2020 Jun 1 - Nature Webcast: Automated quantification of RNA transcripts using dot-counting software “dotdotdot”
Kristen Maynard, Ph.D.,
Research Scientist, Lieber Institute for Brain Development
Watch Video:
Madhavi Tippani, MS,
Research Associate, Lieber Institute for Brain Development
Mohammed Qutaish, Ph.D.,
Senior Image Analysis Scientist, Advanced Cell Diagnostics

Multiplex single-molecule fluorescent in situ hybridization (smFISH) using RNAscope technology is a powerful tool for validating RNA-sequencing and emerging spatial transcriptomic data. But quantification remains a computational challenge. This webcast will present a framework for generating and analyzing smFISH data in complex tissues such as the brain while overcoming confounds associated with autofluorescence.

The speakers developed dotdotdot as an automated software package to quantify RNA transcripts in single nuclei. They will demonstrate the platform’s robustness in quantifying differential and spacial expression of activity-regulated genes, and apply machine learning to predict cell types and perform cell type-specific expression analysis.

This webcast will help you:

  • Acquire multiplex smFISH data in complex tissues
  • Quantify RNA transcripts in single cells from smFISH data
  • Apply computational strategies for analyzing and interpreting smFISH data
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