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:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.
Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.
Project description:To identify epigenetic programs underlying differentiation of mouse retina, we performed ATAC-Seq on bulk native retina (NaR) and iPSC-derived 3D retinal aggregates (3D-RA) at three matched stages of development: embryonic day (E)13 vs differentiation day (DD)13, postnatal day (P)0 vs DD21, and P5 vs DD25. We produced a total of 24 ATAC-seq libraries with two technical replicates (using either 1 ul or 2 ul of TDE1 enzyme) of two biological replicates, and two genomic DNA libraries to use for background controls.
Project description:This study characterized the effect of WEE1 kinase inhibition using AZD1775 treatment on single-cell accessible chromatin and gene expression profile using the 10x Genomics multiome protocol (ATAC + Gene Expression Assay) in the acute lymphoblastic leukemia cell line RS4;11 that represents the KMT2A-rearranged subtype.
Project description:Purpose: The goals of this study are to study the expression of Sfxn3 in C57B/L6 mouse retina and retinal cell types Methods: Library prepared followed by 10X Genomics standard protocol. Transcriptome were generated by high throughput sequencing