|
| Status |
Public on Apr 08, 2020 |
| Title |
Day0_B_S10_R1_001: Proliferation (Day 0) |
| Sample type |
SRA |
| |
|
| Source name |
Myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: C2C12 cells
passages: 5-10
|
| Treatment protocol |
Treated cells were stimulated with TNF alpha (10ng/ml) for 48 hours during differentiation.
|
| Growth protocol |
During myoblast proliferation, cells were supplemented daily with growth media (GM); DMEM with 10% FBS and 1% penicillin/streptomycin. Myogenic differentiation was induced when myoblasts reached 90-100% confluence by exchanging GM with differentiation media (DM), DMEM with 2% horse serum (Sigma) and 1% penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was collected from C2C12 cells using the RNeasy MiniKit (Qiagen). RNA integrity was determined with the Agilent 2100 Bioanalyzer prior to library preparation, RINs ranging from 9.7 to 10.0 were processed with an mRNA-Seq sample preparation kit (Illumina, Inc.; San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Timepoint: 0 h
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomics workbench (Qiagen).Genes with a mean raw count value < 10 were removed from further processing.
Differential gene expression was calculated with raw counts using DESeq2 in R Studio between the experimental groups using filters to select genes with an absolute fold change (FC) > 1.5 and a false discovery rate (FDR) P-value ≤ 0.05.
Genome_build: mm10
|
| |
|
| Submission date |
Sep 28, 2018 |
| Last update date |
Apr 08, 2020 |
| Contact name |
Michael Emmet O'Brien |
| Organization name |
University of Pittsburgh
|
| Department |
Pulmonary, Allergy, and Critical Care Medicine
|
| Lab |
Mallampalli
|
| Street address |
200 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE120600 |
Tumor Necrosis Factor Alpha Regulates Skeletal Myogenesis by Inhibiting SP1 Interaction with cis-Acting Regulatory Elements within the Fbxl2 Gene Promoter |
|
| Relations |
| BioSample |
SAMN10141732 |
| SRA |
SRX4774125 |
