alias: E-MTAB-6785:wt_EpiLC_RRBS_rep2_s
title: Illumina HiSeq 1500 sequencing; Tet1 controls maintenance DNA methylation via the regulation of Dppa3
design: Tet1 controls maintenance DNA methylation via the regulation of Dppa3
library_construction_protocol: Cells were collected by trypsinization To differentiate naïve ESCs into Epiblast-like cells (EpiLCs), flasks were first pre-treated with Geltrex (Life Technologies) diluted 1:100 in DMEM/F12 (Life Technologies) and incubated at 37 °C overnight. Naïve ESCs were plated on Geltrex-treated flasks in defined medium containing 10 ng/mL Fgf2 (R&D Systems), 20 ng/mL Activin A (R&D Systems) and 0.1× Knockout Serum Replacement (KSR) (Life Technologies). Media was changed after 24 h and EpiLCs were harvested for RRBS and RNA-seq experiments after 48 h. Column purification For RRBS, genomic DNA was isolated using the QIAamp DNA Mini Kit (QIAGEN), after an overnight lysis and proteinase K treatment.  RRBS library preparation was performed as described previously (Boyle et al. 2012), with the following differences: bisulfite treatment was performed using the EZ DNA Methylation-Gold™ Kit (Zymo Research Corporation) according to the manufacturer's protocol.
identifiers.namespace: Faculty of Biology Department II Ludwig Maximilians University Munich
identifiers.id: E-MTAB-6785:wt_EpiLC_RRBS_rep2_s
attributes.tag: Experimental Factor: cell type
attributes.value: epiblast-like cell
attributes.tag: Experimental Factor: genotype
attributes.value: wild type genotype