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3 ARTICLES PUBLISHED IN JoVE

Biology

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

R. Scott McIsaac^1,2, Sanford J. Silverman¹, Lance Parsons¹, Ping Xu¹, Ryan Briehof¹, Megan N. McClean¹, David Botstein^1,3

¹The Lewis-Sigler Institute for Integrative Genomics, Princeton University, ²Graduate Program in Quantitative and Computational Biology, Princeton University, ³Department of Molecular Biology, Princeton University

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

JoVE Journal

Rapid Synthesis and Screening of Chemically Activated Transcription Factors with GFP-based Reporters

R. Scott McIsaac^*1,3, Benjamin L. Oakes^*1, David Botstein^1,2, Marcus B. Noyes¹

¹The Lewis-Sigler Institute for Integrative Genomics, Princeton University, ²Department of Molecular Biology, Princeton University, ³Division of Chemistry and Chemical Engineering, California Institute of Technology

This protocol describes an experimental procedure for the rapid construction of artificial transcription factors (ATFs) with cognate GFP reporters and quantification of the ATFs ability to stimulate GFP expression via flow cytometry.

Biology

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Henrik D. Møller¹, Rasmus K. Bojsen², Chris Tachibana³, Lance Parsons⁴, David Botstein⁵, Birgitte Regenberg¹

¹Department of Biology, University of Copenhagen, ²National Veterinary Institute, Technical University of Denmark, ³Group Health Research Institute, ⁴Lewis-Sigler Institute for Integrative Genomics, Princeton University, ⁵Calico Life Sciences LLC

This paper presents a sensitive method called Circle-Seq for purifying extrachromosomal circular DNA (eccDNA). The method encompasses column purification, removal of remaining linear chromosomal DNA, rolling-circle amplification and high-throughput sequencing. Circle-Seq is applicable to genome-scale screening of eukaryotic eccDNA and studying genome instability and copy-number variation.