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| Status |
Public on Mar 12, 2021 |
| Title |
Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.
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| Overall design |
Profiling of C2C12 myoblasts and differentiated C2C12 by short and long-read single-cell RNA-seq as well as single-cell ATAC-seq.
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| |
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| Contributor(s) |
Rebboah E, Reese F, Mortazavi SA |
| Citation(s) |
34620214 |
| |
| Submission date |
Mar 11, 2021 |
| Last update date |
Oct 14, 2021 |
| Contact name |
Elisabeth Rebboah |
| E-mail(s) |
erebboah@uci.edu
|
| Organization name |
University of California, Irvine
|
| Department |
Developmental and Cell Biology
|
| Lab |
Mortazavi Lab
|
| Street address |
2300E Biological Sciences 3
|
| City |
Irvine |
| State/province |
California |
| ZIP/Postal code |
92617 |
| Country |
USA |
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| Platforms (2) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA713904 |
| SRA |
SRP310332 |
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