GSM8306028: TSP77WT_iPSC_p47; Homo sapiens; Bisulfite-Seq
NPCs were collected and pelleted at day 10 of differentiation. Pellets were stored at -80°C until all samples had been collected. All samples gDNA were extracted at the same time. gDNA was extracted following the protocol in Barnett, K.R., et al., ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions. Mol Cell, 2020. 77(6): p. 1350-1364.e6. Briefly, genomic DNA was extracted using phenol-chloroform extraction from 8-12 million cells. Purity and integrity of genomic DNA was confirmed using Nanodrop and Tapestation (Agilent). 50ng of genomic DNA was then incubated with Tn5 assembled with adaptor oligos(produced in-house) and reaction buffer (5x Tris-DMF) at 55C for 8 minutes. Resulting fragments were purified prior to gap repair and oligo replacement. Bisulfite conversion of repaired DNA fragments was performed using the Zymo-Gold Methylation Kit according to the manufacturer's instructions. Libraries were amplified and purified prior to sequencing on a NovaSeq.