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Sample GSM1559494 Query DataSets for GSM1559494
Status Public on Jul 20, 2015
Title mRNA C2C12-H3mm7-D
Sample type SRA
Source name C2C12 cells_H3mm7_Differentiated
Organism Mus musculus
Characteristics cell type: myoblast
cell line: C2C12
culture status: differentiation (D)
Treatment protocol Differentiated cells were transferred to DMEM containing 2% horse serum upon reaching confluence and harvested 48 h later.
Growth protocol Cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 20% fetal bovine serum. Undifferentiated cells were harvested at 60–70% confluence.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated and reversed-transcribed with Takara Prime Script Reverse Transcriptase and an oligo dT primer.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Tet-On-C2C12 cells that harbor the N-terminal-GFP-tagged H3mm7 gene under a doxycycline (Dox)-inducible promoter.
Data processing Illumina RTA 1.17 software used for basecalling.
Sequenced reads were mapped onto the mouse genome (mm9) using Tophat (version 2.0.8) (Trapnell et al., 2012) with the software's default parameter.
Gene expression levels (FPKM; Fragments per kilobase of exon per million mapped sequence reads) were estimated using the cuffdiff program in Cufflinks (version 2.0.1) (Trapnell et al., 2012) using mapped reads and the software’s default parameters.
genome build: mm9
processed data files format and content: tab-delimited text file include FPKM values for each Sample
processed data file: mRNASeq_FPKMTable.txt.gz
Submission date Dec 05, 2014
Last update date May 15, 2019
Contact name Yasuyuki Ohkawa
Organization name Kyushu University
Department Medical Institute of Bioregulation, Medical Institute of Bioregulation
Street address 3-1-1 Maidashi, Higashi-ku, Fukuoka
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platform ID GPL18480
Series (1)
GSE63890 Characterization of mouse histone H3 variants
BioSample SAMD00019358
SRA DRX020485

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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