|
| Status |
Public on Jun 21, 2024 |
| Title |
Quadriceps muscle, COM01 |
| Sample type |
SRA |
| |
|
| Source name |
quadriceps muscle
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Fbxw7 flox/flox
tissue: quadriceps muscle
|
| Treatment protocol |
Mouse quadriceps muscles were harvested and immediately frozen into liquid nitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from powdered quadriceps muscles using Eastep Super Total RNA Extraction Kit (Promega, LS1040) following the manufacturer’s instructions.Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Total RNAs were extracted from powdered quadriceps muscles using Eastep Super Total RNA Extraction Kit (Promega, LS1040) following the manufacturer’s instructions.RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| Data processing |
Quality controlled was done by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA
Fold change and p-value were calculated based on FPKM
Genome_build: MM10
Supplementary_files_format_and_content: Excel file includes read counts for each sample
|
| |
|
| Submission date |
Nov 16, 2019 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Xuelian Xiong |
| E-mail(s) |
xiong.xuelian@zs-hospital.sh.cn
|
| Organization name |
Department of Endocrinology and Metabolism
|
| Department |
Zhongshan Hospital, Fudan University
|
| Street address |
NO. 180, Fenglin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE140503 |
FBXW7 coordinates postprandial muscle glucose metabolism and maintenance of skeletal muscle mass |
|
| Relations |
| BioSample |
SAMN13295233 |
| SRA |
SRX7158672 |
