sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing.
Fuente:
PubMed
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Artículo científico |
| Language: | en |
| Published: |
bioRxiv : the preprint server for biology
2024
|
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1868266260606746625 |
|---|---|
| author | Dehghannasiri, Roozbeh Kokot, Marek Starr, Alexander L Maziarz, Jamie Gordon, Tal Tan, Serena Y Wang, Peter L Voskoboynik, Ayelet Musser, Jacob M Deorowicz, Sebastian Salzman, Julia |
| author_facet | Dehghannasiri, Roozbeh Kokot, Marek Starr, Alexander L Maziarz, Jamie Gordon, Tal Tan, Serena Y Wang, Peter L Voskoboynik, Ayelet Musser, Jacob M Deorowicz, Sebastian Salzman, Julia Dehghannasiri, Roozbeh Kokot, Marek Starr, Alexander L Maziarz, Jamie Gordon, Tal Tan, Serena Y Wang, Peter L Voskoboynik, Ayelet Musser, Jacob M Deorowicz, Sebastian Salzman, Julia |
| collection | PubMed - marine biology |
| contents | sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing. Dehghannasiri, Roozbeh Kokot, Marek Starr, Alexander L Maziarz, Jamie Gordon, Tal Tan, Serena Y Wang, Peter L Voskoboynik, Ayelet Musser, Jacob M Deorowicz, Sebastian Salzman, Julia Typical high-throughput single-cell RNA-sequencing (scRNA-seq) analyses are primarily conducted by (pseudo)alignment, through the lens of annotated gene models, and aimed at detecting differential gene expression. This misses diversity generated by other mechanisms that diversify the transcriptome such as splicing and V(D)J recombination, and is blind to sequences missing from imperfect reference genomes. Here, we present sc-SPLASH, a highly efficient pipeline that extends our SPLASH framework for statistics-first, reference-free discovery to barcoded scRNA-seq (10x Chromium) and spatial transcriptomics (10x Visium); we also provide its optimized module for preprocessing and -mer counting in barcoded data, BKC, as a standalone tool. sc-SPLASH rediscovers known biology including V(D)J recombination and cell-type-specific alternative splicing in human and trans-splicing in tunicate () and when applied to spatial datasets, detects sequence variation including tumor-specific somatic mutation. In sponge () and tunicate (), we uncover secreted repeat proteins expressed in immune-type cells and regulated during development; the sponge genes were absent from the reference assembly. sc-SPLASH provides a powerful alternative tool for exploring transcriptomes that is applicable to the breadth of life's diversity. |
| format | Artículo científico |
| id | pubmed_39763839 |
| institution | PubMed |
| language | en |
| publishDate | 2024 |
| publisher | bioRxiv : the preprint server for biology |
| record_format | pubmed |
| spellingShingle | sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing. Dehghannasiri, Roozbeh Kokot, Marek Starr, Alexander L Maziarz, Jamie Gordon, Tal Tan, Serena Y Wang, Peter L Voskoboynik, Ayelet Musser, Jacob M Deorowicz, Sebastian Salzman, Julia sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing. Dehghannasiri, Roozbeh Kokot, Marek Starr, Alexander L Maziarz, Jamie Gordon, Tal Tan, Serena Y Wang, Peter L Voskoboynik, Ayelet Musser, Jacob M Deorowicz, Sebastian Salzman, Julia Typical high-throughput single-cell RNA-sequencing (scRNA-seq) analyses are primarily conducted by (pseudo)alignment, through the lens of annotated gene models, and aimed at detecting differential gene expression. This misses diversity generated by other mechanisms that diversify the transcriptome such as splicing and V(D)J recombination, and is blind to sequences missing from imperfect reference genomes. Here, we present sc-SPLASH, a highly efficient pipeline that extends our SPLASH framework for statistics-first, reference-free discovery to barcoded scRNA-seq (10x Chromium) and spatial transcriptomics (10x Visium); we also provide its optimized module for preprocessing and -mer counting in barcoded data, BKC, as a standalone tool. sc-SPLASH rediscovers known biology including V(D)J recombination and cell-type-specific alternative splicing in human and trans-splicing in tunicate () and when applied to spatial datasets, detects sequence variation including tumor-specific somatic mutation. In sponge () and tunicate (), we uncover secreted repeat proteins expressed in immune-type cells and regulated during development; the sponge genes were absent from the reference assembly. sc-SPLASH provides a powerful alternative tool for exploring transcriptomes that is applicable to the breadth of life's diversity. |
| title | sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing. |
| url | https://pubmed.ncbi.nlm.nih.gov/39763839/ |