GSM8969507: HCC1428 cells, C48, H3K4me3, biol rep 2; Homo sapiens; OTHER
Samples were processed according to CUT&Tag-IT R-loop, Anti-Rabbit Kit (Active Motif 53160), with the addition of Drosophila spike-in nuclei and spike-in antibody: Drosophila spike-in nuclei CUT&Tag-IT® Spike-In Control, Anti-Rabbit (Active Motif 53168). Spike-in nuclei were added to each sample at a ratio of 1:10 spike-in nuclei to cells, and each were added to ConA beads. Cells, nuclei and ConA beads were mixed by gentle pipetting and strip tubes containing the samples were placed on a room temperature nutator for 10 minutes.  Spike-in antibody was added to each sample according to the kit instructions at the same time as the primary antibody, H3K4me3 (Active Motif 53160). The CUT&Tag-IT Assay Kit protocol was followed as per the manufacturer's instructions for all remaining steps in CUT&Tag-IT Assay Kit. NGS libraries were evaluated on a TapeStation 4150 (Agilent, Santa Clara, CA) using High Sensitivity D1000 ScreenTapes (Agilent 5067-5584) and pooled for equal sequencing depths targeting approximately 30 million reads per sample. Sequencing was conducted on a NovaSeq6000