Dietary Intervention Preserves β-cell Function Through CTCF-mediated Transcriptional Reprogramming

Published: 16 May 2022| Version 2 | DOI: 10.17632/mwgxv7m927.2
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Description

In this study, we established a mouse prediabetic dietary intervention model by switching high fat diet (HFD) to normal chow diet at the prediabetic stage (HFD-CHOW group). Mice continuously fed with normal chow diet (CHOW group) or HFD (HFD group), to mimic the healthy diet or non-intervened conditions, respectively, were used as control groups to understand the genetic and epigenetic networks underlying the dietary intervention-mediated improvement of pancreatic islet β-cell function. This dataset contains processed RNA Seq, scRNA-Seq, ATAC-Seq, and CUT&Tag-Seq data from mouse (Mus musculus) islets. Details in sample collection and data analysis pipeline can be found in the Method section of the manuscript. Wild-type male C57BL/6J mice from the Jackson laboratory at 12-15 weeks of age were subjected to the above treatments for up to 6 months, followed by islet isolation and the subsequent experiments.

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RNA-Seq:  HFD_Time_scale.csv: Islet RNA-Seq data from mice fed with HFD for 1, 2, 3, and 6 months and their respective chow diet fed controls, in 2 technical replicates. Islets were pooled from at least 3 individual animals.  Chow_HFD_HFDtoChow.csv: Islet RNA-Seq data from mice of CHOW group, HFD group, and HFD-CHOW group. Islets were pooled from at least 3 individual animals.  db_AAV-CTCF.csv: Islet RNA-Seq data from db/db mice treatment with AAV-CTCF or saline via pancreatic ductal infusion, in 3 biological replicates. ScRNA-Seq:  Chow.txt, HFD.txt and HFDtoChow.txt: Digital Expression Matrix (dge) of islet scRNA-Seq from mice of CHOW group, HFD group, and HFD-CHOW group. Islets were pooled from at least 3 individual animals. ATAC-Seq:  Chow.bw, HFD.bw and HFDtoChow.bw: BigWig files of islet ATAC-seq from mice of CHOW group, HFD group, and HFD-CHOW group. Islets were pooled from at least 3 individual animals. CUT&Tag-Seq: CTCF binding profile in murine islets:  CTCF_binding_profile_in_murine_islet.bw: BigWig files of islet CTCF CUT&Tag-Seq from mice fed with chow diet for 9 months. Islets were pooled from at least 3 individual animals. Differential CTCF binding differences in Chow, HFD and HFDtoChow:  Chow_islet_CTCF.bw: BigWig files of islet CTCF CUT&Tag-Seq from mice fed with chow diet for 6 months, in 2 technical replicates. Islets were pooled from at least 3 individual animals.  Chow_islet_IgG.bw: BigWig files of islet IgG CUT&Tag-Seq from mice fed chow diet for 6 months. Islets were pooled from at least 3 individual animals.  HFD_islet_CTCF.bw: BigWig files of islet CTCF CUT&Tag-Seq from mice fed with HFD for 6 months, in 3 technical replicates. Islets were pooled from at least 3 individual animals.  HFD_islet_IgG.bw: BigWig files of islet IgG CUT&Tag-seq from mice fed with HFD for 6 months. Islets were pooled from at least 3 individual animals.  HFDtoChow_islet_CTCF.bw: BigWig files of islet CTCF CUT&Tag-Seq from mice of HFD-CHOW group, in 3 technical replicates. Islets were pooled from at least 3 individual animals.  HFDtoChow_islet_IgG.bw: BigWig files of islet IgG CUT&Tag-Seq from mice of HFD-CHOW group. Islets were pooled from at least 3 individual animals.

Institutions

Zhejiang University

Categories

Diabetes, Chromatin Remodeling, Dietary Intervention, Next Generation Sequencing

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