GSM8124443: Cas9 Pcsk9 24h AML12 100k rep1; Mus musculus; OTHER
Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/MRE11/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA. The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. CUT&RUN-MRE11 library was constructed using NEBNext® Ultra™ II DNA Library Prep Kit. For Tracking-seq, cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.  For ChIP-seq, Cells were crosslinked with 1% formaldehyde. After quenching and blocking the beads, MRE11 or H3K4me3 antibody were added. After cell lysis, the lysate was sonicated using a QSONICA sonicator with microtips. DNA was then treated with RNase A and Proteinase K, followed by purification through phenol-chloroform extraction. For ATAC-seq, 100,000 NIH3T3 cells, AML12 cells, mHSPCs, or mESCs were sorted into tube for tagmentation and purifcation. The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. Other libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit.