Résumé
CpG methylation profiles of the somatostatin gene (Sst) and somatostatin receptor genes (Sstr1–Sstr5) were generated from erythrocytes and paraventricular nucleus (PVN) tissue of Magel2 wild-type (WT) and knockout (KO) mice using reduced representation bisulfite sequencing (RRBS).
Overall design: Genomic DNA was extracted from erythrocytes of mouse whole blood samples and from PVN tissue dissected from the brains of Magel2 WT and KO mice. RRBS was performed to assess CpG methylation. Mouse genomic DNA was pooled by 3 per sample to increase representativity in the sequencing. Differentially methylated CpGs were identified using a beta-binomial statistical model (Dispersion Shrinkage for Sequencing data - DSS), comparing Magel2 KO and WT groups separately for blood and PVN samples.
Bisulfite sequencing protocol and data processing:
Genomic DNA (50 ng) was digested with the Mspl enzyme (CCGG), enriched in CpG islands. Restriction ends were filled and 3’-adenylated before bisulfite treatment and PCR amplification (13–15 cycles per pool). Bisulfite conversion efficiency for mouse samples was 1–2.4%.
Libraries were denatured, diluted, hybridized onto NovaSeq 6000 flow cells (Illumina) with dual indexing, and sequenced using the sequencing-by-synthesis method (100 cycles). Thymine was labeled with a green fluorophore, cytosine with a red fluorophore.
Image analysis and base calling were performed using NovaSeq Control Software and RTA. Sequence quality was assessed with FastQC (v0.11.9). Adaptor sequences were trimmed with TrimGalore. Reads were aligned to the mm39 reference genome using Bismark. Contamination was screened using FastQ Screen with Bowtie2.
Organism: Mus musculus
Caractheristics:
Molecule: Genomic DNA
Age: 4months
Sex: both sexes
Strain: C57BL/6-Magel2tm1Stw/J
Replication per sample: 3, except for PVN_WT (5)
Dataset description:
The dataset "CpG_Methylation_Sst_Sstr_PVN_Blood_Magel2_WT_KO.csv" contains DNA methylation percentages at individual genomic positions (mm39) in PVN and blood samples from WT and Magel2 KO mice. CpG positions were selected based on their genomic coordinates within the Sst and Sstr1–Sstr5 genes, according to the Ensembl mm39 gene annotation. Only CpGs located within these gene regions were included. Columns correspond to individual animals per group (e.g., PVN_WT_1 = % methylation in PVN sample 1 from WT mice). Column descriptions:
chr → chromosome
pos → genomic position
other columns → individual sample data (% methylation per CpG per sample)
blank cells → NA values, indicating missing data due to insufficient sequencing coverage or absence of reads at that CpG position.
The datasets "Sst_system_CpGs_DSS_analysis_PVN_Magel_KO_vs_WT.xls" and "Sst_system_CpGs_DSS_analysis_Blood_Magel_KO_vs_WT.xls" contain the results of the Differentially Methylated CpG analysis comparing Magel2 KO and WT groups in PVN and Blood samples, respectively. Each sheet corresponds to one gene of the somatostatin system (Sst and Sstr1–Sstr5). Differentially methylated cytosines were identified using a beta-binomial model, implemented in the DSS package in R. Column descriptions:
chr → chromosome
pos → CpG position
KO, WT → average methylation levels per group
diff → difference in methylation (KO − WT)
diff.se → standard error of the difference
stat → test statistic from the DSS model
phi1, phi2 → dispersion parameters estimated for each group
pval → p-value for methylation difference
fdr → false discovery rate–adjusted p-value
gene → gene name
strand → DNA strand
distance → indicates that CpG sites are located
The dataset "Human_Mouse Orthologous CpGs and TFBS for the SST System.pdf" contains aligned sequences of the Sst system genes (SST, SSTR1–SSTR5) in human (GRCh38) and mouse (GRCm39), highlighting orthologous CpG sites, predicted transcription factor binding sites (TFBS), and functional genomic regions. The dataset was used to investigate conserved epigenetic regulation and transcriptional control in the context of Magel2 KO mice, a model for Schaaf-Yang Syndrome (SYS) and Prader-Willi Syndrome (PWS). Annotations include:
CpG sites (bold)
Predicted TFBS (blue)
Predicted protein-DNA binding sites (boxed in light blue)
Functional exonic/promoter regions (red)
Intergenic/intronic sequences (black)
TSS (ATG)
SNPs (C)
Statistical significance of CpG sites across species (yellow: p<0.001; green: p<0.05)
License / Attribution:This dataset is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0). Users are free to share, copy, redistribute, and adapt the material for any purpose, including commercial use, provided appropriate credit is given to the creators, a link to the license is provided, and any changes made are indicated.