PaintSHOP

PaintSHOP designs oligonucleotide probe sets for fluorescent in situ hybridization (FISH) to enable transcriptome- and genome-scale spatial visualization of nucleic acids.

Key Features:

• Transcriptome- and genome-scale probe design: Designs oligonucleotide probes for transcriptome- and genome-scale FISH experiments.
• Integration of additional sequences: Incorporates additional sequences such as primer pairs into probe designs.
• Machine learning-based specificity prediction: Uses a machine learning model to quantitatively predict probe specificity across the genome and minimize off-target hybridization.
• Ready-to-order probe set generation: Produces finalized oligonucleotide sequences suitable for synthesis and ordering.

Scientific Applications:

• Three-dimensional genome organization: Enables design of probes for super-resolution imaging of 3D chromatin architecture.
• Spatial gene expression profiling: Enables visualization of spatial patterns of gene expression in individual cells using FISH.
• Chromatin organization and gene regulation studies: Supports investigation of chromatin organization and its implications for gene regulation.
• Cellular heterogeneity analysis: Supports examination of cellular heterogeneity through spatially resolved transcriptomic probes.

Methodology:

Users provide experimental targets; PaintSHOP identifies optimal probes, incorporates additional sequences (e.g., primer pairs), and applies a machine learning model to quantitatively predict probe specificity across the genome.