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Visualizing RNA-Seq data

For today's lesson we will be working with RNA-seq data from the publication in ImmunoHorizons by Sabikunnahar et al. (2025).

sab_article

Summary: Innate immune cells rapidly respond to microbial threats, but if unchecked, these responses can harm the host, as seen in septic shock. To explore how genetic variation influences these responses, researchers compared standard lab mice (C57BL/6) with genetically diverse wild-derived mice (PWD).

Experimental Design: The authors isolated bone marrow derived dendritic cells from B6, c11.2, and PWD mice and then either left them unstimulated or stimulated with LPS.

This experiment has:

  • Two treatments: untreated, LPS
  • Three genotypes: B6, c11.2, and PWD

The goal:

  • To test how LPS stimulation affects each genotype
  • Whether the response to LPS differs between genotype

Getting Started: Monday, April 14th

Copy this folder into your home directory:

/gpfs1/cl/mmg3320/course_materials/R_tutorials/ENSM_partIV
  • Open the file RNASeq_Visualizations_PartIV_EDIT.Rmd to start.
  • Slides discussed can be found here

Getting Started: Wednesday, April 16th

  • No in-person class (see Monday's slides for details)