|
| Status |
Public on Feb 26, 2024 |
| Title |
D17-20.Biopsy_125 |
| Sample type |
SRA |
| |
|
| Source name |
Muscle
|
| Organism |
Canis lupus |
| Characteristics |
tissue: Muscle
cell line: all cell types in muscle
cell type: all cell types in muscle
treatment: No treatment (default healing)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from tissues using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254).
One hundred nanograms of total RNA was used to prepare sequencing libraries using the LM-Seq (Ligation Mediated Sequencing) protocol (Hou, Z. et al. A cost-effective RNA sequencing protocol for large-scale gene expression studies. Sci Rep 5, 9570 (2015).)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Post-injury Day:42Wound Zone:Center
|
| Data processing |
FASTQ files were generated by CASAVA (v1.8.2).
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
TPMs were median-by-ratio normalized
Assembly: CanFam3.1
Supplementary files format and content: ExpectedCounts.txt.gz: Text file, mapping read counts
Supplementary files format and content: MedianNorm_TPMs.txt.gz: text file, normalized TPM values
|
| |
|
| Submission date |
Sep 12, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Peng Jiang |
| E-mail(s) |
p.jiang@csuohio.edu
|
| Organization name |
Cleveland State University
|
| Street address |
2121 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44115 |
| Country |
USA |
| |
|
| Platform ID |
GPL33062 |
| Series (1) |
| GSE242973 |
Unraveling the Complex Relationship Between mRNA and Protein Abundance: A Machine Learning-Based Approach for Imputing Protein Levels from RNA-seq Data |
|
| Relations |
| BioSample |
SAMN37361788 |
| SRA |
SRX21758730 |
