GSM3454335: TAPS; Mus musculus; OTHER
Confluent E14 mESC were dissociated from the plates and collected by centrifugation for 5 min at 1000 xg. Genomic DNA was extracted from 40 mln cells with Quick-DNA Plus kit (Zymo Research) according to manufacturer's protocol For Whole Genome TAPS, 1 μg of mESC gDNA was spiked-in with control oligos, fragmented with Covaris M220 instrument and size-selected to 200-400 bp on Ampure XP beads. Subsequently, DNA underwent oxidation with NgTet1. End-repaired and A-tailing reaction and adapter ligation were prepared with KAPA HyperPlus kit according to manufacturer's protocol and sample was reduced with pic-borane. Final sequencing library was amplified with KAPA Hifi Uracil Plus Polymerase for 6 cycles and cleaned-up on 1X Ampure beads. Whole-genome TAPS sequencing library was pair-end 75 bp sequenced on NextSeq Illumina instrument. For Whole Genome Bisulfite Sequencing (WGBS), 200 ng of mESC gDNA spiked-in with 0.5% of unmethylated lambda DNA were fragmented to 200-400 bp. End-repaired and A-tailing reaction and ligation of methylated adapter (NextFlex) were prepared with KAPA HyperPlus kit (Kapa Biosystems) according to manufacturer's protocol. Subsequently, DNA underwent bisulfite conversion with EpiTect Bisulfite Kit (Qiagen) according to manufacturer's protocol. Final library was amplified with KAPA Hifi Uracil Plus Polymerase (Kapa Biosystems) for 6 cycles and cleaned-up on 1X Ampure beads. WGBS sequencing library was pair-end 75 bp sequenced on NextSeq Illumina instrument.
GEO
GSM3454335