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:This study used droplet-based snRNA-seq and joint snRNA-seq and snATAC-seq multiome to profile the gene expression of single nuclei in developing chicken ovaries across three timepoints, from embryonic day (E) 17 to E20. Fertilized chicken eggs (Gallus gallus) were purchased from Granja Santa Isabel and incubated at 37.5 °C in a humidified atmosphere until the required developmental stage. The day when eggs were incubated was considered E0. Single-cell barcoding and library preparation were performed using Chromium Single Cell 3' Reagent Kits (v3 chemistry) for snRNA-seq only and Chromium Single Cell Multiome ATAC + Gene Expression Reagent kits (v1) for multiome experiments with the Chromium Controller instrument (10x Genomics). Sequencing of the libraries was carried out on the Illumina NextSeq 500/550 and initial data processing was performed using Cellranger.
Project description:Mouse embryonic skin samples were collected at E14.5. Dorsolateral skin from littermate control and K14Cre;Shh^fl/fl (Shh cKO) mutant embryos was dissected and processed for 10x Genomics Multiome (simultaneous snRNA-seq and snATAC-seq). Nuclei were isolated and subjected to the Chromium Single Cell Multiome ATAC + Gene Expression protocol.
Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snRNA-seq data is uploaded here.
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:CENP-A, the centromeric histone H3 variant, is essential for the proper segregation of human chromosomes to daughter cells. High CENP-A expression leads to the misincorporation of CENP-A in non-centromeric chromatin and can promote an epithelial-mesenchymal transition (EMT). Here, we explored how CENP-A could promote EMT, considering both its impact on transcription and chromatin structure. For this, we used a MCF10-2A TetOn-CENPA-FLAG-HA cell line where high CENP-A expression can be induced by Doxycycline (Dox) treatment. This cell line is p53-defective (transduction with a dominant-negative (DN) p53 vector). Upon CENP-A overexpression, these cells progressively accumulate mesenchymal states. For the same nuclei, we jointly profiled single-nucleus RNA (snRNA) and single-nucleus ATAC (snATAC) data using 10X Multiome at days 10 and 24 (prior and after the mesenchymal states accumulation). In order to profile changes in transcription and cell states, we compared cells expressing either basal CENP-A levels (non-induced, control with no Dox), or high CENP-A levels (induced with 10 ng/ml Dox).
Project description:A paired single-nuclei RNA and ATAC droplet sequencing atlas of micro dissected human embryonic meningeal development from 6–21 post-conception weeks across cranial regions. Including euploid and Trisomy 21 samples. 10x multiome 3’ v2 was used to perform droplet capture.