slccolon

This repository contains the original count data and analysis files used to produce the figures in the paper: Yang, J.C., Zhao, M., Chernikova, D. et al. ZIP8 A391T Crohn’s Disease-Linked Risk Variant Induces Colonic Metal Ion Dyshomeostasis, Microbiome Compositional Shifts, and Inflammation. Dig Dis Sci (2024). https://doi.org/10.1007/s10620-024-08647-8

Raw data can be found on NCBI, with BioProject accession code PRJNA1004665: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1004665.

Steps to Reproduce the Figures

1. First, clone the repo.

git clone https://github.com/jacobslabucla/slccolon

2. Then, open the Rproj_slccolonpaper folder and open the .Rproj file in RStudio.

3. Load any script in Final_Figures_Paper. By running renv::restore() , all package versions will be synced with the versions used to produce the figures in the paper.

4. Run everything in Functions.R first, to obtain the required custom functions.

5. Now, by running each Figure script (matches the Figures in the paper) you will be able to reproduce the figures in the paper.

ICP MS Data

• ICP-MS / Colon samples from 5-month old mice (WT, MUT) - n = 25, 23

Sex	Genotype	MouseID
Female	MUT	12
Female	WT	13
Male	MUT	11
Male	WT	12

• ICP-MS / Blood - n = 20,20

Sex	Genotype	SampleID
Female	MUT	10
Female	WT	10
Male	MUT	10
Male	WT	10

Microbiome Data

• SLC Long Term / 12-month old mice (WT, HET, MUT) - n= 7, 16, 7

Sex	Genotype	MouseID
Female	HET	10
Female	MUT	6
Female	WT	4
Male	HET	6
Male	MUT	1
Male	WT	3

• SLC Trios / 2-month old mice (WT, HET, MUT) - n = 10, 10, 10

Sex	Genotype	MouseID
Female	HET	4
Female	MUT	4
Female	WT	4
Male	HET	6
Male	MUT	6
Male	WT	6

• Baseline / 3-4 month old mice (WT, HET, MUT) - n = 26, 30, 31

Sex	Genotype	MouseID
Female	HET	10
Female	MUT	14
Female	WT	16
Male	HET	20
Male	MUT	17
Male	WT	11

Histology Data

• 5 months

Sex	Genotype	Score
Female	MUT	4
Female	WT	7
Male	MUT	9
Male	WT	9

• 10 months

Sex	Genotype	Score
Female	HET	7
Female	MUT	5
Female	WT	4
Male	HET	6
Male	MUT	10
Male	WT	4

• Mucin

Sex	Genotype	MouseID
Female	HET	5
Female	MUT	7
Female	WT	6
Male	HET	6
Male	MUT	4
Male	WT	6

Disease model Data

• DSS

Sex	Genotype	MouseID
Female	WT	4
Female	HET	4
Female	MUT	3
Male	WT	9
Male	HET	9
Male	MUT	12

• TNBS

Sex	Genotype	MouseID
Female	WT	8
Female	HET	8
Female	MUT	5
Male	WT	12
Male	HET	14
Male	MUT	12