GEO series

Single-cell Total-RNA Profiling Unveils Regulatory Hubs of Transcription Factors

GSE202126 Mus musculus; Homo sapiens Expression profiling by high throughput sequencing 1089 samples Submitted 2024/05/19 Platform GPL18573Platform GPL19057

Summary

Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from unspliced RNA to spliced RNA (i.e., mature RNA) to degradation. To feed this kinetic analysis, simultaneous measurement of unspliced RNA and spliced RNA in single cells is greatly desired. However, the majority of single-cell RNA-seq chemistry only captures mature RNA species to measure gene expressions. Here, we develop a one-step total-RNA chemistry-based scRNA-seq method: snapTotal-seq. We benchmarked this method with multiple single-cell RNA-seq assays in their performance in kinetic analysis of cell cycle by RNA velocity. Next, with LASSO regression between transcription factors, we identified the critical regulatory hubs mediating the cell cycle dynamics. We also applied snapTotal-seq to profile the oncogene-induced senescence and identified the key regulatory hubs governing the entry of senescence. Furthermore, from the comparative analysis of unspliced RNA and spliced RNA, we identified a significant portion of genes whose expression changes occurred in spliced RNA but not to the same degree in unspliced RNA, indicating these gene expression changes are mainly controlled by post-transcriptional regulation. Overall, we demonstrate that snapTotal-seq can provide enriched information about gene regulation, especially during the transition between cell states.

Published in

Single-cell total-RNA profiling unveils regulatory hubs of transcription factors

Niu Y, Luo J, Zong C · Nature communications 2024 · PMID 39009595 · doi:10.1038/s41467-024-50291-3

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Direct links to NCBI, no account and no request form: the whole study as GSE202126_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 1089 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA834766 and SRA study SRP373434. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39009595) ↗

Study design

40 × HEK293T_A

Supports a between-group comparison across 40 samples.

1 replicated groups read from the first 40 of 1089 sample titles; they account for 40 of them. Check it against the sample list below before relying on it.

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