|
| Status |
Public on May 17, 2019 |
| Title |
GAA-2 |
| Sample type |
SRA |
| |
|
| Source name |
microRNA derived from myotubes after Guanidineacetic acid supplement (GAA)
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129/Rej
tissue source: myoblast
cell line: C2C12
cell type: Murine skeletal muscle cell line
developmental stage: 6 days after differentiation
|
| Treatment protocol |
When the cells density reached about 80 % confluence, the C2C12 myoblasts were induced differentiation by placing differentiation medium that contained high glucose DMEM, 2% horse serum and present or absent 20 mM Guanidineacetic acid.
|
| Growth protocol |
Murine skeletal muscle cell line C2C12 was cultured growth medium that contained high glucose DMEM supplemented with 10% fetal bovine serum, 100000 units/L of penicillin sodium, and 100 mg/L of streptomycin sulfate at 37 ℃ in a humidified atmosphere that contained 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pig reference genome with stringent criteria (0 mismatch in the first 18bp)
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM), then standardized by the formula log2 (RPM+1), which allowed unbiased comparison among samples.
Genome_build: Genome database:mouse genome (assembly GCA_000001635.8); miRbase version: V21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data
|
| |
|
| Submission date |
Aug 14, 2018 |
| Last update date |
May 17, 2019 |
| Contact name |
wang yu jie |
| E-mail(s) |
wangyujie715@163.com
|
| Phone |
+8218227586326
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
211 Huimin Road, Wenjiang District, Chengdu
|
| City |
chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE118528 |
Guanidineacetic acid regulate myogenic differentiation through miR-133a-5 and miR-1a-3p co-mediated PI3K-Akt-mTOR signaling pathway |
|
| Relations |
| BioSample |
SAMN09831643 |
| SRA |
SRX4551582 |
