Project description:we identified 7 families presenting a new cardiac entity associated with a heterozygous deletion of 2 CTCF binding sites on 4q25, inducing TAD fusion and chromatin conformation remodeling. The CTCF binding sites are located in a gene desert at 1 Mb from the Paired-like homeodomain transcription factor 2 gene (PITX2).
Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).
Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.
Project description:The goal of CUT&RUN-seq is to identify the global alteration of H3K27me3 levels by NOP16 overexpression or deletion in triple negative breast cancer cell line MDA-MB231 cells. Three (or Two) biological replicates were assigned for each group and in total 6 groups were prepared for these CUT&RUN-seq libraries. We mapped about 20 million reads per sample to hg38 human reference genome, and counted and normalized each reads number and identified H3K27me3 distribution.
Project description:CUT&RUN experiment was carried out on bovine semeimbranosous muscle satellite cells to identify the locus of the accumulation of the centromeric protein A (CENP-A) on the cattle Y-chromosome. This was carried out to support the annotation of the DNA signal comprising tandem array of a centromeric satellite signal which characterizes the centromere on the Y-chromosome.
Project description:CUT&RUN LoV-U was performed against SMAD4 using two different antibodies in M170117 human melanoma cells under 4 conditions: Control (DMSO), TGFb, MEKi and TGFb + MEKi (Both).