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GEO accession:
Sample GSM2400050
Query DataSets for GSM2400050
Status
Public on Dec 07, 2016
Title
polyA mRNA RNA-seq from C3H10T1/2 (ENCLB357ZZZ)
Sample type
SRA
Source name
Mus musculus C3H10T1/2 immortalized cell line derived from C3H10T1/2
Organism
Mus musculus
Characteristics
line: C3H10T1/2
biomaterial_type: immortalized cell line
description: As a control, this multipotential cell line was treated with a differentiation protocol that will not induce these cells to differentiate into three mesodermal stem cell lineages.
biosample encode accession: ENCBS035ENC (SAMN06044893)
dev stage: unknown
Sex: not collected
age: unknown
health state: unknown
lab: Barbara Wold, Caltech
link: ENCBS035ENC at ENCODE;
https://www.encodeproject.org/ENCBS035ENC/
link: Derived from ENCODE donor ENCDO321TZV;
https://www.encodeproject.org/ENCDO321TZV/
link: growth protocol;
https://www.encodeproject.org/documents/c7dba054-d2e2-46d2-8834-304e37aa4846/@@download/attachment/10ToneHalf_Wold_protocol.pdf
link: ENCODE dbxrefs Cellosaurus CVCL_0190;
http://web.expasy.org/cellosaurus/CVCL_0190
link: ENCODE dbxrefs 10T1/2;
http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=10T1/2
Extracted molecule
total RNA
Extraction protocol
general protocol:
https://www.encodeproject.org/documents/1549840e-0ec9-44c8-adb3-43ceac9d7d6b/@@download/attachment/wgEncodeCaltechRnaSeq.release1.html.pdf
extraction method: Trizol (Invitrogen 15596-026)
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
cDNA
Instrument model
Illumina Genome Analyzer II
Description
https://www.encodeproject.org/experiments/ENCSR000AHX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on mouse 10T1-2 treated with differentiation treatment (control) for 60 hours polyA+
experiment encode accession: ENCSR000AHX
assay title: polyA mRNA RNA-seq
assembly: mm10
encode release date: 2012-05-07
lab: Barbara Wold, Caltech
library encode accession: ENCLB357ZZZ
size range: >200
spikeins used: /references/ENCSR714LOF/
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Nov 22, 2016
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
GPL9250
Series (1)
GSE90172
polyA mRNA RNA-seq from C3H10T1/2 (ENCSR000AHX)
Relations
BioSample
SAMN06044893
SRA
SRX2370365
Named Annotation
GSM2400050_ENCFF509MNU_signal_of_unique_reads_mm10.bigWig
Named Annotation
GSM2400050_ENCFF958IEB_signal_of_all_reads_mm10.bigWig
Supplementary file
Size
Download
File type/resource
GSM2400050_ENCFF139FYR_gene_quantifications_mm10.tsv.gz
2.0 Mb
(ftp)
(http)
TSV
GSM2400050_ENCFF509MNU_signal_of_unique_reads_mm10.bigWig
259.8 Mb
(ftp)
(http)
BIGWIG
GSM2400050_ENCFF916PAI_transcript_quantifications_mm10.tsv.gz
4.4 Mb
(ftp)
(http)
TSV
GSM2400050_ENCFF958IEB_signal_of_all_reads_mm10.bigWig
285.9 Mb
(ftp)
(http)
BIGWIG
GSM2400050_ENCLB357ZZZ_README.txt.gz
646 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
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