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| Status |
Public on Nov 27, 2023 |
| Title |
Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles [scRNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Accurate detection and quantification of mRNA isoforms from nanopore long-read sequencing remains challenged by technical noise, particularly in single cells. To address this, we introduce Isosceles, a computational toolkit that outperforms other methods in isoform detection sensitivity and quantification accuracy across single-cell, pseudo-bulk and bulk resolution levels, as demonstrated using synthetic and biologically-derived datasets. Isosceles improves the fidelity of single-cell transcriptome quantification at the isoform-level, and enables flexible downstream analysis. As a case study, we apply Isosceles, uncovering coordinated splicing within and between neuronal differentiation lineages. Isosceles is suitable to be applied in diverse biological systems, facilitating studies of cellular heterogeneity across biomedical research applications.
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| Overall design |
scRNA-seq sequencing of a mix of three ovarian cancer cell lines using PromethION and Illumina platforms used for benchmarking the Isosceles package.
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| Contributor(s) |
Kabza M, Ritter A, Byrne A, Sereti K, Le D, Stephenson W, Sterne-Weiler T |
| Citation(s) |
39183289 |
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| Submission date |
Nov 17, 2023 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Tim Sterne-Weiler |
| Organization name |
Genentech
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| Department |
Oncology Bioinformatics
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| Street address |
1 DNA Way
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platforms (2) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL26167 |
PromethION (Homo sapiens) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE248118 |
Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles |
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| Relations |
| BioProject |
PRJNA1041796 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE248115_RAW.tar |
35.5 Mb |
(http)(custom) |
TAR (of CSV, MTX) |
| GSE248115_transcript_annotations.csv.gz |
3.5 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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