|
| Status |
Public on Nov 05, 2020 |
| Title |
TA_WT_1 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Tibialis Anterior (TA) muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
genotype: WT
age: 1 month
tissue: Tibialis Anterior (TA) muscle
|
| Growth protocol |
Animals were housed in a 12 h light/dark cycle in a temperature-controlled room in the Animal Research Center of UT Southwestern, with ad libitum access to water and food.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized and TA muscles from WT and D51 mice were dissected. RNA was extracted using the RNeasy mini kit (QIAGEN, 74104) according to the manufacturer's protocol.
Stranded mRNA-Seq libraries were generated using the KAPA mRNA HyperPrep Kit (Roche, KK8580) following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
biological replicate 1
|
| Data processing |
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
Sequencing reads were aligned to mouse GRCm38 (mm10) reference genome using HiSTAT2 (Version 2.0.4) with default settings and --rna-strandness F.
Aligned reads were counted using featurecount (Version 1.6.0) per gene ID.
Differential gene expression analysis was performed with the R package edgeR (Version 3.30.1) using the GLM approach. For each comparison, genes with more than 1 CPM (Count Per Million) in at least three samples were considered as expressed and were used for calculating normalization factor. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.01 were used to select differentially expressed genes between sample group comparisons. Normalized gene CPM values were used to calculate RPKM (Reads Per Kilobase per Million mapped reads) values, which were then used for heatmap plotting.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw count values and RPKM values for each sample, and differential expression analysis results from edgeR.
|
| |
|
| Submission date |
Aug 19, 2020 |
| Last update date |
Nov 05, 2020 |
| Contact name |
Zhaoning Wang |
| E-mail(s) |
zhw063@health.ucsd.edu
|
| Organization name |
UC San Diego
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Bing Ren Lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE156496 |
Transcriptome analysis of the TA muscles from WT and Dmd Exon 51 Knockout mice |
| GSE156498 |
Degenerative and Regenerative Pathways Underlying Duchenne Muscular Dystrophy Revealed by Single-nucleus RNA sequencing |
|
| Relations |
| BioSample |
SAMN15858609 |
| SRA |
SRX8971967 |
