Bioinformatically designed complex oligonucleotide probe sets for FISH

Welcome to the Oligopaints website, with all datasets of genomic targets newly updated with Oligominer (Beliveau, et al. 2018)! Here, you will find database files listing the genomic locations of Oligopaints probes in the C. elegans (ce6 and ce11), Drosophila melanogaster (dm3 and dm6), Arabidopsis (tair10), Mouse (mm9 and mm10), Zebrafish (danRer10) and Human (hg19, hg38, and hg38U) genomes. The Oligominer scripts are available through Github (, with our previous  suite of python scripts and the accompanying guide still here on this website. Finally, there are protocols to guide you through the synthesis of an Oligopaints probe set once you have designed and ordered your oligo library. Check back periodically for database and protocol updates. Happy FISHing!!

Our publications describing/using Oligopaint technologies
(Including HOPs, OligoSTORM, OligoDNA-PAINT)

Beliveau, BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu C-t, and Yin P. OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proc. Nat. Acad. Sci. USA 2018 115:E2183-E2192. PMID: 29463736. PMCID: PMC5877937.

Beliveau BJ, Boettiger AN, Nir G, Bintu B, Yin P, Zhuang X, Wu C-t. In situ super-resolution imaging of genomic DNA with OligoSTORM and OligoDNA-PAINT. Methods Mol Biol 2017 1663:231-252. PMID 28924672.

Wang S, Su J-H, Beliveau BJ, Bintu B, Moffitt JR, Wu C-t, Zhuang X. Spatial organization of chromatin domains and compartments in single chromosomes. Science 2016 353:598-602. doi: 10.1126/science.aaf8084. Epub 2016 Jul 21.

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu C-t, Zhuang X. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature. 2016 529:418-22. doi: 10.1038/nature16496. PMID: 26760202.

Schmidt T, Beliveau B, Uca Y, Theilmann M, Da Cruz F, Wu C-t, Shih W. Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries. Nat Commun 2015 Nov 16;6:8634. doi: 10.1038/ncomms9634. PMID: 26567534 PMCID: PMC4660042.

Murgha Y, Beliveau B, Semrau K, Schwartz D, Wu C-t, Gulari E, Rouillard J-M. Combined in vitro transcription and reverse transcription method to amplify and label complex synthetic oligonucleotide probe libraries. Biotechniques 2015 58:301-7 PMID: 26054766.

Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu C-t. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun 2015 6:7147 doi: 10.1038/ncomms8147. PMID: 25962338 PMCID: PMC4430122.

Beliveau BJ, Apostolopoulos N, Wu C-t. Visualizing genomes with Oligopaint FISH probes. Curr Protocols Mol Biol 2014 14.23. PMID: 24510436 PMCID: PMC3928790.

Beliveau BJ, Joyce ER, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard J-M, Wu, C-t. A versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc. Nat. Acad. Sci. USA 2012 109:21301-6. PMID: 23236188; PMCID: PMC3535588.