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| Status |
Public on Dec 02, 2020 |
| Title |
Spatial RNA sequencing of regenerating mouse hindlimb muscle |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report a series of spatial transcriptomics datasets of regenerating mouse muscle tissue generated with the 10x Genomics Visium platform.
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| Overall design |
Tibialis anterior muscles were injected with notexin and collected two, five, and seven days post-injury. Samples were frozen in OCT. 10 micron tissue sections were assayed using the Visium Spatial Gene Expression Kit (v1). To improve resolution, each spot within the Visium slide was deconvolved using a matched single-cell RNA sequencing reference and BayesPrism (https://github.com/Danko-Lab/TED). Cell type fractions for each spot are included in the metadata files.
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| Contributor(s) |
McKellar DW, Cosgrove BD, De Vlaminck I |
| Citation(s) |
34773081 |
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| Submission date |
Nov 12, 2020 |
| Last update date |
Dec 02, 2021 |
| Contact name |
David William McKellar |
| E-mail(s) |
[email protected]
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| Organization name |
Cornell University
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| Department |
Biomedical Engineering
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| Street address |
237 Tower Rd
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA677872 |
| SRA |
SRP292288 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE161318_RAW.tar |
2.5 Gb |
(http)(custom) |
TAR (of CSV, JSON, TAR, TIFF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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