PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments.
Nat Methods
; 18(8): 937-944, 2021 08.
Article
in En
| MEDLINE
| ID: mdl-34226720
ABSTRACT
Fluorescence in situ hybridization (FISH) allows researchers to visualize the spatial position and quantity of nucleic acids in fixed samples. Recently, considerable progress has been made in developing oligonucleotide (oligo)-based FISH methods that have enabled researchers to study the three-dimensional organization of the genome at super-resolution and visualize the spatial patterns of gene expression for thousands of genes in individual cells. However, there are few existing computational tools to support the bioinformatics workflows necessary to carry out these experiments using oligo FISH probes. Here, we introduce paint server and homology optimization pipeline (PaintSHOP), an interactive platform for the design of oligo FISH experiments. PaintSHOP enables researchers to identify probes for their experimental targets efficiently, to incorporate additional necessary sequences such as primer pairs and to easily generate files documenting library design. PaintSHOP democratizes and standardizes the process of designing complex probe sets for the oligo FISH community.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Repetitive Sequences, Nucleic Acid
/
Oligonucleotide Probes
/
Genome, Human
/
In Situ Hybridization, Fluorescence
/
Computational Biology
/
Chromosome Painting
/
Transcriptome
Limits:
Humans
Language:
En
Journal:
Nat Methods
Journal subject:
TECNICAS E PROCEDIMENTOS DE LABORATORIO
Year:
2021
Type:
Article
Affiliation country:
United States