|
| Status |
Public on Jun 06, 2019 |
| Title |
AMPK-KO_C2C12_D8_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myotubes at day 8
|
| Organism |
Mus musculus |
| Characteristics |
tissue: C2C12 myotubes at day 8
cell type: C2C12
developmental stage: day8
genotype: AMPK-/-
|
| Growth protocol |
C2C12 cells were cultured at 37 °C in DMEM supplemented with 10% fetal bovine serum (Invitrogen) in an incubator with 5% CO2. For in vitro differentiation, fully confluent C2C12 cells were washed twice with 1 x PBS, then subjected to differentiation in DMEM supplemented with 2% equine donor serum (Hyclone).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested at desired time points for total RNA isolation using RNeasy Mini kit (Qiagen).
RNA-seq library was prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: C2C12_WT_AMPK_KO_count.txt
|
| Data processing |
Illumina RTA software was used for basecalling and Illumina bcl2fastq 2.17 software was used for demultiplexing.
Sequencing reads were trimmed for adaptor sequences using TrimGalore v0.4.5 and mapped to mm10 whole genome using STAR v2.5.3a in basic two pass mode for paired-end reads with parameters: --outReadsUnmapped None, --chimSegmentMin 12, --alignIntronMax 100000, --ChimSegmentReadGapMax parameter 3, --alignSJstitchMismatchNmax 5 -1 5 5.
Gene expression was quantified using featureCount v1.5.3 with GENCODE gene annotation (Release M12).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw gene count of RNA-seq samples.
|
| |
|
| Submission date |
Feb 11, 2019 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Gang Li |
| E-mail(s) |
gangli@um.edu.mo
|
| Organization name |
University of Macau
|
| Department |
Faculty of Health Sciences
|
| Lab |
Gang Li's Lab
|
| Street address |
Avenida da Universidade, Taipa
|
| City |
Macau |
| ZIP/Postal code |
999078 |
| Country |
Macau |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE126370 |
Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation [RNA-seq] |
| GSE126371 |
Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation |
|
| Relations |
| BioSample |
SAMN10909722 |
| SRA |
SRX5358401 |
