Multi-omic Chromatin Profiling Reveals SRSF3-, MATR3-, and H1.4-Associated Genome Regulation

This repository contains processed chromatin profiling datasets generated to investigate the roles of SRSF3, MATR3, and linker histone H1.4 in chromatin organization and regulation. The deposited data include Hi-C, ATAC-seq, and CUT&Tag datasets under control and knockdown conditions. Hi-C Hi-C contact matrices are provided for cells before and after SRSF3 knockdown. The processed interaction matrices are stored in Cooler (.cool) format at 10-kb resolution and can be used to analyze changes in higher-order chromatin organization, including chromatin contact frequency, compartmentalization, and other genome-wide interaction features associated with SRSF3 depletion. ATAC-seq ATAC-seq datasets are provided to characterize changes in chromatin accessibility following knockdown of: SRSF3 MATR3 H1.4 The corresponding processed files are provided as compressed archives. Histone modification CUT&Tag CUT&Tag datasets profiling multiple histone modifications are provided for control and knockdown conditions of SRSF3 and MATR3. The histone marks include: H3K4me1 H3K4me3 H3K9ac H3K9me3 H3K27ac H3K27me3 IgG samples are included as negative controls. For the SRSF3 knockdown histone-modification CUT&Tag dataset, files beginning with “0” represent the control condition, whereas files beginning with “500” represent the SRSF3 knockdown condition. For the MATR3 knockdown histone-modification CUT&Tag dataset, files beginning with “S” represent the control condition, whereas files beginning with “6” represent the MATR3 knockdown condition. Genome-wide CUT&Tag signal tracks are provided in bigWig (.bw) format and can be visualized directly in genome browsers such as IGV or the UCSC Genome Browser. Supplementary heatmaps and signal profiles around transcription start sites (TSSs) and scaled genomic regions are also included. SRSF3 and MATR3 CUT&Tag CUT&Tag datasets profiling the genome-wide chromatin occupancy of SRSF3 and MATR3 are also included. In addition to their respective baseline/control profiling datasets, reciprocal knockdown experiments were performed to investigate the relationship between SRSF3 and MATR3 chromatin association: MATR3 CUT&Tag following SRSF3 knockdown SRSF3 CUT&Tag following MATR3 knockdown