DNA Methylation Profiling of Fallopian Tube

Whole-genome methylation profiling data from normal human fallopian tube samples from Morrison et al. (40 (link)) were used. We used two technical replicates each profiled with two methods (EM-seq with the New England Biolabs kit and WGBS with the Swift Biosciences kit). The data was aligned as described in (40 (link)), then each kit's technical replicates were merged, and individual epiBED files created for each kit. The resulting epiBED files were merged into a single epiBED file for generating the figure. The SNRPN-SNURF imprinted region was selected based on annotations for imprinted CpG probes in the Illumina MethylationEPIC array (41 (link)). After creating the epiBED file, it was imported into R using biscuiteer (version 1.13.1) and the figure was created using bisplotti (version 0.0.19, https://github.com/huishenlab/bisplotti). Reads were subsetted to those that covered both the SNP and CpG and sorted based on their methylation status.

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Zhou W., Johnson B.K., Morrison J., Beddows I., Eapen J., Katsman E., Semwal A., Habib W.A., Heo L., Laird P.W., Berman B.P., Triche TJ J.r, & Shen H. (2024). BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nucleic Acids Research, 52(6), e32.

Publication 2024

MethylationEPIC array

Corresponding Organization : Van Andel Institute

Other organizations : Hebrew University of Jerusalem

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Variable analysis

independent variables

Methylation profiling method (EM-seq vs. WGBS)

dependent variables

Methylation levels in the SNRPN-SNURF imprinted region

control variables

Normal human fallopian tube samples
Technical replicates for each profiling method

Annotations

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