Designing Oligonucleotide-Based FISH Probe Sets with PaintSHOP.
Chromatin
Chromosomes
Cytogenetics
FISH
Oligonucleotide
Spatial genomics
Spatial transcriptomics
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2024
2024
Historique:
medline:
19
3
2024
pubmed:
19
3
2024
entrez:
19
3
2024
Statut:
ppublish
Résumé
Fluorescent in situ hybridization (FISH) enables the visualization of the position and abundance of nucleic acid molecules in fixed cell and tissue samples. Many FISH-based methods employ sets of synthetic, computationally designed DNA oligonucleotide (oligo) FISH probes, including massively multiplexed imaging spatial transcriptomics and spatial genomics technologies. Oligo probes can either be designed de novo or accessed from an existing database of pre-discovered probe sequences. This chapter describes the use of PaintSHOP, a user-friendly, web-based platform for the design of sets of oligo-based FISH probes. PaintSHOP hosts large collections of pre-discovered probes from many model organisms and also provides collections of functional sequences such as primers and readout domains and interactive tools to add these functional sequences to selected probes. Detailed examples are provided for three common experimental scenarios.
Identifiants
pubmed: 38502486
doi: 10.1007/978-1-0716-3766-1_12
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
177-189Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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