Unveiling Early Responses of Mouse β-Cells to High Fat Diet feeding through Single-Cell Multiome Analysis

Phenotyping of mice

To investigate early adaptive changes to short-term HFD, we fed eleven-week-old male C57BL/6JBomTac mice with a HFD (60% energy from fat) or purified low-fat diet (LFD) (10% energy from fat) as a control, for one and three weeks.

To capture the early genomic changes within islets of Langerhans following short-term HFD exposure, we utilized a single-nucleus method known as chromium single-cell multiome ATAC + Gene expression from 10X Genomics (snMultiome) using nuclei from isolated islets. snMultiome enables simultaneous capture of gene expression data and chromatin accessibility data from the same single nuclei through RNA-sequencing (snRNA-seq) and transposase-accessible chromatin with sequencing (snATAC-seq), respectively.

A) Schematic overview of the experimental setup: 8-week-old male C57BL/6JBomTac mice underwent a three-week acclimatization period during which they were fed a low-fat-diet (LFD). Subsequently, mice were divided into groups receiving either LFD (orange, as a control) or high-fat-diet (blue, HFD) for one or three weeks.

B) Macronutrient composition of LFD (7 % energy from sucrose 10 % energy from fat) and HFD (7 % energy from sucrose, 60 % energy from fat) presented in % Kcal. Following one or three weeks of diet the metabolic phenotype of these mice was characterized on several parameters

Brief description of folder

The following folders contain:

• R/: This folder contains scripts for quality control and analysis performed in R
• illustrations/: Illustrations used for this readme file

Description of scripts

• R/: r_library.txt
  • weight.R: Calculation of weight gain from week 0
  • GTT.R: Analysis of Intraperitoneal glucose tolerance test
  • ITT.R: Analysis of Intraperitoneal insulin tolerance test
  • fasted_glucose.R: Fasted blood glucose levels.
  • beta_cell_function.R: Quantification of insulin levels and beta-cell function
  • weight_multiome_samples.R: Check if multiome or revisions samples are outliers based on weight gain

Other scripts

• R/:
  • Package_load.R: to load packages