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| Status |
Public on Oct 16, 2023 |
| Title |
Common Mitochondrial Deletions in RNA-Seq: Evaluation of Bulk, Single-Cell and Spatial Transcriptomic Datasets |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
To investigate whether large mitochondrial DNA (mtDNA) deletions can be quantified and detected using the high-throughput bioinformatics tool Splice-Break (https://github.com/brookehjelm/Splice-Break2).
This dataset contains 8 human middle temporal gyrus (MTG) samples (from 4 patients) that underwent spatial transcriptomic RNA-Sequencing following 10x Genomics visium protocols as well as 2 samples (from spatial transcriptomics patient 144107/144108) that underwent bulk RNA-Sequencing (one with a ribosomal depletion library preparation and one without).
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| |
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| Overall design |
10x Visium spatial transcriptomics profiles of middle temporal gyrus tissue taken from 4 patient samples (two tissue sections of each), consisting of 2 controls, 1 Alzheimer's Disease (AD), and 1 Parkinson's Disease (PD). Bulk RNA-Sequencing of one patient with no neurodegenerative diagnosis was included for methods comparison.
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| Web link |
https://pubmed.ncbi.nlm.nih.gov/38368460/
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| |
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| Contributor(s) |
Omidsalar AA, Hjelm BE |
| Citation(s) |
38368460 |
| |
| Submission date |
Mar 05, 2023 |
| Last update date |
Mar 05, 2024 |
| Contact name |
Brooke Hjelm |
| E-mail(s) |
bhjelm@usc.edu
|
| Organization name |
USC
|
| Department |
Translational Genomics
|
| Street address |
1450 Biggy Street
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA941074 |
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