole cells, HAoEC isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQY
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens thoracic aorta endothelial primary cell female adult (22 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4b5849dd-d15b-4153-a164-e4f8e7fe8515/@@download/attachment/LID47022.pdf

value: thoracic aorta endothelial cell

value: primary cell

value: Aortic Endothelial cells (HAoEC) that were surgically resected from a 22 year old caucasian female.

value: 22 year

value: female

value: ENCBS488ENC at ENCODE; https://www.encodeproject.org/ENCBS488ENC/

value: Derived from ENCODE donor ENCDO127AAA; https://www.encodeproject.org/ENCDO127AAA/

value: ENCODE dbxrefs HAoEC_7071706.1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HAoEC_7071706.1


title: total RNA-seq from melanocyte of skin (ENCLB555ALL)

description:
https://www.encodeproject.org/experiments/ENCSR000CUQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on humn skin melanocytes primary whole cells (NHEM-M2) from rRNA-depleted total RNA greater than 200 nucleotides in size.
experiment encode accession: ENCSR000CUQ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALL
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens melanocyte of skin primary cell male child (3 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/956a126d-c876-475b-9cc4-81ae754fff6b/@@download/attachment/LID47257.pdf

value: melanocyte of skin

value: Epidermal Melanocytes (NHEM.f_M2) from the foreskin of a lightly pigmented 3 year old male

value: 3 year

value: child

value: male

value: ENCBS479ENC at ENCODE; https://www.encodeproject.org/ENCBS479ENC/

value: Derived from ENCODE donor ENCDO144AAA; https://www.encodeproject.org/ENCDO144AAA/

value: ENCODE dbxrefs NHEM.f_M2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=NHEM.f_M2

value: PromoCell sample source; http://www.promocell.com/nc/products/human-primary-cells/melanocytes/?sword_list%5B%5D=NHEM


title: total RNA-seq from fibroblast of the aortic adventitia (ENCLB555AXD)

description:
https://www.encodeproject.org/experiments/ENCSR000CUJ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from aortic adventital fibroblast primary whole cells, HAoAF isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUJ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AXD
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens fibroblast of the aortic adventitia primary cell male adult (47 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9da37917-0dcc-4722-acdd-13133e1cf014/@@download/attachment/LID47021.pdf

value: fibroblast of the aortic adventitia

value: Aortic Adventitial Fibroblasts (HAoAF) from the tunica adventitia region that was surgically resected from a 47 year old caucasian male.

value: 47 year

value: adult

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: Thomas Gingeras, CSHL

value: ENCBS486ENC at ENCODE; https://www.encodeproject.org/ENCBS486ENC/

value: Derived from ENCODE donor ENCDO125AAA; https://www.encodeproject.org/ENCDO125AAA/

value: ENCODE dbxrefs HAoAF_6090101.11; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HAoAF_6090101.11

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


title: total RNA-seq from vein endothelial cell (ENCLB555ARM)

description:
https://www.encodeproject.org/experiments/ENCSR000CUG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from saphenous vein endothelial primary whole cells, HSaVEC isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ARM
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens vein endothelial primary cell male adult (48 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/49cc7045-94fb-4bba-8607-ebaa2b2be47f/@@download/attachment/LID47260.pdf

value: vein endothelial cell

value: primary cell

value: Saphenous Vein Endothelial Cells (HSaVEC) from the thigh of a 48 year old caucasian male

value: 48 year

value: ENCBS468ENC at ENCODE; https://www.encodeproject.org/ENCBS468ENC/

value: Derived from ENCODE donor ENCDO148AAA; https://www.encodeproject.org/ENCDO148AAA/

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


title: total RNA-seq from skeletal muscle satellite cell (ENCLB555APQ)

description:
https://www.encodeproject.org/experiments/ENCSR000CUI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from skeletal muscle myosatellite cells isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUI
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555APQ
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens skeletal muscle satellite primary cell male adult (21 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/52d47489-86d9-489b-b958-bd50874b6e7d/@@download/attachment/LID47246.pdf

value: skeletal muscle satellite cell

value: Skeletal muscle myosatellite cells from the striated Mm. intercostales muscle that were surgically resected from a 21 year old caucasian male.

value: 21 year

value: male

value: ENCBS482ENC at ENCODE; https://www.encodeproject.org/ENCBS482ENC/

value: Derived from ENCODE donor ENCDO017AAA; https://www.encodeproject.org/ENCDO017AAA/

value: ENCODE dbxrefs SkMC_8121902.17; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=SkMC_8121902.17

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


title: total RNA-seq from placental epithelial cell (ENCLB555AQF)

description:
https://www.encodeproject.org/experiments/ENCSR000CUP/
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biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from placental epithelial primary whole cells, HPIEpC isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CUP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQF
size range: >200
spikeins used: /references/ENCSR470JZL/

source_name: Homo sapiens placental epithelial primary cell female newborn

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/479832f5-6d4f-4074-9754-c2c1fe99de5c/@@download/attachment/LID47253.pdf

value: placental epithelial cell

value: Epithelial Cells (HPIEpC) from amniotic membrane from the placenta of a newborn caucasian female

value: unknown

value: newborn

value: female

value: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: Thomas Gingeras, CSHL

value: ENCBS465ENC at ENCODE; https://www.encodeproject.org/ENCBS465ENC/

value: Derived from ENCODE donor ENCDO140AAA; https://www.encodeproject.org/ENCDO140AAA/

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

value: ENCODE dbxrefs HPIEpC_9012801.2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HPIEpC_9012801.2