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| Status |
Public on Oct 11, 2022 |
| Title |
Spatial transcriptomics tools allow for regional exploration of heterogeneous muscle pathology in the pre-clinical rabbit model of rotator cuff tear |
| Organism |
Oryctolagus cuniculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Conditions affecting skeletal muscle, such as chronic rotator cuff tears, low back pain, dystrophies, and many others often share changes in muscle phenotype: intramuscular adipose and fibrotic tissue increase while contractile tissue is lost. The underlying changes in cell populations and cell ratios observed with these phenotypic changes complicate the interpretation of tissue-level transcriptional data. Novel single cell transcriptomics has limited capacity to address this problem because muscle fibers are too long to be engulfed in single cell droplets and single nuclei transcriptomics are complicated by muscle fibers’ multinucleation. Therefore, the goal of this project was to evaluate the potential and challenges of a spatial transcriptomics technology to add dimensionality to transcriptional data in an attempt to better understand regional cellular activity in heterogeneous skeletal muscle tissue.
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| Overall design |
Fresh and 6 years old snapfrozen healthy and tenotomized rabbit supraspinatus muscle sections were mounted on 10x Visium slides
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| Web link |
https://josr-online.biomedcentral.com/articles/10.1186/s13018-022-03326-8
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| Contributor(s) |
Ruoss S, Esparza MC, Vasquez-Bolanos LS, Nasamran CA, Fisch KM, Engler AJ, Ward SR |
| Citation(s) |
36195913 |
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| Submission date |
Aug 08, 2022 |
| Last update date |
Oct 14, 2022 |
| Contact name |
Samuel Richard Ward |
| E-mail(s) |
srward@ucsd.edu
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| Phone |
8585344918
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| Organization name |
University of California San Diego
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| Department |
Orthopaedic Surgery, Radiology, and Bioengineering
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| Lab |
Muscle Physiology
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| Street address |
9500 Gilman Drive (0863)
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL26786 |
Illumina NovaSeq 6000 (Oryctolagus cuniculus) |
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| Samples (4)
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| GSM6436954 |
6L: muscle, 2 weeks tenotomy, stored 6 years |
| GSM6436955 |
14L: muscle, 16 weeks tenotomy, stored 6 years |
| GSM6436956 |
14R: muscle, healthy, stored 6 years |
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| Relations |
| BioProject |
PRJNA867403 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE210773_RAW.tar |
157.9 Mb |
(http)(custom) |
TAR (of JPG, JSON, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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