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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

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

  2. 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.

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

  4. 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