Jul 6, 2020

PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments

BioRxiv : the Preprint Server for Biology
E. A. HershbergBrian J Beliveau

Abstract

Fluorescent 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. These methods 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. While considerable progress has been made in developing new molecular methods that harness complex oligo libraries for FISH, there are few existing computational tools to support the bioinformatics workflows necessary to carry out these experiments. Here, we introduce Paint Server and Homology Optimization Pipeline (PaintSHOP), an interactive platform for the reproducible 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 standardized files documenting the design of their libraries. Our platform integrates a machine learning model that quantitatively predicts probe specificity on the genome scale into a dynamic ...Continue Reading

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Mentioned in this Paper

Fish extract
Drug Carriers
In Situ Hybridization
Fluorescent in Situ Hybridization
Nucleic Acids
Positioning Attribute
Oligonucleotides
cDNA Library
Bio-Informatics
Probes

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