Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [Tumor_stained_for_EpCam_CD45]
Ontology highlight
ABSTRACT: A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).
Project description:A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).
Project description:A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).
Project description:A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).
Project description:A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).
Project description:A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).
Project description:A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).
Project description:A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).
Project description:Aging is a universal biological phenomenon linked to many diseases, such as cancer or neurodegeneration. However, the molecular mechanisms underlying aging, or how lifestyle interventions such as cognitive stimulation can ameliorate this process, are yet to be clarified. Here, we performed a multi-omic profiling, including RNA-seq, ATAC-seq, ChIP-seq, EM-seq, SWATH-MS and single cell Multiome scRNA and scATAC-seq, in the dorsal hippocampus of young and old mouse subjects which were subject to cognitive stimulation using the paradigm of environmental enrichment. In this study we were able to describe the epigenomic landscape of aging and cognitive stimulation.
Project description:Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. We identify a dominant role for hypoxia, marked by HIF1α protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells.
Project description:The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, only a few studies have been done at the single cell level (scATAC-seq) due to technical difficulties. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk tagmentation with single-nuclei sorting, to investigate open chromatin regions. We applied this method on mouse splenocytes and unbiasedly revealed key regulatory regions and transcription factors that define each cell (sub)type.