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Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA

Nat Protoc. 2021-02; 
Leslie J Mateo, Nasa Sinnott-Armstrong, Alistair N Boettiger
Products/Services Used Details Operation
Custom DNA/RNA Oligos The Oligopaint library from Twist Biosciences or Genscript typically ships at 30–100-ng/μl final concentration and should be stored at −20 °C Get A Quote

摘要

Chromatin conformation capture (3C) methods and fluorescent in situ hybridization (FISH) microscopy have been used to investigate the spatial organization of the genome. Although powerful, both techniques have limitations. Hi-C is challenging for low cell numbers and requires very deep sequencing to achieve its high resolution. In contrast, FISH can be done on small cell numbers and capture rare cell populations, but typically targets pairs of loci at a lower resolution. Here we detail a protocol for optical reconstruction of chromatin architecture (ORCA), a microscopy approach to trace the 3D DNA path within the nuclei of fixed tissues and cultured cells with a genomic resolution as fine as 2 kb and a throughp... More

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