|
| Status |
Public on Jul 31, 2024 |
| Title |
Cpt2_PKO_1 |
| Sample type |
SRA |
| |
|
| Source name |
Muscle stem cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6NJ
genotype/variation: Cpt2PKO
age: 2 months
cell type: Hind limb muscle stem cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA from 1 ug of total RNA is enriched using oligo(dT) beads for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA
Cpt2_PKOvsWT_DEG.xlsx
|
| Data processing |
The original raw data from Illumina HiSeq are transformed to sequenced reads by base calling.
Raw reads are filtered to remove reads containing adapters or reads of low quality, then mapped to GRCm38/mm10 whole genome using TopHat2.
For the quantification of gene expression level, HTSeq V0.6.1 was used to analyze the read numbers mapped for each gene. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on the gene read counts mapped to genes or exons.
A differential expression analysis was performed using the DESeq2 R/EdgeR R package with the threshold of significance set as adjusted p < 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Cpt2PKOvsWT_DEG.xlsx: Matrix table with raw gene counts and FPKM for every gene and every sample.
|
| |
|
| Submission date |
Oct 01, 2020 |
| Last update date |
Jul 31, 2024 |
| Contact name |
Shihuan Kuang |
| E-mail(s) |
skuang@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Animal Sciences
|
| Street address |
270 S Russel St
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN16338441 |
| SRA |
SRX9233801 |
