Project description:NCIH2170 is a lung cancer cell line harboring a large amount of extrachromosomal DNA (ecDNA) with high cell-to-cell variation. We performed 10X sc-multiome sequencing on this cell line to study the pattern of gene expression and chromatin accessibility with the existence of ecDNA.
Project description:We performed single-nucleus ATAC-seq (snATAC-seq) to profile chromatin accessibility across eight brain regions from male C57BL/6J mice and 10x Multiome to jointly profile chromatin accessibility and gene expression in the same regions from female C57BL/6J mice, at 2, 9, and 18 months of age. Nuclei were isolated from frozen dissected brain tissue, tagmented with barcoded Tn5 transposase, and sequenced using either combinatorial barcoding (male samples) or 10x Multiome (female samples). Our analysis reveals region- and age-specific chromatin accessibility changes, highlighting regulatory programs associated with brain aging in distinct cell types.
Project description:Mouse retina is heterogeneous, composed of multiple neuronal and non-neuronal cell types. Among them, bipolar cells (BC), which connect photoreceptors (cones and rods) to inner retina, are traditionally dissected into rare subtypes of subtle functional and morphological differences. While high-resolution single-cell transcriptomic profiles of BCs are availabl, little is known about the corresponding single-cell chromatin landscapes. Although it is now possible to directly generate multiome data, there are often restrictions on cost, feasibility, and data quality. Therefore, integrating single-cell ATAC and RNA profiles obtained independently from the same retina sample may provide an exciting opportunity to comprehensively characterize these rare cell subtypes and discover transcription factors (TFs) important in establishing or maintaining the cell identities
Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.
Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.