Article ; Online: Cost-Efficient Transcriptomic-Based Drug Screening.
Journal of visualized experiments : JoVE
2024 , Issue 204
Abstract: Transcriptomics allows to obtain comprehensive insights into cellular programs and their responses to perturbations. Despite a significant decrease in the costs of library production and sequencing in the last decade, applying these technologies at the ... ...
Abstract | Transcriptomics allows to obtain comprehensive insights into cellular programs and their responses to perturbations. Despite a significant decrease in the costs of library production and sequencing in the last decade, applying these technologies at the scale necessary for drug screening remains prohibitively expensive, obstructing the immense potential of these methods. Our study presents a cost-effective system for transcriptome-based drug screening, combining miniaturized perturbation cultures with mini-bulk transcriptomics. The optimized mini-bulk protocol provides informative biological signals at cost-effective sequencing depth, enabling extensive screening of known drugs and new molecules. Depending on the chosen treatment and incubation time, this protocol will result in sequencing libraries within approximately 2 days. Due to several stopping points within this protocol, the library preparation, as well as the sequencing, can be performed time-independently. Processing simultaneously a high number of samples is possible; measurement of up to 384 samples was tested without loss of data quality. There are also no known limitations to the number of conditions and/or drugs, despite considering variability in optimal drug incubation times. |
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MeSH term(s) | Transcriptome ; Drug Evaluation, Preclinical ; Gene Expression Profiling ; Gene Library ; Costs and Cost Analysis |
Language | English |
Publishing date | 2024-02-23 |
Publishing country | United States |
Document type | Journal Article ; Video-Audio Media |
ZDB-ID | 2259946-0 |
ISSN | 1940-087X ; 1940-087X |
ISSN (online) | 1940-087X |
ISSN | 1940-087X |
DOI | 10.3791/65930 |
Database | MEDical Literature Analysis and Retrieval System OnLINE |
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