OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
Abstract
FISH enables researchers to visualize the subcellular distribution of RNA and DNA molecules in individual cells. The recent development of FISH methods employing probes composed of synthetic DNA oligonucleotides (oligos) allows researchers to tightly control aspects of probe design such as binding energy and genomic specificity. Although oligo FISH probes are central to many recently developed massively multiplexed and superresolution imaging methods, no dedicated computational utility exists to facilitate the design of such probes on the genome-wide scale. Here, we introduce a streamlined pipeline for the rapid, genome-scale design of oligo FISH probes and validate our approach by using conventional and superresolution imaging. Our method provides a framework with which to design oligo-based hybridization experiments.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Feb 20, 2018
- Source ID
- 10.1073/pnas.1714530115
Entities
People
- Brian J Beliveau
- Chao-Ting Wu
- Guy Nir
- Hiroshi M. Sasaki
- Jocelyn Y. Kishi
- Peng Yin
- Sinem K Saka
- Son C. Nguyen
Organizations
- Damon Runyon Cancer Research Foundation
- European Molecular Biology Organization
- Harvard Medical School
- Harvard University
- Human Frontier Science Program
- National Institutes of Health
- National Science Board
- Office of Naval Research
- Office of Naval Research Global
- Uehara Memorial Foundation