Dead-Seq: Discovering Synthetic Lethal Interactions from Dead Cells Genomics.

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Version: Final published version
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Serval ID
serval:BIB_F76D5A9A3A60
Type
A part of a book
Publication sub-type
Chapter: chapter ou part
Collection
Publications
Institution
Title
Dead-Seq: Discovering Synthetic Lethal Interactions from Dead Cells Genomics.
Title of the book
Methods in Molecular Biology
Author(s)
Blanco-Fernandez J., Jourdain A.A.
Publisher
Springer
ISSN
1940-6029 (Electronic)
ISSN-L
1064-3745
Publication state
Published
Issued date
2023
Peer-reviewed
Oui
Volume
2661
Pages
329-342
Language
english
Notes
Publication Status: ppublish
Abstract
Pooled genetic screens have revolutionized the field of functional genomics, yet perturbations that decrease fitness, such as those leading to synthetic lethality, have remained difficult to quantify at the genomic level. We and colleagues previously developed "death screening," a protocol based on the purification of dead cells in genetic screens, and used it to identify a set of genes necessary for mitochondrial gene expression, translation, and oxidative phosphorylation (OXPHOS), thus offering new possibilities for the diagnosis of mitochondrial disorders. Here, we describe Dead-Seq, a refined protocol for death screening that is compatible with most pooled screening protocols, including genome-wide CRISPR/Cas9 screening. Dead-Seq converts negative-selection screens into positive-selection screens and generates high-quality data directly from dead cells, at limited sequencing costs.
Keywords
Genomics/methods, Genome, Genetic Testing/methods, CRISPR-Cas Systems, Annexin V, Apoptosis, Auxotrophy, Drop-out screen, Galactose, Genome-wide screening, MACS, Metabolism, Mitochondria, Mitochondrial translation, Necroptosis, ORFeome, RNAi, Synthetic lethality, Systems genetics, sgRNA, shRNA
Pubmed
Open Access
Yes
Funding(s)
Swiss National Science Foundation / 310030_200796
Create date
15/05/2023 12:47
Last modification date
26/05/2023 6:16
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