title: polyA mRNA RNA-seq from HepG2 (ENCLB256SCK)

description:
https://www.encodeproject.org/experiments/ENCSR985KAT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HepG2 Long Poly-A+ from Graveley
experiment encode accession: ENCSR985KAT
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB256SCK
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line

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

tag: line

value: immortalized cell line

value: RNA Evaluation HepG2 Long Poly-A+ from Graveley (HepG2-LZ-2)

value: 15 year

tag: dev stage

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS883DWI at ENCODE; https://www.encodeproject.org/ENCBS883DWI/

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: RN319 B

status: Public on Mar 18 2016

type: SRA

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

library_source: genomic

data_processing:
Data were mapped using BOWTIE
For each nucleotide, the amount of mapped fragments was considered (= coverage)
Data files were compressed by merging neighbouring nucleotides with equal coverages into single rows, with indication of start and end position of nucleotides with that specific coverage
Genome_build: HG19
Supplementary_files_format_and_content: txt files with columns containing resp. line number, chromosome, start and end position (nucleotide) and amount of mapped fragments

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney sample_Nephrectomie

extract_protocol:
DNA extracted using Qiagen Blood and Tissue Kit according to manufacturers Instuctions
Libraries were prepared using standard multiplexed paired-end Chip-seq protocol (Illumina). In summary, 500 ng of DNA per sample was fragmented by ultrasound mediated DNA shearing (Covaris S2, Covaris, Woburn, Massachusetts, USA) set to obtain fragments with an average length of 200bp. We employed the MethylCap kit (Diagenode AF-100-0048, Liège, Belgium) to obtain methylated DNA fragments using the highest salt concentration single elution step option. This was followed by the library preparation for the enriched DNA, which was performed with a modified 'multiplexed paired-end ChIP protocol' (Illumina, San Diego, California, USA). Therefore, the NEBNext® DNA Sample Prep Master Mix Set 1 (New England BioLabs (NEB) E6040, Ipswich, Massachusetts, USA) was combined with the Multiplexing Sample Preparation Oligo Kit (Illumina PE-400-1001). Per sample, 22µl of the prepared sample was subjected to PCR (21 cycles) following the Illumina Library Amplification Index Protocol. After purification (Qiaquick PCR Purification columns, Qiagen), elution and concentration (evaporation), the libraries were pooled and denaturated (NaOH), followed by Illumina HiSeq 2000 sequencing ('multiplexed paired-end run, 2 times 45 cycles) of 10pM/pool.

tag: gender

value: male

tag: age (yrs)

tag: fuhrman grade

tag: t stage

tag: m stage

tag: warm ischemia time* (mins)

tag: previous treatment

tag: tissue

value: kidney

tag: tissue type

value: Nephrectomie


title: total RNA-seq from MG63 (ENCLB854NNF)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR971KNW/
***************
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 MG63. They are stranded PE101 Illumina HiSeq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR971KNW
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB854NNF
size range: >200
spikeins used: /references/ENCSR156CIL/

library_source: transcriptomic

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

molecule: total RNA

source_name: Homo sapiens MG63 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4cc595c0-4e78-443d-8e33-ccb3989585ee/@@download/attachment/291649.pdf

tag: biosample encode accession

tag: age

value: 14 year

tag: Sex

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS091SUW at ENCODE; https://www.encodeproject.org/ENCBS091SUW/

value: Derived from ENCODE donor ENCDO987OSE; https://www.encodeproject.org/ENCDO987OSE/

value: ENCODE dbxrefs Cellosaurus CVCL_0426; http://web.expasy.org/cellosaurus/CVCL_0426


title: total RNA-seq from MG63 (ENCLB094OJT)

description:
https://www.encodeproject.org/experiments/ENCSR971KNW/
***************
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 MG63. They are stranded PE101 Illumina HiSeq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR971KNW
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB094OJT
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7e952cee-b6a6-4c40-9f36-4dce4c7c901b/@@download/attachment/291650.pdf

value: immortalized cell line

value: ENCBS462PMF at ENCODE; https://www.encodeproject.org/ENCBS462PMF/


title: total RNA-seq from bipolar spindle neuron (ENCLB056VRK)

description:
https://www.encodeproject.org/experiments/ENCSR968WKR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of bipolar neurons that were differentiated from induced pluripotent stem cells. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR968WKR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB056VRK
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/43d8219c-6d99-4b29-b2b6-d8a9b0e8542c/@@download/attachment/292526.pdf

value: bipolar spindle neuron

value: in vitro differentiated cells

tag: description

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

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

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

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


title: total RNA-seq from HT-29 (ENCLB133LNX)

description:
https://www.encodeproject.org/experiments/ENCSR971GPJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line HT-29, a colorectal adenocarcinoma from a 44 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR971GPJ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB133LNX
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens HT-29 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/f4c0e974-7e0c-44f1-9182-37c15ad3c3e2/@@download/attachment/LID288375.pdf

tag: line

value: adenocarcinoma colon cells

value: 44 year

tag: passage number

value: female

tag: health state

value: colorectal adenocarcinoma

value: Bradley Bernstein, Broad

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

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

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

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


title: total RNA-seq from bipolar spindle neuron (ENCLB168YKQ)

description:
https://www.encodeproject.org/experiments/ENCSR968WKR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of bipolar neurons that were differentiated from induced pluripotent stem cells. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR968WKR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB168YKQ
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/24b6f06a-e18d-4e05-acf5-c08d776daf8b/@@download/attachment/292527.pdf

value: bipolar spindle neuron

tag: dev stage

value: male

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


title: polyA mRNA RNA-seq from HepG2 (ENCLB257SKY)

description:
https://www.encodeproject.org/experiments/ENCSR985KAT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HepG2 Long Poly-A+ from Graveley
experiment encode accession: ENCSR985KAT
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB257SKY
size range: >200
spikeins used: /references/ENCSR449DXG/

value: immortalized cell line

value: RNA Evaluation HepG2 Long Poly-A+ from Graveley (HepG2-LZ-1)

value: 15 year

value: child

value: hepatocellular carcinoma

value: Brenton Graveley, UConn

value: ENCBS574ZRE at ENCODE; https://www.encodeproject.org/ENCBS574ZRE/

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 induced pluripotent stem cell (ENCLB984FOR)

description:
https://www.encodeproject.org/experiments/ENCSR938LSP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line GM23338, an induced pluripotent stem cell (iPSC) line derived from cell line GM23248.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR938LSP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB984FOR
size range: >200
spikeins used: /references/ENCSR156CIL/

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

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/1b20a77a-bc0f-43ba-ab44-87497a17c9dc/@@download/attachment/291183.pdf

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

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

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

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

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


title: total RNA-seq from HT-29 (ENCLB951FSA)

description:
https://www.encodeproject.org/experiments/ENCSR971GPJ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line HT-29, a colorectal adenocarcinoma from a 44 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR971GPJ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB951FSA
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/e423884e-c120-46af-8a02-dda70aa150ad/@@download/attachment/LID288376.pdf

value: immortalized cell line

value: adenocarcinoma colon cells

value: 44 year

value: female

value: colorectal adenocarcinoma

value: Bradley Bernstein, Broad

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

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

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

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


title: total RNA-seq from induced pluripotent stem cell (ENCLB779JPG)

description:
https://www.encodeproject.org/experiments/ENCSR938LSP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line GM23338, an induced pluripotent stem cell (iPSC) line derived from cell line GM23248.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR938LSP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB779JPG
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/468b1df9-f3b7-462c-922e-028b4075769f/@@download/attachment/291184.pdf

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: 53 year

value: male

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


title: total RNA-seq from H4 (ENCLB652BFV)

description:
https://www.encodeproject.org/experiments/ENCSR919QJT/
***************
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 H4. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR919QJT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB652BFV
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens H4 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/81f79cf1-8512-46e2-bb8f-7f27262f416d/@@download/attachment/291692.pdf

value: 37 year

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS836LDB at ENCODE; https://www.encodeproject.org/ENCBS836LDB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_1239; http://web.expasy.org/cellosaurus/CVCL_1239


title: total RNA-seq from hepatocyte (ENCLB670RJP)

description:
https://www.encodeproject.org/experiments/ENCSR908ZAS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from stem cells that were differentiated down a hepatocytic pathway.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR908ZAS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB670RJP
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d9b87d58-8b77-4e9f-80ac-49a0ca76e4a0/@@download/attachment/293970.pdf

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like 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: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

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


title: total RNA-seq from hepatocyte (ENCLB615ALX)

description:
https://www.encodeproject.org/experiments/ENCSR908ZAS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from stem cells that were differentiated down a hepatocytic pathway.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR908ZAS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB615ALX
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/50dd7adf-e8a2-4a9d-af22-70f67f412795/@@download/attachment/293969.pdf

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/


title: total RNA-seq from epithelial cell of alveolus of lung (ENCLB088PVJ)

description:
https://www.encodeproject.org/experiments/ENCSR897KTO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of epithelial cell of alveolus of lung primary of cell type (HPAE EpiC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR897KTO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB088PVJ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens epithelial of alveolus lung primary cell female fetal (21 week)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/454bbda4-30de-4243-8e6c-62aacc55ce6b/@@download/attachment/295048.pdf

value: epithelial cell of alveolus of lung

value: primary cell

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

value: 21 week

value: fetal

value: Thomas Gingeras, CSHL

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

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

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


title: total RNA-seq from H4 (ENCLB738UVO)

description:
https://www.encodeproject.org/experiments/ENCSR919QJT/
***************
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 H4. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR919QJT
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB738UVO
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/20952fb2-f48e-4fd6-abd4-a22774878d8b/@@download/attachment/291691.pdf

value: immortalized cell line

value: 37 year

value: adult

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS381KGR at ENCODE; https://www.encodeproject.org/ENCBS381KGR/

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

value: ENCODE dbxrefs Cellosaurus CVCL_1239; http://web.expasy.org/cellosaurus/CVCL_1239


title: total RNA-seq from LHCN-M2 (ENCLB561XGM)

description:
https://www.encodeproject.org/experiments/ENCSR894WMQ/
***************
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 after 4 days of differentiation. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR894WMQ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB561XGM
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fe2e646a-5452-4af0-80f8-fd1151ab66fe/@@download/attachment/292338.pdf

value: in vitro differentiated cells

value: 41 year

value: ENCBS231OMQ at ENCODE; https://www.encodeproject.org/ENCBS231OMQ/

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


title: total RNA-seq from endometrial microvascular endothelial cells (ENCLB260JQO)

description:
https://www.encodeproject.org/experiments/ENCSR919MZM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of endometrial microvascular endothelial primary cell line HEMEC.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR919MZM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB260JQO
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens endometrial microvascular endothelial cells primary cell female adult (34 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/76f50dd2-f38a-49f2-9b3e-1d20d6244ba2/@@download/attachment/294915.pdf

value: primary cell

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

value: 34 year

value: female

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

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

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


title: total RNA-seq from endometrial microvascular endothelial cells (ENCLB925VWI)

description:
https://www.encodeproject.org/experiments/ENCSR919MZM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of endometrial microvascular endothelial primary cell line HEMEC.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR919MZM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB925VWI
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/63e0d5f6-07b8-4635-af11-a328633fb316/@@download/attachment/294916.pdf

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

value: adult

value: Thomas Gingeras, CSHL

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


title: total RNA-seq from epithelial cell of alveolus of lung (ENCLB755HPY)

description:
https://www.encodeproject.org/experiments/ENCSR897KTO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of epithelial cell of alveolus of lung primary of cell type (HPAE EpiC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR897KTO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB755HPY
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens epithelial of alveolus lung primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/83e43b73-1bac-4abf-b24d-ea082022b20e/@@download/attachment/295049.pdf

value: epithelial cell of alveolus of lung

value: Human Pulmonary Alveolar Epithelial Cells (HPAEpiC).

value: unknown

value: not collected

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

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

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


title: total RNA-seq from SJSA1 (ENCLB542ORM)

description:
https://www.encodeproject.org/experiments/ENCSR880EGO/
***************
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 SJSA1. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR880EGO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB542ORM
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens SJSA1 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/7fd2c665-35b6-43ac-8d17-2114150dfcfd/@@download/attachment/291392.pdf

value: immortalized cell line

value: 19 year

value: male

value: John Stamatoyannopoulos, UW

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

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

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


title: total RNA-seq from myotube (ENCLB255LXZ)

description:
https://www.encodeproject.org/experiments/ENCSR828TEI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of primary cell line HSMM that has been differentiated into myotubes.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR828TEI
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB255LXZ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens myotube in vitro differentiated cells derived from skeletal muscle myoblast

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b0eec905-dd1d-46c4-a0cf-1cd5df3e33a4/@@download/attachment/291755.pdf

value: myotube

value: in vitro differentiated cells

value: skeletal muscle myotubes differentiated from the HSMM cell line

value: ENCBS526ENC at ENCODE; https://www.encodeproject.org/ENCBS526ENC/

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

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


title: total RNA-seq from myotube (ENCLB796YUI)

description:
https://www.encodeproject.org/experiments/ENCSR828TEI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of primary cell line HSMM that has been differentiated into myotubes.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR828TEI
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB796YUI
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens myotube in vitro differentiated cells

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/89049476-90fc-478a-bd97-6999eaffc307/@@download/attachment/291756.pdf

value: unknown

value: not collected

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


title: total RNA-seq from LHCN-M2 (ENCLB534MTC)

description:
https://www.encodeproject.org/experiments/ENCSR894WMQ/
***************
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 after 4 days of differentiation. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR894WMQ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB534MTC
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/37686b0b-9c41-4422-ad5e-7333c4f367bb/@@download/attachment/292337.pdf

value: skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor; differentiated for 4 days; 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: adult

value: ENCBS234AAA at ENCODE; https://www.encodeproject.org/ENCBS234AAA/

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

value: ENCODE dbxrefs DIFF_4d; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=DIFF_4d

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 airway epithelial cell (ENCLB271TJH)

description:
https://www.encodeproject.org/experiments/ENCSR822SUG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from airway epithelial cells (HSA EpiC). They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR822SUG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB271TJH
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens airway epithelial primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b741ed6c-d17a-42fa-a499-889d369fffb1/@@download/attachment/295146.pdf

value: airway epithelial cell

value: primary cell

value: Human Small Airway Epithelial Cells

value: Thomas Gingeras, CSHL

value: ENCBS408ZXF at ENCODE; https://www.encodeproject.org/ENCBS408ZXF/

value: Derived from ENCODE donor ENCDO749MBK; https://www.encodeproject.org/ENCDO749MBK/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=3235


title: total RNA-seq from airway epithelial cell (ENCLB473OOB)

description:
https://www.encodeproject.org/experiments/ENCSR822SUG/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from airway epithelial cells (HSA EpiC). They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR822SUG
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB473OOB
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f224b0fe-90f9-4d3a-b15d-5584f0b7bda0/@@download/attachment/295147.pdf

value: unknown

value: ENCBS050ADW at ENCODE; https://www.encodeproject.org/ENCBS050ADW/


title: total RNA-seq from mammary microvascular endothelial cell (ENCLB311NPN)

description:
https://www.encodeproject.org/experiments/ENCSR815UVL/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of mammary microvascular endothelial cell primary cell line (HMMEC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR815UVL
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB311NPN
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens mammary microvascular endothelial primary cell female adult (26 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dd98cf09-a3a8-44bd-99e4-aa9f2837a997/@@download/attachment/295050.pdf

value: mammary microvascular endothelial cell

value: Human Mammary Microvascular Endothelial Cells (HMMEC) from the breast tissue of a 26 year old female.

value: 26 year

value: female

value: ENCBS291IGF at ENCODE; https://www.encodeproject.org/ENCBS291IGF/

value: Derived from ENCODE donor ENCDO779FJA; https://www.encodeproject.org/ENCDO779FJA/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=7605


title: total RNA-seq from mammary microvascular endothelial cell (ENCLB652XFG)

description:
https://www.encodeproject.org/experiments/ENCSR815UVL/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of mammary microvascular endothelial cell primary cell line (HMMEC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR815UVL
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB652XFG
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bf7b2601-201c-4579-b6eb-739bb941d8f5/@@download/attachment/295051.pdf

value: Human Mammary Microvascular Endothelial Cells (HMMEC).

value: adult

value: ENCBS118XHF at ENCODE; https://www.encodeproject.org/ENCBS118XHF/


title: RNAseq-ALL21

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

data_processing:
AB SOLID data:  Primary alignment with Lifescope software version 2.1
ILLUMINA data: Primary alignment with STAR
Mark duplicate with PICARD version 1.107
SplitNCigar with GATK version 3.2-2
Read counts using HTSeq version 0.6.1p1 with Ensembl GRCH37 version 75
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: pre-B leukemic cell line

growth_protocol: Cells were cultured in RPMI 1640 media supplemented with 10% Fetal Bovine Serum

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis for all patients using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. The Allprep DNA/RNA Mini kit (Qiagen) was used for all REH samples .Following a DNAse I treatment, total RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) and the Illumina TruSeq Stranded Total RNA kit (relapse samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System or the Illumina HiSeq 2500 System.

tag: disease state

value: acute lymphoblastic leukemia

tag: cell line

value: REH

tag: etv6 status

value: Clone 2-1 stably expressing His-tagged ETV6


title: total RNA-seq from fibroblast of arm (ENCLB099WXD)

description:
https://www.encodeproject.org/experiments/ENCSR797BPP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line GM23248, a fibroblast primary cell line derived from an arm skin punch of a 53 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR797BPP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB099WXD
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

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/bd66e0d3-e847-4e93-abc4-5d678014b779/@@download/attachment/291182.pdf

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: RNAseq-ALL23

description: REHWT

value: Wild type (ETV6 -/-)


title: RNAseq-ALL22

value: Clone 2-1 with plasmid backbone only


title: total RNA-seq from fibroblast of arm (ENCLB011AUM)

description:
https://www.encodeproject.org/experiments/ENCSR797BPP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line GM23248, a fibroblast primary cell line derived from an arm skin punch of a 53 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR797BPP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB011AUM
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/66e15587-02f1-4b08-b9a6-a142304af2cd/@@download/attachment/291181.pdf

value: adult

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/


title: RNAseq-ALL20

value: acute lymphoblastic leukemia

value: Clone 2-1 stably expressing DNA-binding deficient His-tagged ETV6


title: RNAseq-ALL18

value: REH

value: Clone 2-11 stably expressing His-tagged ETV6


title: total RNA-seq from SJSA1 (ENCLB870ILB)

description:
https://www.encodeproject.org/experiments/ENCSR880EGO/
***************
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 SJSA1. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR880EGO
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB870ILB
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/8f1739ab-9c4f-4695-b11a-f1d1544a8761/@@download/attachment/291393.pdf

value: immortalized cell line

value: 19 year

value: John Stamatoyannopoulos, UW

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

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

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


title: RNAseq-ALL19

value: Clone 2-11 with plasmid backbone only


title: RNAseq-ALL17

value: Clone 2-11 stably expressing DNA-binding deficient His-tagged ETV6


title: total RNA-seq from hair follicular keratinocyte (ENCLB470CZF)

description:
https://www.encodeproject.org/experiments/ENCSR680USE/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from hair follicular keratinocytes (HHFK). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR680USE
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB470CZF
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens hair follicular keratinocyte primary cell male adult (55 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e3ae259d-7279-4925-b837-71bbeac81cd1/@@download/attachment/295148.pdf

value: hair follicular keratinocyte

value: primary cell

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

value: 55 year

value: male

value: Thomas Gingeras, CSHL

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

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

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


title: total RNA-seq from M059J (ENCLB617TPR)

description:
https://www.encodeproject.org/experiments/ENCSR696SMK/
***************
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 M059J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR696SMK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB617TPR
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens M059J 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/09a92c07-8d90-423d-9987-c3e12493769a/@@download/attachment/291693.pdf

value: immortalized cell line

value: 33 year

value: adult

value: malignant glioblastoma

value: ENCBS062ILC at ENCODE; https://www.encodeproject.org/ENCBS062ILC/

value: Derived from ENCODE donor ENCDO000ACY; https://www.encodeproject.org/ENCDO000ACY/

value: ENCODE dbxrefs Cellosaurus CVCL_0400; http://web.expasy.org/cellosaurus/CVCL_0400


title: total RNA-seq from neural tube (ENCLB672ISU)

description:
https://www.encodeproject.org/experiments/ENCSR004XCU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-Seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR004XCU
assay title: total RNA-seq
assembly: mm10
encode release date: 2015-10-13
lab: Barbara Wold, Caltech
library encode accession: ENCLB672ISU
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10
nucleic acid starting quantity units: ng

organism: Mus musculus

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (15.5 days)

value: neural tube

value: tissue

value: Neural tube from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS206NRE at ENCODE; https://www.encodeproject.org/ENCBS206NRE/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: single cell RNA-seq from induced pluripotent stem cell (ENCLB237OAE)

description:
https://www.encodeproject.org/experiments/ENCSR368QPC/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on PGP human IPS cells (13pgs)
experiment encode accession: ENCSR368QPC
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB237OAE
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

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

extract_protocol:
extraction method: Ambion mirVana
extraction protocol: https://www.encodeproject.org/documents/428a184d-7fa1-4599-9d8d-749c2eba7edd/@@download/attachment/cms_055740.pdf, extraction protocol: https://www.encodeproject.org/documents/f0cc5a7f-96a5-4970-9f46-317cc8e2d6a4/@@download/attachment/cms_055423.pdf, general protocol: https://www.encodeproject.org/documents/5f5193b0-0c61-40c6-a286-b1f6d6f0c0da/@@download/attachment/SmartSeqProtocol.pdf

tag: antibody

value: Control

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: 53 year

value: male

value: Thomas Gingeras, CSHL

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

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

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

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


title: total_RNAseq_thoc5_mut_ov

city: Pasadena

first: Maria

last: Ninova

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

description: total RNA

data_processing:
For consistency between different sequencing datasets, 100 bp reads were trimmed to 50 bp before processing.
Standard illumina 3' adaptor sequence was removed using Reaper (Davis et al. 2013)  or Cutadapt tool (Martin et al. 2011).
Data was filtered against Drosophila melanogaster  ribosomal RNA sequences using Bowtie 0.12.7 (Langmead et al., 2009), allowing up to 3 mismatches.
Remaining reads were mapped to D. melanogaster genome (UCSC dm3) allowing 0 mismatches, and only uniquely mapping reads were retained (-m 1).
Genome_build: UCSC dm3
Supplementary_files_format_and_content: Genome coverage histograms for uniquely mapped reads in bigWig format

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were maintained under standard conditions.

extract_protocol:
Total RNA from dissected ovaries was purified using Trizol according to manufacturer's instructions. Chromatin-associated RNAs were isolated as described previously (Khodor et al., 2011), with modifications.  For total RNA-sequencing and input RNA in Thoc5-GFP RIP experiment, ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit (human/mouse/rat, Epicenter) with additional Drosophila-specific probes. Thoc5-GFP and GFP-bound RNA (negative control) was isolated from immunopurified protein bound RNA fraction from ovarian lysates using antibodies against GFP. Detailed protocols for chromatin-associated RNAs and protein-bound RNA extraction is available in the accompanying manuscript.
Total and chromatin-associated RNA libraries were generated using the NEBNext library preparation kit (NEB) according to the manufacturer's instructions. For small RNA librarires, 19-29 nt RNAs were isolated from total RNA of dissected ovaries using 12% polyacrylamide gels, and library construction was performed as described in previous studies (Aravin et al., 2008; Brennecke et al., 2007).

treatment_protocol: No treatment (such as fixation) prior to extraction

tag: genotype

value: 1 week old


title: total_RNAseq_thoc5_het_ov

description: total RNA


title: single cell RNA-seq from bipolar spindle neuron (ENCLB941VYE)

description:
https://www.encodeproject.org/experiments/ENCSR225BBK/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on PGP human bipolar spindle neurons (13pgs)
experiment encode accession: ENCSR225BBK
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB941VYE
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

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

value: bipolar spindle neuron

value: in vitro differentiated cells

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

value: adult

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


title: total RNA-seq from G401 (ENCLB798FHZ)

description:
https://www.encodeproject.org/experiments/ENCSR653DFZ/
***************
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 G401. They are stranded PE101 Illumina Hhi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR653DFZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB798FHZ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens G401 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6ad72b1c-0487-479f-b598-6c896d34bc6b/@@download/attachment/291648.pdf

value: immortalized cell line

value: 3 month

value: child

value: John Stamatoyannopoulos, UW

value: ENCBS659PBH at ENCODE; https://www.encodeproject.org/ENCBS659PBH/

value: Derived from ENCODE donor ENCDO572LRN; https://www.encodeproject.org/ENCDO572LRN/

value: ENCODE dbxrefs Cellosaurus CVCL_0270; http://web.expasy.org/cellosaurus/CVCL_0270


title: total RNA-seq from MCF-7 (ENCLB240JZT)

description:
https://www.encodeproject.org/experiments/ENCSR667JTA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation MCF7 Long Total from Graveley
experiment encode accession: ENCSR667JTA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB240JZT
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens MCF-7 immortalized cell line

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

value: RNA Evaluation MCF7 Long Total from Graveley (MCF7-1)

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: Brenton Graveley, UConn

value: ENCBS328UKJ at ENCODE; https://www.encodeproject.org/ENCBS328UKJ/

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: total RNA-seq from SK-MEL-5 (ENCLB059TNM)

description:
https://www.encodeproject.org/experiments/ENCSR669KQU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SK-MEL-5, a metastatic malignant melanoma from a 24 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR669KQU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB059TNM
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens SK-MEL-5 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/cf45f92c-c735-47e5-8c5b-eb781bce38e5/@@download/attachment/287677.pdf

value: 24 year

value: adult

value: ENCBS518AAA at ENCODE; https://www.encodeproject.org/ENCBS518AAA/

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

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


title: total RNA-seq from G401 (ENCLB208TJF)

description:
https://www.encodeproject.org/experiments/ENCSR653DFZ/
***************
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 G401. They are stranded PE101 Illumina Hhi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR653DFZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB208TJF
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a8987139-caa9-4717-b002-3410cc260791/@@download/attachment/291647.pdf

value: immortalized cell line

value: 3 month

value: child

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS062JBT at ENCODE; https://www.encodeproject.org/ENCBS062JBT/


title: total RNA-seq from hair follicular keratinocyte (ENCLB764KEB)

description:
https://www.encodeproject.org/experiments/ENCSR680USE/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from hair follicular keratinocytes (HHFK). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR680USE
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB764KEB
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/33861c4f-b2cf-4919-8f64-88f20b98d447/@@download/attachment/295149.pdf

value: hair follicular keratinocyte

value: primary cell

value: Human Hair Follicular Keratinocyte Cells (HHFK).

value: 55 year

value: Thomas Gingeras, CSHL

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

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


title: total RNA-seq from MCF-7 (ENCLB188STW)

description:
https://www.encodeproject.org/experiments/ENCSR667JTA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation MCF7 Long Total from Graveley
experiment encode accession: ENCSR667JTA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB188STW
size range: >200
spikeins used: /references/ENCSR449DXG/

value: RNA Evaluation MCF7 Long Total from Graveley (MCF7-2)

value: 69 year

value: adult

value: female

value: breast cancer (adenocarcinoma)

value: Brenton Graveley, UConn

value: ENCBS174OTK at ENCODE; https://www.encodeproject.org/ENCBS174OTK/

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 NCI-H460 (ENCLB297PER)

description:
https://www.encodeproject.org/experiments/ENCSR625QJI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR625QJI
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB297PER
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/789f89ea-d988-4619-ba45-82882fbe7c40/@@download/attachment/293551.pdf

value: immortalized cell line

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

value: 37 year

value: male

tag: subcellular fraction term name

value: nucleus

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

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

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

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


title: single cell RNA-seq from bipolar spindle neuron (ENCLB463KOX)

description:
https://www.encodeproject.org/experiments/ENCSR225BBK/
***************
biological replicate number: 1
technical replicate number: 1
description: Total RNA-seq on PGP human bipolar spindle neurons (13pgs)
experiment encode accession: ENCSR225BBK
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB463KOX
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: bipolar spindle neuron

value: in vitro differentiated cells

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

value: 53 year

value: Thomas Gingeras, CSHL

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

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


title: smallRNAseq_thoc5_ovary

description: Size-selected small RNA 19-29 nt

value: 1 week old


title: polyA mRNA RNA-seq from NCI-H460 (ENCLB794DVD)

description:
https://www.encodeproject.org/experiments/ENCSR625QJI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from nuclear fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR625QJI
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB794DVD
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/da942e1d-25f3-4387-8d6d-5df618a4682b/@@download/attachment/293552.pdf

value: immortalized cell line

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

value: adult

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


title: total RNA-seq from M059J (ENCLB374MEK)

description:
https://www.encodeproject.org/experiments/ENCSR696SMK/
***************
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 M059J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR696SMK
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB374MEK
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/45306207-b13a-4a6b-9034-1d2ea4bf7d4e/@@download/attachment/291694.pdf

value: 33 year

value: male

value: malignant glioblastoma

value: John Stamatoyannopoulos, UW

value: ENCBS304XWS at ENCODE; https://www.encodeproject.org/ENCBS304XWS/

value: Derived from ENCODE donor ENCDO000ACY; https://www.encodeproject.org/ENCDO000ACY/

value: ENCODE dbxrefs Cellosaurus CVCL_0400; http://web.expasy.org/cellosaurus/CVCL_0400


title: total RNA-seq from bronchus fibroblast of lung (ENCLB463QPI)

description:
https://www.encodeproject.org/experiments/ENCSR620NSN/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from primary bronchial fibroblast cells (HBF).  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR620NSN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB463QPI
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens bronchus fibroblast of lung primary cell

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bbf154b3-2e7d-4b85-af80-88e4b2bf7a2e/@@download/attachment/LID294954.pdf

value: bronchus fibroblast of lung

value: primary cell

value: Bronchial primary cell fibroblasts (HBF) from an unknown donor (no metadata associated with the donor).

value: unknown

value: not collected

value: ENCBS302ZPK at ENCODE; https://www.encodeproject.org/ENCBS302ZPK/

value: Derived from ENCODE donor ENCDO108OFX; https://www.encodeproject.org/ENCDO108OFX/

value: ScienCell sample source; http://www.sciencellonline.com/site/productInformation.php?keyword=3425


title: single cell RNA-seq from induced pluripotent stem cell (ENCLB171NYD)

description:
https://www.encodeproject.org/experiments/ENCSR368QPC/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on PGP human IPS cells (13pgs)
experiment encode accession: ENCSR368QPC
assay title: single cell RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-09-29
lab: Barbara Wold, Caltech
library encode accession: ENCLB171NYD
size range: >200
spikeins used: /references/ENCSR013YHQ/, /references/ENCSR133ALU/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cell-equivalent

value: Control

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

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

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

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

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


title: total RNA-seq from bronchus fibroblast of lung (ENCLB333MHE)

description:
https://www.encodeproject.org/experiments/ENCSR620NSN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from primary bronchial fibroblast cells (HBF).  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR620NSN
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2015-05-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB333MHE
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f55ccbcb-bf04-4e8b-af08-e43bf26fd5ba/@@download/attachment/LID294953.pdf

value: bronchus fibroblast of lung

value: primary cell

value: Human Bronchial Fibroblasts (HBF) from ScienCell Research Laboratories are isolated from human bronchus tissue.  They resemble a mesenchymal stem cell phenotype and their principle function is the production of type III collagen, elastin, and proteoglycans of the extracellular matrix.

value: ENCBS787BHC at ENCODE; https://www.encodeproject.org/ENCBS787BHC/


title: total RNA-seq from Caki2 (ENCLB908GTT)

description:
https://www.encodeproject.org/experiments/ENCSR584JXD/
***************
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 Caki2. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR584JXD
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB908GTT
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens Caki2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0b1919ec-b91f-420c-8749-8c8c5759d1dc/@@download/attachment/291646.pdf

value: immortalized cell line

value: 69 year

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS461KDA at ENCODE; https://www.encodeproject.org/ENCBS461KDA/

value: Derived from ENCODE donor ENCDO140IFG; https://www.encodeproject.org/ENCDO140IFG/

value: ENCODE dbxrefs Cellosaurus CVCL_0235; http://web.expasy.org/cellosaurus/CVCL_0235


title: total RNA-seq from A172 (ENCLB989OBQ)

description:
https://www.encodeproject.org/experiments/ENCSR580GSX/
***************
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 A172. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR580GSX
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB989OBQ
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens A172 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/d95c8c50-20dd-4015-b292-60bc8d31d0ba/@@download/attachment/291389.pdf

value: 53 year

value: adult

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

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

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


title: total RNA-seq from Caki2 (ENCLB771RHM)

description:
https://www.encodeproject.org/experiments/ENCSR584JXD/
***************
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 Caki2. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR584JXD
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-11-20
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB771RHM
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/12f9805e-6155-45a3-8866-bb3bbf3b9362/@@download/attachment/291645.pdf

value: ENCBS768KGZ at ENCODE; https://www.encodeproject.org/ENCBS768KGZ/


title: RNAPII ChIP-seq

city: Atlanta

first: Chun-hui

last: Hou

address: 1510 Clifton Rd NE

institute: Emory University

description: Normal culture

data_processing:
ChIP-seq datasets were analyzed with MACS.
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

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:
ChIP experiments were carried out as described (Proc Natl Acad Sci U S A 105, 20398-403, 2008). Five ChIP on Heat shocked Kc167 cells with antibodies against BEAF, CP190, CTCF, SuHw and RNAPII, one ChIP on normal Kc167 cells with antibody against total RNAPII.
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: chip antibody

value: RNAPII (gift from John T. Lis; Adelman et al., Mol. Cell, 2005)

tag: treatment

value: Normal culture


title: HS CTCF ChIP-seq

description: Heat shocked

value: CTCF (Bushey et al., Genes & Dev. 2009)

value: Heat shocked


title: ChIP Input DNA

description: Heat shocked


title: HS SuHw ChIP-seq

description: Heat shocked

value: SuHw (Bushey et al., Genes & Dev. 2009)


title: total RNA-seq from SK-MEL-5 (ENCLB695YMT)

description:
https://www.encodeproject.org/experiments/ENCSR669KQU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SK-MEL-5, a metastatic malignant melanoma from a 24 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR669KQU
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB695YMT
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/b4bcdbf0-2d1a-4dd7-9a70-1cb29d08ca4a/@@download/attachment/287678.pdf

value: immortalized cell line

tag: biosample encode accession

tag: age

value: 24 year

tag: Sex

value: female

value: ENCBS519AAA at ENCODE; https://www.encodeproject.org/ENCBS519AAA/

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

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


title: HS RNAPII ChIP-seq

description: Heat shocked


title: total RNA-seq from A172 (ENCLB954KLQ)

description:
https://www.encodeproject.org/experiments/ENCSR580GSX/
***************
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 A172. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR580GSX
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB954KLQ
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/246e4934-babf-489c-8323-8b2ade394bed/@@download/attachment/291388.pdf

value: 53 year

value: adult

value: male

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

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


title: Hi-C library HS1

description:
Heat shocked
supplementary file: AllHS_hotint_NB_10000rs_allchr.txt

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

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.

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

tag: hi-c enzyme

value: HindIII


title: polyA mRNA RNA-seq from SK-N-DZ (ENCLB519UOV)

description:
https://www.encodeproject.org/experiments/ENCSR569JKX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a neuroblastoma immortalized cell line SK-N-DZ erived 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: ENCSR569JKX
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB519UOV
size range: >200
spikeins used: /references/ENCSR156CIL/

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bdb46b9c-71d7-4742-9de6-c56bd589269b/@@download/attachment/293601.pdf

tag: line

value: SK-N-DZ

tag: description

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: Thomas Gingeras, CSHL

value: cytosol

value: ENCBS580YYW at ENCODE; https://www.encodeproject.org/ENCBS580YYW/

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: HS BEAF ChIP-seq

description: Heat shocked

value: BEAF (Bushey et al., Genes & Dev. 2009)

value: Heat shocked


title: HS CP190 ChIP-seq

description: Heat shocked

value: CP190 (Bushey et al., Genes & Dev. 2009)


title: polyA mRNA RNA-seq from SK-N-DZ (ENCLB071UME)

description:
https://www.encodeproject.org/experiments/ENCSR569JKX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from cytoplasmic fractions of a neuroblastoma immortalized cell line SK-N-DZ erived 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: ENCSR569JKX
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-12-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB071UME
size range: >200
spikeins used: /references/ENCSR156CIL/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c71b93aa-a575-4147-bf59-144253f6d646/@@download/attachment/293600.pdf

value: immortalized cell line

tag: dev stage

value: female

value: ENCBS715HTH at ENCODE; https://www.encodeproject.org/ENCBS715HTH/


title: total RNA-seq from SJCRH30 (ENCLB879IMG)

description:
https://www.encodeproject.org/experiments/ENCSR568YRP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SJCRH30, a metastatic rhabdomyosarcoma from a 17 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR568YRP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB879IMG
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens SJCRH30 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/3213c5ca-da44-4d5d-b7f6-0746a7f68f3d/@@download/attachment/287489.pdf

value: This immortalized cell line was established from cells from the metastatic site of the bone marrow of a child with rhabdomyosarcoma

value: 17 year

value: unknown

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS516AAA at ENCODE; https://www.encodeproject.org/ENCBS516AAA/

value: Derived from ENCODE donor ENCDO339AAA; https://www.encodeproject.org/ENCDO339AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0041; http://web.expasy.org/cellosaurus/CVCL_0041


title: smallRNAseq_het_ovary

description: Size-selected small RNA 19-29 nt

extract_protocol:
Total RNA from dissected ovaries was purified using Trizol according to manufacturer's instructions. Chromatin-associated RNAs were isolated as described previously (Khodor et al., 2011), with modifications.  For total RNA-sequencing and input RNA in Thoc5-GFP RIP experiment, ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit (human/mouse/rat, Epicenter) with additional Drosophila-specific probes. Thoc5-GFP and GFP-bound RNA (negative control) was isolated from immunopurified protein bound RNA fraction from ovarian lysates using antibodies against GFP. Detailed protocols for chromatin-associated RNAs and protein-bound RNA extraction is available in the accompanying manuscript.
Total and chromatin-associated RNA libraries were generated using the NEBNext library preparation kit (NEB) according to the manufacturer's instructions. For small RNA librarires, 19-29 nt RNAs were isolated from total RNA of dissected ovaries using 12% polyacrylamide gels, and library construction was performed as described in previous studies (Aravin et al., 2008; Brennecke et al., 2007).

value: 1 week old


title: total RNA-seq from H7-hESC (ENCLB638ZFC)

description:
https://www.encodeproject.org/experiments/ENCSR490SQH/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of uninduced embryonic stem cell line H7-hESC.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR490SQH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB638ZFC
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens H7-hESC stem 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/ff3febef-f644-4923-9b4e-f84958492806/@@download/attachment/291754.pdf

value: stem cell

value: not collected

value: ENCBS624XJG at ENCODE; https://www.encodeproject.org/ENCBS624XJG/

value: Derived from ENCODE donor ENCDO221AAA; https://www.encodeproject.org/ENCDO221AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_9772; http://web.expasy.org/cellosaurus/CVCL_9772


title: total RNA-seq from SJCRH30 (ENCLB427PQN)

description:
https://www.encodeproject.org/experiments/ENCSR568YRP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line SJCRH30, a metastatic rhabdomyosarcoma from a 17 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR568YRP
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB427PQN
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/3f0f8953-f109-4062-b222-89f9bbf51984/@@download/attachment/287490.pdf

value: immortalized cell line

value: This immortalized cell line was established from cells from the metastatic site of the bone marrow of a child with rhabdomyosarcoma.

value: ENCBS517AAA at ENCODE; https://www.encodeproject.org/ENCBS517AAA/


title: total RNA-seq from A375 (ENCLB509MRG)

description:
https://www.encodeproject.org/experiments/ENCSR504VXC/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line A375, a malignant melanoma from a 54 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR504VXC
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB509MRG
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens A375 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/1f9bea9a-6532-4f11-960a-9b0b31ee386c/@@download/attachment/LID287570.pdf

value: Epithelial cells, malignant melanoma

value: 54 year

value: adult

tag: passage number

value: female

tag: health state

value: malignant melanoma

value: Bradley Bernstein, Broad

value: ENCBS607AAA at ENCODE; https://www.encodeproject.org/ENCBS607AAA/

value: Derived from ENCODE donor ENCDO348AAA; https://www.encodeproject.org/ENCDO348AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0132; http://web.expasy.org/cellosaurus/CVCL_0132

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1619.aspx


title: total RNA-seq from A375 (ENCLB516QBX)

description:
https://www.encodeproject.org/experiments/ENCSR504VXC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line A375, a malignant melanoma from a 54 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR504VXC
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB516QBX
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/9c83c5ac-0415-4045-94d1-0d8059829610/@@download/attachment/LID287569.pdf

value: ENCBS606AAA at ENCODE; https://www.encodeproject.org/ENCBS606AAA/


title: total RNA-seq from HT1080 (ENCLB151WWC)

description:
https://www.encodeproject.org/experiments/ENCSR535VTR/
***************
biological replicate number: 2
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: ENCLB151WWC
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/c330770e-6e47-4865-90e3-1d5b348a28f4/@@download/attachment/LID288370.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: male

value: fibrosarcoma

value: John Stamatoyannopoulos, UW

value: ENCBS513AAA at ENCODE; https://www.encodeproject.org/ENCBS513AAA/

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 H7-hESC (ENCLB811KMY)

description:
https://www.encodeproject.org/experiments/ENCSR490SQH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of uninduced embryonic stem cell line H7-hESC.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR490SQH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB811KMY
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/bec773a0-39b5-4500-9fa2-9102f5645540/@@download/attachment/291753.pdf

value: stem cell

value: undifferentiated embryonic stem cells

value: unknown

value: not collected

value: ENCBS293AAA at ENCODE; https://www.encodeproject.org/ENCBS293AAA/

value: Derived from ENCODE donor ENCDO221AAA; https://www.encodeproject.org/ENCDO221AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_9772; http://web.expasy.org/cellosaurus/CVCL_9772

value: ENCODE dbxrefs H7-hESC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H7-hESC


title: total RNA-seq from skeletal muscle myoblast (ENCLB550ATC)

description:
https://www.encodeproject.org/experiments/ENCSR444WHQ/
***************
biological replicate number: 2
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: ENCLB550ATC
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/89f6158b-c42e-4a1d-b1cd-b4c72b8d2865/@@download/attachment/291758.pdf

value: skeletal muscle myoblast

value: primary cell

value: ENCBS665DRD at ENCODE; https://www.encodeproject.org/ENCBS665DRD/

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