|
| Status |
Public on Oct 03, 2019 |
| Title |
MT_si-hnRNPL_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
C2C12
|
| Organism |
Mus musculus |
| Characteristics |
cell type: C2C12 myoblasts
cell line: C2C12
culture conditions: DM 48 hours
|
| Treatment protocol |
C2C12 myoblasts were induced to differentiation by switching to DMEM supplemented with 2% horse serum, 100 U/ml penicillin and 100 μg of streptomycin (differentiation medium, DM) when cell confluence reached 80%-90%. The cells were then cultured in DM for 48 h or 72 h.
|
| Growth protocol |
C2C12 myoblasts were grown in DMEM supplemented with 10% FBS, 100 U/ml penicillin and 100 μg of streptomycin (growth medium, GM) in a 5% CO2 humidified incubator at 37°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For total RNA-seq, total RNAs were extracted from MB or MT C2C12 cells using TRIzol reagent (Invitogen) and then delivered to BGI HK for rRNA depletion; for poly A+ RNA-seq, RNA-seq was performed following the procedures described before (Chen et al., 2017; Zhou et al., 2015). Total RNAs were extracted from C2C12 cells using TRIzol reagent (Invitogen) following the manufacturer’s instructions and then subjected to poly(A) selection (Ambion, 61006).
For total RNA-seq, RNAs were submitted to Beijing Genomic Center, Hong Kong. The libraries were prepared following strand specific RNA-seq library preparation procedures and sequenced on the HiSeq2000 platform; for polyA+ RNA-seq, we prepared the libraries using NEBNext® Ultra™ II RNA Library Preparation Kit (NEB, E7770S) and barcoded libraries were pooled at equal concentration and sequenced on the HiSeq1500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
poly A+ RNA
|
| Data processing |
Illumina Casava1.8 software was used for basecalling.
RNA-seq reads were mapped to mm9 genome using TopHat2. If multiple reads aligned to the same genomic position, only one read per position was kept for downstream analyses.
Gene expression level was quantified by Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are plain text files. Each entry represents expression level (RPKM) of all genes in mm9.
|
| |
|
| Submission date |
May 18, 2018 |
| Last update date |
Oct 03, 2019 |
| Contact name |
Jiajian Zhou |
| E-mail(s) |
[email protected]
|
| Organization name |
Southern Medical University
|
| Department |
Dermatology Hospital
|
| Street address |
No. 2 Lujing Road, Yuexiu District,
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
NA |
| Country |
China |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE114658 |
MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [RNA-Seq] |
| GSE114659 |
MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation |
|
| Relations |
| BioSample |
SAMN09225190 |
| SRA |
SRX4101065 |
