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GEO accession:
Sample GSM2453411
Query DataSets for GSM2453411
Status
Public on Feb 03, 2017
Title
polyA mRNA RNA-seq from MEL cell line (ENCLB409VHC)
Sample type
SRA
Source name
Mus musculus strain MEL MEL immortalized cell line treated with 2% dimethyl sulfoxide for 5 days
Organism
Mus musculus
Characteristics
line: MEL cell line
biomaterial_type: immortalized cell line
description: Leukemia (K562 analog)
biosample encode accession: ENCBS050ENC (SAMN06044898)
dev stage: unknown
treatments: treatment_term_id: CHEBI:28262; treatment_term_name: dimethyl sulfoxide; treatment_type: chemical; duration: 5; duration_units: day; UCSC-ENCODE-cv:DMSO_2.0pct;
Sex: not collected
age: unknown
health state: unknown
lab: Michael Snyder, Stanford
link: ENCBS050ENC at ENCODE;
https://www.encodeproject.org/ENCBS050ENC/
link: Derived from ENCODE donor ENCDO073AAA;
https://www.encodeproject.org/ENCDO073AAA/
link: ENCODE dbxrefs Cellosaurus CVCL_2111;
http://web.expasy.org/cellosaurus/CVCL_2111
link: ENCODE dbxrefs MEL;
http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL
Extracted molecule
total RNA
Extraction protocol
extraction method: see document
general protocol:
https://www.encodeproject.org/documents/d6ec08a9-8b45-424d-aad9-55cbc02d527f/@@download/attachment/wgEncodePsuRnaSeq.html.pdf
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
cDNA
Instrument model
Illumina HiSeq 2000
Description
https://www.encodeproject.org/experiments/ENCSR000CIE/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on mouse erythroleukemia cells treated with dimethylsulfoxide 2.0% (single end)
experiment encode accession: ENCSR000CIE
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-08-13
lab: Ross Hardison, PennState
library encode accession: ENCLB409VHC
size range: >175
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Jan 11, 2017
Last update date
May 15, 2019
Contact name
ENCODE DCC
E-mail(s)
encode-help@lists.stanford.edu
Organization name
ENCODE DCC
Street address
300 Pasteur Dr
City
Stanford
State/province
CA
ZIP/Postal code
94305-5120
Country
USA
Platform ID
GPL13112
Series (1)
GSE93476
polyA mRNA RNA-seq from MEL cell line (ENCSR000CIE)
Relations
BioSample
SAMN06044898
SRA
SRX2487469
Supplementary file
Size
Download
File type/resource
GSM2453411_ENCFF343IAQ_signal_of_all_reads_mm10.bigWig
147.6 Mb
(ftp)
(http)
BIGWIG
GSM2453411_ENCFF474KPJ_transcript_quantifications_mm10.tsv.gz
4.8 Mb
(ftp)
(http)
TSV
GSM2453411_ENCFF619TEZ_gene_quantifications_mm10.tsv.gz
2.5 Mb
(ftp)
(http)
TSV
GSM2453411_ENCFF691DSC_signal_of_unique_reads_mm10.bigWig
78.5 Mb
(ftp)
(http)
BIGWIG
GSM2453411_ENCLB409VHC_README.txt.gz
610 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
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