A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

Magda Bienko; Nicola Crosetto; Leonid Teytelman; Sandy Klemm; Shalev Itzkovitz; Alexander van Oudenaarden

doi:10.1038/nmeth.2306

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

Nat Methods. 2013 Feb;10(2):122-124. doi: 10.1038/nmeth.2306. Epub 2012 Dec 23.

Authors

Magda Bienko^#¹, Nicola Crosetto^#¹, Leonid Teytelman¹, Sandy Klemm², Shalev Itzkovitz¹, Alexander van Oudenaarden^{1

3}

Affiliations

¹ Departments of Physics and Biology, and the Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
² Departments of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
³ Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlandss.

^# Contributed equally.

Abstract

We developed a cost-effective genome-scale PCR-based method for high-definition DNA FISH (HD-FISH). We visualized gene loci with diffraction-limited resolution, chromosomes as spot clusters and single genes together with transcripts by combining HD-FISH with single-molecule RNA FISH. We provide a database of over 4.3 million primer pairs targeting the human and mouse genomes that is readily usable for rapid and flexible generation of probes.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
DNA Primers*
Genomic Library*
Humans
In Situ Hybridization, Fluorescence / methods*
Mice
Polymerase Chain Reaction
Sequence Analysis, DNA / methods*

Substances

DNA Primers

Abstract

Publication types

MeSH terms

Substances

Grants and funding