|
| Status |
Public on Sep 22, 2020 |
| Title |
RNA_C2C12_deltapro#3_day0_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
time course: day0
treatment: none
cell line: C2C12
cell type: myoblasts
|
| Treatment protocol |
At the confluence, cells were treated for 48 hours in medium containing 10% FBS, 0.5mM isobuylmethylxanthine, 125nM indomethacin, 1 μM dexamethosone, 850nM insulin, 1nM T3 and 1 μM rosiglitazone. After 48 hours, cells were switched to medium containing 10% FBS, 850nM insulin, 1nM T3 and 1 μM rosiglitazone.
|
| Growth protocol |
C2C12 myoblasts were mainteined in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Life Techologies) and RNeasy Mini Kit (Qiagen).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads were aligned to the mm9 genome assembly using STAR version 2.5.3a with the following parameters --runThreadN 10 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --limitBAMsortRAM 16000000000 --genomeDir MMUC --readFilesIn Read1.fastq Read2.fastq --outFilterMultimapNmax 1
Read counts for each gene were derived from the STAR output file named "ReadsPerGene.out.tab" and the matched strand count was used for further processes.
Genome_build: mm9
Supplementary_files_format_and_content: txt files showing FPKM value of each samples .
|
| |
|
| Submission date |
Apr 26, 2019 |
| Last update date |
Sep 22, 2020 |
| Contact name |
Hironori Waki |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Tokyo
|
| Street address |
Hongo 7-3-1, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
1138655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE130389 |
NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure adipocyte differentiation [RNA-seq] |
| GSE130390 |
NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure adipocyte differentiation |
|
| Relations |
| BioSample |
SAMN11518887 |
| SRA |
SRX5759164 |
