Project description:We present a transcriptomic atlas of abiotic stress tolerance in wheat. We employed a systems biology approach to study physiological, metabolomic and transcriptomic responses associated with heat, drought, salinity and their possible combinations. Our objectives were to (1) rank stress treatments based on the overall physiological and growth impacts, (2) identify the core sets of genes common to a particular stress type, (3) examine pathways that are uniquely expressed in the various stress combinations, (4) detect associations between phenotypic and transcriptomic responses, (5) suggest possible transcription factors for further characterization and use in improving wheat performance in multi-stress environments.
Project description:Integration of multi-omics data can provide information on biomolecules from different layers to illustrate the complex biology systematically. Here, we built the first global quantitative atlas containing transcriptomes, proteomes, phospho-proteomes and acetyl-proteomes of 20 tissues in common wheat. We identified 132,570 transcripts, 32,256 proteins, 69,364 phosphorylation sites, and 34,974 acetylation sites across wheat development stages. Our data demonstrated that homoeolog expression bias exists divergence at different omics layers. Regulatory networks dissected critical proteins or genes controlling important biology processes. Four wheat trait-gene families refer to timely flowering, disease resistance, starch biosynthesis-related genes, and seed storage proteins were used as examples to verify our data and shed novel inlight on the importance of post-translational modifications in wheat previously unknown. Importantly, a novel Fusarium crown rot (FCR) resistant gene delta-1-pyrroline-5-carboxylate synthase (TaP5CS1) was identified by FCR-responsive multi-omics techniques. We found that TaP5CS1 confers FCR tolerance via increased proline content and is regulated by histone deacetylase 9 (TaHDA9). Our multi-omics atlas data will accelerate function and mechanism studies of important traits in wheat.
Project description:In this study, we set to take advantage of Marchantias less complex signalling architecture to better understand how plants respond to environmental cues such as stress and time of the day, to modulate the expression of genes and biological pathways. To this end, we constructed an abiotic stress gene expression atlas of Marchantia comprising seven abiotic stresses (darkness, high light, cold, heat, nitrogen deficiency, salt, mannitol) and their pairwise combinations (e.g., cold + salt). We also measured gene expression at six timepoints of a day (12h light/ 12h darkness)
Project description:Microfluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high throughput sequencing enables the construction of high-spatial-resolution multi-omics atlas at the genome scale. Applying it to mouse embryo tissues revealed major tissue (sub)types in early-stage organogenesis, brain micro-vasculatures, and the fine structure of an optical vesicle at the single-cell-layer resolution.
Project description:Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).
Project description:Cell types in the human retina are highly heterogeneous with their abundance varies by several orders of magnitude. To decipher the complexity of gene expression and regulation of the human retinal cell types, we generated a multi-omics single-cell atlas of the adult human retina, including over 250K nuclei for single-nuclei RNA-seq and 150K nuclei for single-nuclei ATAC-seq. Over 60 cell subtypes have been identified based on their transcriptomic profiles, reaching a sensitivity of 0.01%. Integrative analysis of this single-cell multi-omics dataset identified gene regulatory elements across the genome for each cell subtype. In addition, when combined with other data modalities, such as eQTL, potential causal variants can be identified through fine mapping. Taken together, this new dataset represents the most comprehensive single-cell multi-omics profiling for the human retina that enables in-depth molecular characterization of most cell subtypes.
Project description:The pituitary regulates growth, reproduction and other endocrine systems. To investigate transcriptional network epigenetic mechanisms in this gland, we generated paired single nucleus (sn) transcriptome and chromatin accessibility profiles in single mouse pituitaries, and genome-wide sn methylation datasets. Our analysis provided insight into cell type epigenetics, regulatory circuit and gene control mechanisms. Latent variable transcriptome and accessibility data representation resolved both inter-sexual and inter-individual variation in gene control programs. Multi-omics analysis of cell type-specific gene regulatory networks distinguished distinct mechanisms. Particularly, the FoxL2 gonadotrope network is controlled both by FoxL2 expression and by target gene epigenetic status. Co-accessibility analysis comprehensively identified putative regulatory regions, including a region that overlapped the fertility-linked rs11031006 human polymorphism. In vitro CRISPR-deletion at this locus increased Fshb levels, supporting this domain’s predicted regulatory role. The public pituitary atlas [link] is a resource for elucidating cell-type specific gene regulatory mechanisms and principles of transcription circuit control.