|Public on Feb 15, 2012
|strain: Cast/EiJ x 129X1/SvJ
tissue: frontal cortex
|The crosses of the two mouse strains 129x1/SvJ (129) and Cast/EiJ (Cast) were performed at Jackson Laboratories (http://jaxmice.jax.org/) and the male mice F1 offspring and males of each of the two parental strains were shipped to investigator laboratories at 8 to 9 weeks of age.
|A total of 500ng genomic DNA isolated from IMR90, MEF, and the frontal cortex of F1i and F1r was digested in parallel by the DNA methylation dependent restriction enzyme FspEI. FspEI recognizes the CmC site (the second cytosine is methylated and can be in the context of CG, CHG or CHH) and creates a 5’ protruding end 17 bases downstream of the methylcytosine. A similar experiment was performed by incubating the F1i genomic DNA with a DNA methylation independent restriction enzyme BstNI. The digested DNA was gel purified, size selected for fragments within 100-600bp. The resulting DNA was then prepared as genomic DNA libraries for high-throughput sequencing (Illumina).
|Illumina Genome Analyzer II
|FspEI-Seq reads were mapped using Novoalign (Novocraft, Malaysia) with adapter sequences stripped. Novoalign permits gapped alignment by allowing more than two mismatches per read (up to 8 for high quality base calls on single end reads and 16 on paired-end reads) that particularly benefits sequencing read mapping around SNPs and indels. Only reads that were perfectly mapped were used to determine the positions of methylcytosines on the same strand.
|Nov 09, 2011
|Last update date
|May 15, 2019
|9500 Gilman Dr. CMM East, Room 2071
|Base-resolution analyses of parent-of-origin and sequence dependent allele specific DNA methylation in the mouse genome (MRE-seq)
|Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation