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Sample GSM538828 Query DataSets for GSM538828
Status Public on Jul 06, 2010
Title SAGE_T0-3
Sample type SRA
Source name Mouse C2C12 myoblasts
Organism Mus musculus
Characteristics time: T0 (days)
cell type: Mouse C2C12 myoblasts
cell line: C2C12
protocol: SAGE
Treatment protocol To induce fusion into myotubes, proliferating cells were serum deprived by changing to a medium of DMEM supplemented with 2% FBS
Growth protocol Proliferating C2C12 mouse myoblasts were grown out on collagen coated plates in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS).
Extracted molecule total RNA
Extraction protocol For DeepCAGE, we used the protocol of Valenet al. 2009, but we used modified adapters in the 5' and 3' end ligation steps that have linker sequences (proliferating – CCGACAGGTTCAGAGTTCTACAGAGACAGCAG and differentiated - CCGACAGGTTCAGAGTTCTACAGCTTCAGCAG) for Illumina Genome Analyzer II sequencing and have a recognition site for EcoP15I used instead of MmeI. For DeepSAGE we used a FC-102-1005 DGE-Tag Profiling NlaIII SamplePrepKit from Illumina
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Description DeepSAGE (3' sequencing)
Data processing Illumina GAPipeline, GAPSS analysis (, custom Perl and R scripts
Submission date Apr 28, 2010
Last update date May 15, 2019
Contact name Peter A.C. 't Hoen
Phone +31 71 5269421
Fax +31 71 5268285
Organization name Leiden University Medical Center
Department Center for Human and Clinical Genetics
Street address PO Box 9600
City Leiden
ZIP/Postal code 2300 RC
Country Netherlands
Platform ID GPL9250
Series (1)
GSE21580 DeepCAGE and DeepSAGE with proliferating and differentiated C2C12 mouse myoblasts
SRA SRX019939
BioSample SAMN00012306

Supplementary file Size Download File type/resource
GSM538828_sage_prolif-3_f.wig.gz 3.6 Mb (ftp)(http) WIG
GSM538828_sage_prolif-3_r.wig.gz 3.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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