ABSTRACT: Genomic DNA of a Holstein male, that was used for multiple tissue ATAC-seq experiments, was sequenced. The sequences were used for ATAC-seq peak calling as a background.
Project description:We performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq) using 88 tissue samples to profile open chromatin regions in the cattle genome.
Project description:To test the chromatin accessibility of different immune cell subsets, we isolated CD4+T cells, CD8+T cells, CD19+B cells and CD14+ monocytes from human PBMCs and performed ATAC assay.
Project description:Differential gene transcription enables development and homeostasis in all animals and is regulated by two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers. While enhancers have been thoroughly characterized, the properties and mechansisms of silencers remain largely unknown. By an unbiased genome-wide functional screen in Drosophila melanogaster S2 cells, we discover a class of silencers that bind one of three transcription factors (TFs) and are generally not included in chromatin-defined CRE catalogs, as they mostly lack detectable DNA accessibility. The silencer-binding TF CG11247, which we term Saft, safeguards cell fate decisions in vivo and functions via a highly-conserved domain we term ZAC and the corepressor G9a, independently of G9a’s H3K9-methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanisms has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.
Project description:CD4+ T cells were extracted from mouse and human. They were activated in vitro with CD3/28 and cultured with Il4. ATAC-seq was then performed at different time points
Project description:Open chromatin regions were analyzed by ATAC-seq in t(3;8) K562 and wild type K562 to characterize the MYC super-enhancer region. ATAC-seq was performed as described (Buenrostro et al., 2013) with a modification in the lysis buffer to reduce mitochondrial DNA contamination.
Project description:In order to identify the open chromatin profiles in the U2OS cell, ATAC-seq technology was used to determine the accessible chromatin landscape in U2OS cell.
Project description:Bulk ATAC-seq was performed on human, chimpanzee, bonobo, and macaque stem cell-derived cerebral organoids. ATAC-seq was performed on day 60 (2 months old) and day 120 (4 months old) cerebral organoids.
Project description:Open chromatin regions were analyzed by ATAC-seq in MUTZ3 and MOLM1 cell lines (both inv(3) AML) to characterize the GATA2 super-enhancer region. ATAC-seq was performed as described (Buenrostro et al., 2013) with a modification in the lysis buffer to reduce mitochondrial DNA contamination.