GSM6560971: ileum, G33T, non-NEC; Homo sapiens; Bisulfite-Seq
Snap-frozen specimens were mounted on appropriate embedding molds with clear Optimal Cutting Temperature Embedding Medium and cryostat sectioned at 7 um. These sections were mounted on memebrane slides, stained with toluidine blue and air dried. Tissue DNA was extracted using the Nucleospin Tissue XS Kit. Extracted DNA was quantified by using the KAPA hgDNA Quantification and QC Kit. DNA was sheared with Covaris to a size of ~175bp. Libraries were prepared using the KAPA HyperPrep Kit. Libraries were bisulfite converted post-ligation using the EZ DNA Methylation-Direct Kit and amplified 13-15 cycles. Bisulfite-converted DNA libraries underwent targeted capture using the SeqCap Epi CPGiant Enrichment Kit and amplified 10 cycles. Samples were sequenced on a HiSeq with 100 bp paired-end reads to a mean targeted read depth of ~24x.