GSM9450630: V6.5 WGS; Mus musculus; OTHER
Genomic DNA was isolated from three mouse ES cell lines, which are V6.5, V6.5-meGFP-Brd4-meGFP and V6.5-meGFP-Med1, using the QIAGEN AllPrep DNA/RNA Mini kit (QIAGEN, Cat# 80204) and quantified using a Qubit fluorometer with the dsDNA BR kit (Thermo Fisher Scientific, Cat# Q32853). High-molecular-weight DNA was used for library preparation. Whole-genome sequencing libraries were prepared using the KAPA HyperPrep Library Preparation kit (Roche, Ref# KR0961) according to the manufacturer's instructions. Briefly, 500 ng of genomic DNA of each cell line was sheared to an average insert size of approximately 350 bp using a Covaris LE220, followed by end repair, A-tailing, and ligation of adapters from ITD for Illumina TrueSeq DNA UDI v2 (Illumina, Ref# 20042113). Adapter-ligated DNA was purified using AmPure XP beads (Beckman Coulter, Ref# A63881) and amplified by 3 cycles of PCR. Amplified libraries were assessed for size distribution and concentration using HS D1000 Screen Tape (Agilent, part# 5067) on a TapeStation system (Agilent, part# 4200) prior to sequencing. Further QC of Libraries was performed using Illumina MiSeq Nano kits. Libraries were pooled at equimolar concentrations and loaded according to Illumina's recommended loading concentrations. The final sequencing was performed on an Illumina NextSeq 2000 platform using a P1 flow cell with a 300-cycle kit, generating paired-end 150 bp, and 25M PF reads for each sample. Base calling and demultiplexing were carried out using Illumina's onboard software.