|
| Status |
Public on May 23, 2018 |
| Title |
TS5.026_Inj_RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Day03_VML_Run_MMG
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Lewis rat
injury: VML
run: Run
repair: MMG
timepoint: day 3
tissue: tibialis anterior muscle
|
| Treatment protocol |
while under isoflurane anesthesia a unilateral full-thickness VML injury was created using a 6 mm punch biopsy to the middle third of the TA muscle. On average, the tissue removed from the TA weighed 90.5 ± 3.2 mg.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The muscles were thawed, minced and homogenized (Tissue Ruptor, Qiagen) for 30 seconds at room temperature and total RNA was isolated from the slurry using the miRNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions.
1 μg of isolated total RNA was used to produce cDNA libraries using the Truseq protocol (Illumina), as per the manufacturer’s instructions. Biological replicates or triplicates were produced from each condition and individual libraries were pooled and sequenced using 76 base-pair (bp) paired-end reads on a Hi-Seq. 2500 in high output mode to an average depth of 55 M reads per library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TS5.026_Inj
|
| Data processing |
RNA data was pseudoaligned to the University of California, Santa Cruz, annotated Sus scrofa (pig) genome (build 9.2)
Transcript abundances were quantified using Kallisto with default parameters
R/Bioconductor DESeq 2 was used to calculate differential expression (DE) of transcripts
R was used to analyze expression data for set analysis (GAGE), principal component analysis, and correlation of inter-treatment gene expression
Cound data was log2 transformed, after adding a pseudocount of 0.5 to all measurements
Genome_build: Rattus norvegicus (rat) genome (build 6.0)
Supplementary_files_format_and_content: Excel format worksheet for genes
|
| |
|
| Submission date |
May 22, 2018 |
| Last update date |
May 24, 2018 |
| Contact name |
Darrell Orlyn Ricke |
| E-mail(s) |
Darrell.Ricke@ll.mit.edu
|
| Phone |
1-781-981-8323
|
| Organization name |
MIT Lincoln Laboratory
|
| Department |
Group 48 Bioengineering Systems & Technology
|
| Lab |
Bioinformatics
|
| Street address |
244 Wood Street
|
| City |
Lexington |
| State/province |
MA |
| ZIP/Postal code |
02421-6426 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE114799 |
Multiscale analysis of a regenerative therapy for treatment of volumetric muscle loss injury |
|
| Relations |
| BioSample |
SAMN09239071 |
| SRA |
SRX4116434 |
