GSM8124512: ATAC mouse HSPCs; Mus musculus; ATAC-seq
100,000 NIH3T3 cells, AML12 cells, mHSPCs, or mESCs were sorted into tube for tagmentation and purifcation. Tagged DNA were PCR amplified with primers containing barcodes to construct the sequencing libraries. 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.