|
| Status |
Public on Jul 20, 2015 |
| Title |
mRNA C2C12-H3.3-D |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 cells_H3.3_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 H3.3 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 |
| E-mail(s) |
yohkawa@bioreg.kyushu-u.ac.jp
|
| 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 |
|
| Relations |
| BioSample |
SAMD00019353 |
| SRA |
DRX020484 |
