About the speaker:
Johan Henriksson is an associate professor at the Umeå university, department of Molecular biology. Starting out as a mechanical engineer, he did a PhD in biology at Karolinska Institutet, working on gene regulation during C.elegans embryogenesis. Seeing how progress in biology is effectively driven by technology, he continued with a postdoc at Sanger institute, developing tools for single-cell analysis and CRISPR screening. This led to the recruitment to MIMS at Umeå university, where he has further improved these technologies with one goal in mind: what more experiments are needed before we can consider ourselves done with biology?
Abstract:
How do we most efficiently map gene regulation using modern molecular biology? This talk will cover two popular tools with the aim of uncovering the technical challenges that are seldom mentioned: For CRISPR screening, the common statistical assumptions commonly break down, resulting in biases to be aware of when interpreting this type of data. These assumptions can however be fixed by using an alternative to PCR: the molecular inversion probe. The lessons learned are of relevance also for interpreting other advanced high-throughput sequencing protocols. This analysis will be followed by a case study of multiome RNA+ATACseq single-cell data. It will be shown how these modalities represent two different cell state spaces, questioning the current trend of batch integrating separately produced scRNA-seq and scATAC-seq datasets. All-in-all, modern tools present plenty of challenges and opportunities for those interested in efficiently dissecting gene regulation!