TIRE-seq simplifies transcriptomics via integrated RNA capture and library preparation

O&#39;Keeffe, P; Nouri, Y; Saw, HS; Moore, Z; Baldwin, TM; Olechnowicz, SWZ; Jabbari, JS; Squire, DM; Leslie, S; Wang, C; You, Y; Ritchie, ME; Cross, RS; Jenkins, MR; Audiger, C; Naik, SH; Whittle, JR; Freytag, S; Best, SA; Hickey, PF; Amann-Zalcenstein, D; Bowden, R; Brown, DV

Author(s): O'Keeffe, P; Nouri, Y; Saw, HS; Moore, Z; Baldwin, TM; Olechnowicz, SWZ; Jabbari, JS; Squire, DM; Leslie, S; Wang, C; You, Y; Ritchie, ME; Cross, RS; Jenkins, MR; Audiger, C; Naik, SH; Whittle, JR; Freytag, S; Best, SA; Hickey, PF; Amann-Zalcenstein, D; Bowden, R; Brown, DV;
Details: Publication Year 2025-05-02,Volume 15,Issue #1,Page 15385
Journal Title: Scientific Reports
Publication Type: Research article
Abstract: RNA sequencing (RNA-seq) is widely used in biomedical research, advancing our understanding of gene expression across biological systems. Traditional methods require upstream RNA extraction from biological inputs, adding time and expense to workflows. We developed TIRE-seq (Turbocapture Integrated RNA Expression Sequencing) to address these challenges. TIRE-seq integrates mRNA purification directly into library preparation, eliminating the need for a separate extraction step. This streamlined approach reduces turnaround time, minimizes sample loss, and improves data quality. A comparative study with the widely used Prime-seq protocol demonstrates TIRE-seq's superior sequencing efficiency with crude cell lysates as inputs. TIRE-seq's utility was demonstrated across three biological applications. It captured transcriptional changes in stimulated human T cells, revealing activation-associated gene expression profiles. It also identified key genes driving murine dendritic cell differentiation, providing insights into lineage commitment. Lastly, TIRE-seq analyzed the dose-response and time-course effects of temozolomide on patient-derived neurospheres, identifying differentially expressed genes and enriched pathways linked to the drug's mechanism of action. With its simplified workflow and high sequencing efficiency, TIRE-seq offers a cost-effective solution for large-scale gene expression studies across diverse biological systems.
Publisher: Springer Nature
Keywords: Humans; *Gene Library; Animals; Mice; *Transcriptome; *Gene Expression Profiling/methods; *Sequence Analysis, RNA/methods; High-Throughput Nucleotide Sequencing/methods; T-Lymphocytes/metabolism; *RNA-Seq/methods; Cell Differentiation/genetics; Dendritic Cells/metabolism/cytology; Temozolomide/pharmacology; RNA, Messenger/genetics/isolation & purification; Extraction; High throughput; Rna; Transcriptomics
Department(s): Medical Oncology
Publisher's Version: https://doi.org/10.1038/s41598-025-98282-8
Open Access at Publisher's Site: https://doi.org/10.1038/s41598-025-98282-8
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2025-06-03 03:44:07

Last Modified: 2025-06-03 03:44:24