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Pipeline publication

[…] . For each TF, its peak binding region for measuring methylation level is defined as a length of 2000 bp centered on TSS (TSS ± 1000 bp), mainly for covering each promoter region., We selected the RRBS data for measuring each TF’s methylation status. With the aggregated DNA methylation level from the 82 TFs across all the 19 cell types, we constructed their methylation distribution background model with the normalization and fitting. Then we adopted the K-S test for determining the statistic p-value between TF’s methylation distribution density and the background model. We defined those entries with p-value ≤ 0.05 as the significantly differential methylated compared with background model., Bowtie2 was used to align sequencing reads, SAMtools and BAMtools were used to process the aligned sequencing reads, methylKit was used to analyze part of RRBS data, and DESeq was used to analyze RNA-seq data., Integration of multi-platform and cross-cell-types omics information enables the thorough interrogation of genomic features with undiscovered biological functions. Till now, there is still limited systematic analysis for hundreds of data sets across different data types and multiple cell types., Our work conducted the systems integration of 19 ENCODE cell types about the cell type-specific DNA methylation and its impacts on transcriptional regulation. The systematic analysis on DNA methylation within predefined genomic regions or segments revealed that DNA methylation in CpG islands and CpG islands […]

Pipeline specifications

Software tools Bowtie2, SAMtools, BamTools, methylKit