|
| Status |
Public on Oct 11, 2022 |
| Title |
6L: muscle, 2 weeks tenotomy, stored 6 years |
| Sample type |
SRA |
| |
|
| Source name |
M. supraspinatus
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
tissue: M. supraspinatus
treatment: Harvested and snapfrozen at 2w after tenotomy
|
| Treatment protocol |
snapfrozen in liquid nitrogen-cooled isopentane and stored at -80°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Permeabilization protocol by 10x Genomics CG000238 Rev E. 18 min incubation time.
10x Genomics Protocol CG000239 Rev E
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics Visium
|
| Data processing |
Space Ranger 1.2.0
Loupe Browser v.6.0.0
Ensembl release 104 (Oryctolagus_cuniculus.OryCun2.0.104.chr.gtf)
Assembly: OryCun2.0 (Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa
Supplementary files format and content: tsv: barcodes, features
Supplementary files format and content: mtx: matrix
Supplementary files format and content: jpg: H&E staining
Supplementary files format and content: json: spot pixel coordinates
|
| |
|
| Submission date |
Aug 08, 2022 |
| Last update date |
Oct 13, 2022 |
| 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 |
GPL26786 |
| Series (1) |
| GSE210773 |
Spatial transcriptomics tools allow for regional exploration of heterogeneous muscle pathology in the pre-clinical rabbit model of rotator cuff tear |
|
| Relations |
| BioSample |
SAMN30197908 |
| SRA |
SRX16984429 |
