Published June 10, 2024 | Version v3
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ASO mouse model metabolomics | data & code

Creators

  • 1. California Institute of Technology

Description

ASO Model Metabolomics

Overview

This repository contains the data and code used for the analysis presented in our study: https://www.biorxiv.org/content/10.1101/2024.06.07.597975v1.abstract on the metabolomics of ASO mouse models with SPF and germ-free microbiomes.

Data and Code Availability

Data Availability

The Zenodo deposit includes:

  • Raw metabolomics data
  • Processed data files
  • Analysis scripts
  • Supplementary materials

Repository Structure

The repository is organized as follows:

ASO_model_metabolomics/
│
#################################################################################
#######   Code for processing raw and performing core statistical tests   #######

├── Sia - github/
│   ├── 5370_Gut_brain_axis_study_Sub1_Pilot_study_Report_2020-04-27.pdf
│   ├── Cal_Tech_PD_Mice/
│   │   ├── 5370_Gut_brain_axis_study_Sub1_Pilot_study_Data_2020-04-27.xlsx
│   │   ├── 5370_Gut_brain_axis_study_Sub1_Pilot_study_Report_2020-04-27.pdf
│   │   ├── MxP-Quant-500-kit_MetaboINDICATOR™_V01-2019.xlsx
│   │   └── Sample_reconciliation_messages/
│   │       ├── RE_Sample_reception_(BC_No._5370_Duke).msg
│   │       ├── Sample_information_From_PD_Mice_2019_LHM_AKa_DSo.xlsx
│   │       ├── Sample_information_From_PD_Mice_2019_LHM_original.xlsx
│   │       └── Sample_overview_complete.xlsx
│   └── ...
│
├── data/
│   ├── 5370_Cal_Tech_PD_Mouse_Model_Gut_brain_axis_study_09112020.xlsx
│   ├── Metadata_Metabolomics_2019_checked_2020_updated.xlsx
│   ├── Metadata_Metabolomics_2019.xlsx
│   ├── normalized/
│   │   ├── 5370_Gut_brain_axis_study_Sub1_Pilot_study_Data_2020-04-27.xlsx
│   └── unnormalized/
│       ├── 5370_Gut_brain_axis_study_Sub1_not_normalized_2020-11-04.xlsx
│       ├── 5370_Gut_brain_axis_study_Sub1_not_normalized_2020-11-05.xlsx
│   └── ...
│
├── figures/
│   ├── August_2021/ ...
│
├── results/
│   ├── caltech.PD_mice.122622.xlsx
│
├── scripts/
│   ├── Cal_Tech_PD_Mice.q500.analysis.R
│   ├── Cal_Tech_PD_Mice.q500.figures.R
│   ├── Cal_Tech_PD_Mice.q500.preprocess.R
│   ├── Cal_Tech_PD_Mice.q500.regression.R
│   └── impute.knn.obs.sel.R


#################################################################################
##############   Code for interpretation and figure generation   ##############

├── ASO_model_metabolomics.Rproj
│
├── src/
│   ├── analyte_class_correlations.R
│   ├── analyte_class_enrichment.R
│   ├── body-weight-correlation-analysis.html
│   ├── body-weight-correlation-analysis.qmd
│   ├── body-weight-correlation-analysis.R
│   ├── boxplots.R
│   ├── correlations_vis.R
│   ├── correlations.R
│   ├── functions.R
│   ├── interaction_effect_plots.R
│   ├── load_packages.R
│   └── tissue_shared_analytes.R
│
├── figures/
│   ├── Analyte_class_estimates/
│   ├── Correlations/
│   ├── Heatmaps/
│   ├── Interaction_plots/
│   ├── Venn_Diagrams/
│   └── ...
│
├── files/
│   ├── 2023-01-22_body-weight-correlations.rds
│   ├── 2023-01-24_lm-comparisons-BWQuant.rds
│   ├── 5370_Cal_Tech_PD_Mouse_Model_Gut_brain_axis_study_09112020.xlsx
│   ├── analyte_class_colors_grouped.rds
│   ├── analyte_class_colors.RData
│   ├── caltech.PD_mice_G_by_M_results.xlsx
│   ├── caltech.PD_mice.022223.xlsx
│   ├── caltechdata.csv
│   ├── Metadata_Metabolomics_2019_checked_2020_updated.xlsx
│   ├── plasma_correlation_data.rds
│   └── ...
│
├── renv/ ... # for reproducibility 
├── README.md  # This file
└── LICENSE
 

Data Dictionary

Raw Data

  • 5370_Gut brain axis study_Sub1_Pilot study_gut content data_not normalized_2020-11-05.xlsx:
    • Raw data for gut samples.
  • 5370_Gut brain axis study_Sub1_Pilot study_Data_not normalized_2020-11-04.xlsx:
    • Raw data for all other samples (Plasma & brain)

Processed Data

  • 5370_Gut_brain_axis_study_Sub1_Pilot_study_Data_2020-04-27.xlsx:
    • Contains aggregated data for the gut-brain axis study, sub1 pilot study conducted on 2020-04-27.
  • caltechdata.csv:
    • Imputated and unimputed abundances for all metabolites and samples.

Results and Statistical Reports

  • caltech.PD_mice.022223.xlsx:
    • Contains statistical results for linear models, ANOVAs, t-tests, and conditional testing.
  • plasma_correlation_data.rds:
    • Correlation results for each metabolite between plasma and all other tissue levels.
  • 2023-01-22_body-weight-correlations.rds:
    • Mouse body weight correlation results.
  • 2023-01-24_lm-comparisons-BWQuant.rds:
    • Contains linear model results for body weight quantification.

Supplementary Data

  • Metadata_Metabolomics_2019_checked_2020_updated.xlsx:
    • Metadata for samples and mice.

How to cite this material

DOI:10.5281/zenodo.10841427

Files

ASO_model_metabolomics.zip

Files (177.8 MB)

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Additional details

Software

Repository URL
https://github.com/jboktor/ASO_model_metabolomics.git
Programming language
R