Module 6: Cell Cell Communication

By Gregory Schwartz, Veronique Voisin, Chaitra Sarathy and Ruth Isserlin

Module 6 lecture : Cell-Cell Communication.

Gregory Schwartz

Lecture

scRNA lab praticals

scRNA-lab1_PBMC

  • This lab starts from scRNA data from peripheral blood mononuclear cells.

  • The cells from similar cell types were grouped into clusters.

  • We extracted the gene lists corresponding to each cluster and run pathway analysis on it using g:Profiler.

  • We also created pseudobulk from the data, ran GSEA and created an enrichment map.

scRNAlab2_Glioblastoma

  • Similar to lab1, we extracted gene lists from scRNA clustering from glioblastoma data.

  • We created a mastermap by uploading in EnrichmentMap the pathway enrichment results for all the cluster gene lists.

scRNAlab_CellPhoneDB

  • Similar to lab1 , we start from scRNA data from peripheral blood mononuclear cells and we are going to study the cell-cell communication between different cell types using CellPhoneDB.

scRNAlab_NEST

  • In this lab, we are exploring cell-cell communication in spatial trancriptomic of a pancreatic cancer (PDAC) tissue section using the tool NEST.