0.5-1 million undifferentiated HUDEP2, HUDEP2 at day 2 of differentiation, or primary cells at day 8 of differentiation were used for CUT&RUN. We followed the experimental procedures published by Henikoff laboratory with minor adaptations35 . Antibody incubations were performed in 300 μl PCR tubes for 2 h at 4 °C with rotation. pAG-MNase were obtained from Cell Signaling. Antibodies used in this study were: IgG (Cell signaling, #3900), anti-NFIA (Thermo Fisher Scientific, PA5-52252), anti-NFIX (Sigma Aldrich, SAB1401263), anti-H3K27ac (Invitrogen, MA5-23516). anti-NFIA antibodies used in Extended Data Figure 6 were obtained from Sigma, #HPA008884; Active Motif, #39397; Invitrogen, #535936. Approximately 2 μg antibody were used per 200 μl reaction. The released DNA fragments were quantified by Qubit and sequencing libraries were generated using NEB Kits (E7645 and E6440S) with 15-30 ng input DNA6 (link). The barcoded libraries were pooled and paired-end (2×50 bp) sequenced on the Illumina Nextseq 2000 platform.
Sequencing data from CUT&RUN were analyzed by CUT-RUNTOOLS-2.064 (link) using default settings (https://github.com/fl-yu/CUT-RUNTools-2.0 ).
Sequencing data from CUT&RUN were analyzed by CUT-RUNTOOLS-2.064 (link) using default settings (