GSM1833755: shallow TABseq on a PyMT-induced breast tumor from a sFlk1-overexpressing mouse 1; Mus musculus; OTHER
Nucleic acids were subsequently extracted using the Wizard Genomic DNA Purification (Promega, Leiden, The Netherlands) kit according to instructions, with all buffers supplemented with DFO (200 µM), dissolved in 80 µL PBS-DFO with RNAse A (200 units, NEB, Ipswich, MA, USA), incubated for 10 minutes at 37°C. After proteinase K addition (200 units) and incubation for 30 minutes at 56°C, DNA was purified using the QIAQuick blood and tissue kit (all buffers supplemented with DFO), eluted in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -80°C until further processing. library preparations and TAB-conversion were as described by Yu and colleagues (Nat Protoc 2012), except that bisulfite conversion was done using the EZ DNA Methylation-Lightning Kit (ZYMO), and libraries were amplified using the KAPA Uracil+ 2x master mix. tet-assisted-bisulfite-seq
GEO Accession
GSM1833755