|
Status |
Public on Feb 26, 2024 |
Title |
D17-20.Biopsy_127 |
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:Intermediate
|
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 |
SAMN37361786 |
SRA |
SRX21758732 |