GSM8833112: PBS 1hr treated BMDM, IgG CUT&Run (Input); Mus musculus; OTHER
CUT&Run : We performed Cleavage Under Targets & Release Using Nuclease (CUT&RUN) on bone marrow-derived macrophages (BMDMs) using the CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, 14-1048) following the manufacturer's protocol. Briefly, 1 × 10⁵ cells were immobilized on Concanavalin A-coated magnetic beads and incubated with H3K4me1 (EpiCypher, 13-0057) and H3K27ac (EpiCypher, 13-0045) antibodies. After antibody binding, the cells were treated with pAG-MNase for targeted chromatin cleavage at 37°C. The cleaved chromatin fragments were purified and used for downstream library preparation. CUT&Run : CUT&RUN libraries were prepared using the CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001) following the manufacturer's instructions. Approximately 5 ng of purified DNA was used for library preparation. The process included end repair, A-tailing, adapter ligation, and uracil excision, followed by dual-indexed PCR amplification using i5 and i7 primers. Libraries were purified and size-selected using AMPure XP beads to remove contaminants and enrich for fragments of the desired size. The final libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end (2 × 150 bp) reads, ensuring high coverage for downstream analysis.