Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.
Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 91,922 nuclei in the mouse cerebellum across eleven developmental stages, from the beginning of neurogenesis (e10.5) till adulthood (P63). The study included two biological replicates per stage, one from each sex. Cerebelli were dissected as whole or in two halves, nuclei were extracted and profiled using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).
Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 19,204 nuclei in the opossum (Monodelphis domestical) cerebellum across two developmental stages (postnatal day 21 and adult). The study included two biological replicates per stage, one from each sex, and an additional adult sample enriched for white matter. Cerebelli were dissected in two halves, nuclei were extracted from one half and profiled using 10x single-cell ATAC reagent kit (v1.1) and a Chromium controller. The white matter enriched sample was dissected from coronal cerebellum slices. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).
Project description:The aim of the experiment was to identify HAND1 target genes and its impact on chromatin accessibility in relation to cardiac development. A HAND1-null hESC line was used, in which a doxycycline-inducible HAND1-T2A-BFP transgene had been integrated in approximately half of the cells for HAND1 rescue / overexpression. The hESCs were differentiated with BMP4, Activin A and CHIR. On day 2.5, doxycycline was added. On day 3, cells were dissociated and sorted by BFP level using FACS. Samples were immediately processed for RNA-seq and ATAC-seq.
Project description:The experiment aimed to resolve cellular heterogeneity in cardiac differentiation through the purification of different cell populations by lineage markers and analysis of their transcriptomes and chromatin accessibility. The differentiation protocol was designed to promote cell diversity. The addition of SB at day 2, inhibited SMAD2/3 phosphorylation and created a high BMP signalling bias to restrict cardiac differentiation in favour of other mesodermal lineages, whereas the addition of DMH1 at day 2, inhibited SMAD1/5/8 phosphorylation to create a high Activin signaling bias to promote the co-differentiation of endoderm. Cells were sorted based on SOX17-tomato and NKX2-5-GFP knock-in reporters into their major classes: Pop1 = SB_G0_T0 Pop2 = SB_G1_T0 Pop3 = CTRL_G0_T0 Pop4 = CTRL_G1_T0 Pop5 = DM_G0_T0 Pop6 = DM_G1_T0 Pop7 = DM_G1_T1 Pop8 = DM_G0_T1
Project description:A map of open chromatin in control and Irx3-KO beige ME3 preadipocytes cells on days 0, 1 and 7 of adipogenic differentiation. Cells were differentiated for indicated number of days, pelleted and snap-frozen in liquid nitrogen. After thawing, cells were treated with DNase to remove exogenous DNA released from cells that died prior to freezing. Remaining cells were lysed in ATAC-seq lysis buffer from the ATAC-seq. Crude nuclear extracts was isolated by centrifugation and resuspended in Tagmentation buffer. Nuclear integrety was verified under microscope, and 50,000 nuclei were transferred for tagmentation. Tagmentation and indexing was performed according to the instructions of the ATAC-seq Kit (Active Motif Catalog No. 53150). Library QC was performed on a Bioanalyzer, and the library was sequenced on a HiSeq4000 Illumina platform using 75 bp paired end sequencing. Reads were filtered to remove low quality mappings, duplicates and mitochondrial mappings. Peaks were called by Macs2 and ENCODE blacklisted regions were excluded. Differentially open chromatin was identified by featurecounts and DESeq2.
Project description:Here, we generated multiome (coupled scRNA-seq and scATAC-seq) data over a time course of mid- and hindbrain organoid development to map cell composition and explore the regulatory mechanisms underlying cell type maturation. The dataset incorporates 5 time points from day 7 to day 120 from 3 human induced pluripotent stem cell (iPSC) lines using 2 previously established protocols. The protocols differentially generate ventral and dorsal cell types, and together cover regions such as floor-plate, dorsal and ventral midbrain, cerebellum, and additional parts of hindbrain. Comparing the data to a reference atlas of the developing human brain and to an integrated neural organoid cell atlas, we find that the gene regulatory architecture in organoid cells is predictive of primary counterparts and also that multiple regions are under-represented in existing organoid models.
Project description:This study used droplet-based 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 E19. 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 Multiome ATAC + Gene Expression Reagent kits (v1) 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:ATAC-seq was performed in the ovarian cancer cell lines COV-434, ES-2, Kuramochi, OAW28, OAW42, OVISE, SKOV-3, TOV-112D. The aim of this experiment was to detect open chromatin sites. Enhancers are associated with open chromatin sites flanked by histones with H3K4me1 and H3K27ac marks. Therefore, the combination of this ATAC-seq experiment with histone ChIP-seq is complementary for the detection of enhancers. Omni-ATAC-seq was performed as described by Corces et al. 2017 with some modifications, which are described in detail in the protocol.