Mabe872

The following inhibitors used in this study were purchased from Selleckchem: ATM inhibitor (KU60019), ATR inhibitor (VE822), DNA-PK inhibitor (NU7441) and PARP inhibitor (Olaparib). Antibodies against H2B (17–10054), H3.3 (MABE872), H3 (06-755), H4 (05-858), H2A.X (ABE1960) and H2A.Z (ABE1348) were purchased from Millipore.

Anti- beta III Tubulin (MAB1637, Millipore), Anti- beta III Tubulin (T2200, Sigma), anti-NeuN (MAB377), anti-PCNA (SC7907, SANTA CRUZ), anti-PAX6 (AB2237, Millipore, Darmstadt, Germany), anti-H3.3 (MABE872, Millipore), anti-Tri-Methyl-Histone H3(Lys4) (05-1339, Millipore), anti-Histone H3 (4499, Cell Signaling Technology, Beverly, MA, USA), anti-H4K16ac (07-329, Millipore), anti-β-ACTIN (20536-1-Ap, Proteintech, Rosemont, IL, USA), anti-NESTIN (MAB353, Millipore), anti-SOX2 (3728, Cell Signaling Technology), anti-SOX2 (MAB2018, R&D, Minneapolis, MN, USA), anti-Flag (F1804, Sigma), anti-phospho-Histone H3(Ser10) (3377, Cell Signaling Technology), anti-HA (M20003, Abmart, Shanghai, China), anti-Tri-Methyl-Histone H3(Lys36) (9763, Cell Signaling Technology), anti-BrdU (AB6326, Abcam, Cambridge, UK), anti-GLI1 (SC20687, SANTA CRUZ, Delaware Avenue, CA, USA), IgG (bs0295P, Bioss, Beijing, China), and anti-Caspase3 (9662, Cell Signaling Technology) anti-Lamin A/C (bs1446, bioworld, Nanjing, China).

Low-cell-number ChIP-seq (5,000 HSCs) was performed, as described previously, with a native ChIP-seq protocol (Hu et al., 2019 (link)). MNase-digested samples were used for ChIP with anti-H3.3 antibodies (MABE872, Millipore). The input and immunoprecipitated DNA was cleaned using SPRI beads, and the NEBNext Ultra II kit was used to generate bar-coded libraries for Illumina sequencing. Reads were mapped to mm10 with Bowtie, peaks were called using both PePr and MACS2, and deepTools was used to generate all heatmaps.