Cells of eukaryotic multicellular organisms have inherent heterogeneity.Recent advances in single-cell gene expression studies enable us to explore transcriptional regulation in dynamic development processes and highl...Cells of eukaryotic multicellular organisms have inherent heterogeneity.Recent advances in single-cell gene expression studies enable us to explore transcriptional regulation in dynamic development processes and highly heterogeneous cell populations.In this study,using a high-throughput single-cell RNA-sequencing assay,we found that the cells in Arabidopsis root are highly heterogeneous in their transcriptomes.A total of 24 putative cell clusters and the cluster-specific marker genes were identified.The spatial distribution and temporal ordering of the individual cells at different developmental stages illustrate their hierarchical structures and enable the reconstruction of continuous differentiation trajectory of root development.Moreover,we found that each root cell cluster exhibits distinct patterns of ion assimilation and hormonal responses.Collectively,our study reveals a high degree of heterogeneity of root cells and identifies the expression signatures of intermediate states during root cell differentiation at single-cell resolution.We also established a web server(http://wanglab.sippe.ac.cn/rootatlas/)to facilitate the use of the datasets generated in this study.展开更多
Gliomas are the most common and malignant intracranial tumors in adults.Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments.However,access to compr...Gliomas are the most common and malignant intracranial tumors in adults.Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments.However,access to comprehensive genomic data and analytical platforms is often limited.Here,we developed the Chinese Glioma Genome Atlas(CGGA),a user-friendly data portal for the storage and interactive exploration of cross-omics data,including nearly 2000 primary and recurrent glioma samples from Chinese cohort.Currently,open access is provided to whole-exome sequencing data(286 samples),mRNA sequencing(1018 samples)and microarray data(301 samples),DNA methylation microarray data(159 samples),and microRNA microarray data(198 samples),and to detailed clinical information(age,gender,chemoradiotherapy status,WHO grade,histological type,critical molecular pathological information,and survival data).In addition,we have developed several tools for users to analyze the mutation profiles,mRNA/microRNA expression,and DNA methylation profiles,and to perform survival and gene correlation analyses of specific glioma subtypes.This database removes the barriers for researchers,providing rapid and convenient access to high-quality functional genomic data resources for biological studies and clinical applications.CGGA is available at http://www.cgga.org.cn.展开更多
基金the State Key Basic Research Program of China(2013CB127000)National Natural Science Foundation of China(31430013+5 种基金31222029912173023,31525004)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27030101)Young Elite Scientists Sponsorship Program by CAST(2016QNRC001)National Postdoctoral Program for Innovative Talents(BX201600178)the Sanofi-SI BS 2017 Post-doctoral Fellowship.
文摘Cells of eukaryotic multicellular organisms have inherent heterogeneity.Recent advances in single-cell gene expression studies enable us to explore transcriptional regulation in dynamic development processes and highly heterogeneous cell populations.In this study,using a high-throughput single-cell RNA-sequencing assay,we found that the cells in Arabidopsis root are highly heterogeneous in their transcriptomes.A total of 24 putative cell clusters and the cluster-specific marker genes were identified.The spatial distribution and temporal ordering of the individual cells at different developmental stages illustrate their hierarchical structures and enable the reconstruction of continuous differentiation trajectory of root development.Moreover,we found that each root cell cluster exhibits distinct patterns of ion assimilation and hormonal responses.Collectively,our study reveals a high degree of heterogeneity of root cells and identifies the expression signatures of intermediate states during root cell differentiation at single-cell resolution.We also established a web server(http://wanglab.sippe.ac.cn/rootatlas/)to facilitate the use of the datasets generated in this study.
基金supported by the National Natural Science Foundation of China(Grant Nos.81702460 and 81802994)
文摘Gliomas are the most common and malignant intracranial tumors in adults.Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments.However,access to comprehensive genomic data and analytical platforms is often limited.Here,we developed the Chinese Glioma Genome Atlas(CGGA),a user-friendly data portal for the storage and interactive exploration of cross-omics data,including nearly 2000 primary and recurrent glioma samples from Chinese cohort.Currently,open access is provided to whole-exome sequencing data(286 samples),mRNA sequencing(1018 samples)and microarray data(301 samples),DNA methylation microarray data(159 samples),and microRNA microarray data(198 samples),and to detailed clinical information(age,gender,chemoradiotherapy status,WHO grade,histological type,critical molecular pathological information,and survival data).In addition,we have developed several tools for users to analyze the mutation profiles,mRNA/microRNA expression,and DNA methylation profiles,and to perform survival and gene correlation analyses of specific glioma subtypes.This database removes the barriers for researchers,providing rapid and convenient access to high-quality functional genomic data resources for biological studies and clinical applications.CGGA is available at http://www.cgga.org.cn.
