alias: GSM1676715
title: GSM1676715: Whole Genome Bisulfite Sequencing from Mouse Embryonic Fibroblasts; Mus musculus; Bisulfite-Seq
library_construction_protocol: Nanog-CreER reporter MEFs were reprogrammed in for 6 or 9 days, and sorted for tdTomato+ the end of OSKM induction step, at day 6 and 9 respectively. DNA was isolated from snap-frozen intermediate sorted cells using the Quick-gDNA mini prep kit (Zymo). DNA was then bisulfite converted using the EZ DNA Methylation-Gold kit (Zymo). Sequencing libraries were created using the EpiGnome Methyl-Seq (Epicentre) and sequenced on an Illumina HiSeq 1500 system. The sequencing reads were aligned to the Mouse Genome Build 37 (mm9) using a proprietary script based on Bowtie 2. Due to the low sequencing depth of some of the samples, the methylation calls were down-sampled so that each CpG was covered by a single call (being either ‘methylated’ or ‘non-methylated’). Mean methylation was then calculated over all CpGs that had calls in all samples (either methylated “1” or non-methylated “0”) EpiGnome Methyl-Seq (Epicentre)
identifiers.namespace: GEO
identifiers.id: GSM1676715