2023-12-11

Presentation by Marcelo Zossi, Lappalainen Lab

Generation and characterization of a Cas3 reporter in CRISPRi and CRISPRa K562 cells

The apoptopic role in K562 cells is controversial. They study the apoptopic activity of K562 cells in presence of TNF-alpha.

CRISPRa perturbation of TNFR1 increase TNF induced apoptosis, but CRISPRi pertutbation of TNRF1 does not change TNF induced apoptosis.

CRISPRi genome-wide screen.

Identify mechanisms involved in TNF-alpha resistance. Perturn 18000 genes using the CIAPO system. Sort GFP-(non-apoptopic) and GPP+(apoptopic) cells.

The samples were indexed as: - TNF-/GFP- - TNF-/GFP+ - TNF+/GFP- - TNF+/GFP+

Guides recovered from the samples were genotyped using NextSeq.

Statistical analysis target: Compare guides in 4 diffferent samples.

• Methods for sgRNA analysis for CRISPR screens
• High content CRISPR screening
• Comparing fold changes

Presentation by Stella Park, Knowles Lab

Alternative splicing produces different mRNAs. Identify both annotated and unannotated RBPs.