|
| Status |
Public on Jul 14, 2021 |
| Title |
Week1_sham WRE1.4R |
| Sample type |
SRA |
| |
|
| Source name |
supraspinatus
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
time post-tenotomy: 1
group: sham
|
| Treatment protocol |
tenotomy, or a sham were performed(cut of the skin)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
muscle was extracted and flash frozen
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Week1_sham
|
| Data processing |
quality control on raw fastq uisng FASTQC
aligned to rabbit genome
read quanitification using RSEM and Ensembl Orycun annotation
edgeR, limma-voom, followed by empirical bayes, TMM applied
design (Tenotomy - Sham)
Genome_build: Orycun2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 23, 2021 |
| Last update date |
Jul 14, 2021 |
| Contact name |
Samuel Richard Ward |
| E-mail(s) |
srward@ucsd.edu
|
| Phone |
8585344918
|
| Organization name |
University of California San Diego
|
| Department |
Orthopaedic Surgery, Radiology, and Bioengineering
|
| Lab |
Muscle Physiology
|
| Street address |
9500 Gilman Drive (0863)
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL25392 |
| Series (1) |
| GSE173234 |
Transcriptional Changes Associated with Acute to Chronic Stage Muscle Adaptations in a Model of Rotator Cuff Tendon Tear |
|
| Relations |
| BioSample |
SAMN18857404 |
| SRA |
SRX10671771 |
