Instructions:

We provide all differential epigenetic modification regions to exploring the dynamics informations in specific genomic regions by yourself. Based on the genomic coordinate files (BED format) provided by users, this study employed bedtools for efficient genomic interval operations and utilized the ChIPseeker package to achieve precise annotation and localization of differentially modified epigenetic regions with long non-coding RNAs (lncRNAs). You can retrieve information on interesting genomic regions associated with epigenomics.

Method:

This study employed the "dmr" analysis strategy of CGmapTools software to systematically accomplish the following key steps: (1) detection and localization of differentially methylated regions (DMRs); (2) precise calculation of average methylation levels in each region, thereby accurately identifying genomic regions with significant methylation changes across different samples or experimental conditions.

For ChIP-seq data analysis, we integrated both DiffBind and DESeq2 methods for statistical significance analysis. By applying stringent thresholds for fold change and p-values, we reliably identified biologically significant differential binding peaks.

Help Note:

1. Choose the Genomes; 2. Select Factors; 3. Tissues; 4. Upload input.bed file; 5. Click "Submit" buttom and show results. The uploaded file needs to be in BED format (tab-separated), eg. "Chr1 19589 24058 lncRNA1". Furthermore, clicking on "Example" buttom will download Example_input.bed for you to test.