GSM8972914: HCC1428 cells, C48, S96, biol rep 2; Homo sapiens; OTHER
Samples were processed according to CUT&Tag-IT R-loop Assay Kit (Active Motif 53167), with the addition of Drosophila spike-in nuclei and spike-in antibody: Drosophila spike-in nuclei CUT&Tag-IT® Spike-In Control, Anti-Mouse (Active Motif 53174). 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, S9.6 (included in R-loop Assay Kit). The CUT&Tag-IT R-loop Assay Kit protocol was followed as per the manufacturer's instructions for all remaining steps for R-loop samples and CUT&Tag-IT Assay Kit, Anti-Rabbit for the H3K4me3 samples. 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
GEO
GSM8972914_r1