A Minimal Book Example
1 Microbial Bile Acid Metabolism Shapes T Cell Responses During Inflammation
2 Introduction: load the datasets
- 2.1 Load packages
- 2.2 Load datasets
3 Analyze the effect of UDCA administration on the bile acid pool (supplementary figure 5)
4 Create the bile acid pools (figure 4, supplementary figure 6,8)
- 4.1 Create BA pools first for peri-GVHD-onset timepoint
  - 4.1.1 Plot: TBAs (total_BAs), PBAs (primary_pool), SBAs (secondary_pool), nonUDCA SBAs (secondary_nonUDCA), conjugated (conjugated_pool), unconjugated (unconjugated_pool), sulfated (sulfated_pool)
  - 4.1.2 Create pies
- 4.2 Create BA pools for peri-engraftment timepoint
  - 4.2.1 Plot BA pools and GVHD; can plot total BAs (total_BAs), PBAs (primary_pool), SBAs (secondary_pool), nonUDCA SBAs (secondary_nonUDCA), conjugated (conjugated_pool), unconjugated (unconjugated_pool), sulfated_pool, secondary/primary ratio and secondary*/primary ratio
  - 4.2.2 Create pies
5 Evaluate T cell modulatory BAs in patients with GVHD vs controls (figure 4)
6 Shotgun metagenomic sequencing: Evaluate genes of interest (figure 5, supplement figure 10)
7 Create landscape of all peri-GVHD-onset samples (figure 5)
8 Diversity, bai operon and domination
9 Evaluation of UDCA exposure and clinical outcomes: Teng Fei
10 scRNA seq Data: Anastasia Kousa
- 10.1 GSEA RESULTS
- 10.2 FOLD CHANGE vs FOLD CHANGE
11 RNA sequncing in mice (Figure 2): Anastasia Kousa
Published with bookdown

Microbial Bile Acid Metabolism Shapes T Cell Responses During Inflammation

Oriana Miltiadous

2023-08-18

Chapter 1 Microbial Bile Acid Metabolism Shapes T Cell Responses During Inflammation