scholarly journals High-throughput single-cell transcriptome profiling of plant cell types

2018 ◽  
Author(s):  
Christine N. Shulse ◽  
Benjamin J. Cole ◽  
Gina M. Turco ◽  
Yiwen Zhu ◽  
Siobhan M. Brady ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Marker Genes ◽  
Single Cell Rna Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Heterogeneous Tissues ◽  
Genomic Basis

AbstractSingle-cell transcriptome analysis of heterogeneous tissues can provide high-resolution windows into the genomic basis and spatiotemporal dynamics of developmental processes. Here we demonstrate the feasibility of high-throughput single-cell RNA sequencing of plant tissue using the Drop-seq approach. Profiling of >4,000 individual cells from the Arabidopsis root provides transcriptomes and marker genes for a diversity of cell types and illuminates the gene expression changes that occur across endodermis development.

scholarly journals High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Cell Reports ◽  
2019 ◽  
Vol 27 (7) ◽  
pp. 2241-2247.e4 ◽  
Author(s):  
Christine N. Shulse ◽  
Benjamin J. Cole ◽  
Doina Ciobanu ◽  
Junyan Lin ◽  
Yuko Yoshinaga ◽  
...  
Keyword(s):  
Single Cell ◽  
Plant Cell ◽  
High Throughput ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

scholarly journals A single cell transcriptome atlas of the developing zebrafish hindbrain

2019 ◽  
Author(s):  
Monica Tambalo ◽  
Richard Mitter ◽  
David G. Wilkinson
Keyword(s):  
Single Cell ◽  
Neuronal Differentiation ◽  
Cell Types ◽  
Spatial Patterning ◽  
Rna Seq ◽  
Valuable Resource ◽  
Dorsoventral Axis ◽  
Single Cell Rna Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractSegmentation of the vertebrate hindbrain leads to the formation of rhombomeres, each with a distinct anteroposterior identity. Specialised boundary cells form at segment borders that act as a source or regulator of neuronal differentiation. In zebrafish, there is spatial patterning of neurogenesis in which non-neurogenic zones form at bounderies and segment centres, in part mediated by Fgf20 signaling. To further understand the control of neurogenesis, we have carried out single cell RNA sequencing of the zebrafish hindbrain at three different stages of patterning. Analyses of the data reveal known and novel markers of distinct hindbrain segments, of cell types along the dorsoventral axis, and of the transition of progenitors to neuronal differentiation. We find major shifts in the transcriptome of progenitors and of differentiating cells between the different stages analysed. Supervised clustering with markers of boundary cells and segment centres, together with RNA-seq analysis of Fgf-regulated genes, has revealed new candidate regulators of cell differentiation in the hindbrain. These data provide a valuable resource for functional investigations of the patterning of neurogenesis and the transition of progenitors to neuronal differentiation.

scholarly journals DSAVE: Detection of misclassified cells in single-cell RNA-Seq data

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243360
Author(s):  
Johan Gustafsson ◽  
Jonathan Robinson ◽  
Juan S. Inda-Díaz ◽  
Elias Björnson ◽  
Rebecka Jörnsten ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Types ◽  
Rna Seq ◽  
Cell Type ◽  
Log Likelihood ◽  
Single Cell Rna Sequencing ◽  
Cell Transcriptome ◽  
Average Gene ◽  
Single Cell Transcriptome

Single-cell RNA sequencing has become a valuable tool for investigating cell types in complex tissues, where clustering of cells enables the identification and comparison of cell populations. Although many studies have sought to develop and compare different clustering approaches, a deeper investigation into the properties of the resulting populations is lacking. Specifically, the presence of misclassified cells can influence downstream analyses, highlighting the need to assess subpopulation purity and to detect such cells. We developed DSAVE (Down-SAmpling based Variation Estimation), a method to evaluate the purity of single-cell transcriptome clusters and to identify misclassified cells. The method utilizes down-sampling to eliminate differences in sampling noise and uses a log-likelihood based metric to help identify misclassified cells. In addition, DSAVE estimates the number of cells needed in a population to achieve a stable average gene expression profile within a certain gene expression range. We show that DSAVE can be used to find potentially misclassified cells that are not detectable by similar tools and reveal the cause of their divergence from the other cells, such as differing cell state or cell type. With the growing use of single-cell RNA-seq, we foresee that DSAVE will be an increasingly useful tool for comparing and purifying subpopulations in single-cell RNA-Seq datasets.

scholarly journals Single Cell Transcriptome Data Analysis Defines the Heterogeneity of Peripheral Nerve Cells in Homeostasis and Regeneration

2021 ◽  
Vol 15 ◽  
Author(s):  
Bing Chen ◽  
Matthew C. Banton ◽  
Lolita Singh ◽  
David B. Parkinson ◽  
Xin-peng Dun
Keyword(s):  
Endothelial Cells ◽  
Data Analysis ◽  
Single Cell ◽  
Schwann Cells ◽  
Peripheral Nerves ◽  
Cell Types ◽  
Transcriptome Data ◽  
Single Cell Rna Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

The advances in single-cell RNA sequencing technologies and the development of bioinformatics pipelines enable us to more accurately define the heterogeneity of cell types in a selected tissue. In this report, we re-analyzed recently published single-cell RNA sequencing data sets and provide a rationale to redefine the heterogeneity of cells in both intact and injured mouse peripheral nerves. Our analysis showed that, in both intact and injured peripheral nerves, cells could be functionally classified into four categories: Schwann cells, nerve fibroblasts, immune cells, and cells associated with blood vessels. Nerve fibroblasts could be sub-clustered into epineurial, perineurial, and endoneurial fibroblasts. Identified immune cell clusters include macrophages, mast cells, natural killer cells, T and B lymphocytes as well as an unreported cluster of neutrophils. Cells associated with blood vessels include endothelial cells, vascular smooth muscle cells, and pericytes. We show that endothelial cells in the intact mouse sciatic nerve have three sub-types: epineurial, endoneurial, and lymphatic endothelial cells. Analysis of cell type-specific gene changes revealed that Schwann cells and endoneurial fibroblasts are the two most important cell types promoting peripheral nerve regeneration. Analysis of communication between these cells identified potential signals for early blood vessel regeneration, neutrophil recruitment of macrophages, and macrophages activating Schwann cells. Through this analysis, we also report appropriate marker genes for future single cell transcriptome data analysis to identify cell types in intact and injured peripheral nerves. The findings from our analysis could facilitate a better understanding of cell biology of peripheral nerves in homeostasis, regeneration, and disease.

scholarly journals Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine

2019 ◽  
Vol 217 (2) ◽  
Author(s):  
Yalong Wang ◽  
Wanlu Song ◽  
Jilian Wang ◽  
Ting Wang ◽  
Xiaochen Xiong ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Intestine ◽  
Hormone Secretion ◽  
Cell Types ◽  
Nutrient Absorption ◽  
Marker Genes ◽  
Human Intestine ◽  
Colon And Rectum ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

The intestine plays an important role in nutrient digestion and absorption, microbe defense, and hormone secretion. Although major cell types have been identified in the mouse intestinal epithelium, cell type–specific markers and functional assignments are largely unavailable for human intestine. Here, our single-cell RNA-seq analyses of 14,537 epithelial cells from human ileum, colon, and rectum reveal different nutrient absorption preferences in the small and large intestine, suggest the existence of Paneth-like cells in the large intestine, and identify potential new marker genes for human transient-amplifying cells and goblet cells. We have validated some of these insights by quantitative PCR, immunofluorescence, and functional analyses. Furthermore, we show both common and differential features of the cellular landscapes between the human and mouse ilea. Therefore, our data provide the basis for detailed characterization of human intestine cell constitution and functions, which would be helpful for a better understanding of human intestine disorders, such as inflammatory bowel disease and intestinal tumorigenesis.

scholarly journals Single cell transcriptome atlas of the Drosophila larval brain

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Clarisse Brunet Avalos ◽  
G Larisa Maier ◽  
Rémy Bruggmann ◽  
Simon G Sprecher
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Marker Genes ◽  
Neural Cells ◽  
Larval Brain ◽  
Cell Diversity ◽  
Transcriptional Changes ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
The Brain

Cell diversity of the brain and how it is affected by starvation, remains largely unknown. Here, we introduce a single cell transcriptome atlas of the entire Drosophila first instar larval brain. We first assigned cell-type identity based on known marker genes, distinguishing five major groups: neural progenitors, differentiated neurons, glia, undifferentiated neurons and non-neural cells. All major classes were further subdivided into multiple subtypes, revealing biological features of various cell-types. We further assessed transcriptional changes in response to starvation at the single-cell level. While after starvation the composition of the brain remains unaffected, transcriptional profile of several cell clusters changed. Intriguingly, different cell-types show very distinct responses to starvation, suggesting the presence of cell-specific programs for nutrition availability. Establishing a single-cell transcriptome atlas of the larval brain provides a powerful tool to explore cell diversity and assess genetic profiles from developmental, functional and behavioral perspectives.

scholarly journals High throughput, error corrected Nanopore single cell transcriptome sequencing

2019 ◽  
Author(s):  
Kevin Lebrigand ◽  
Virginie Magnone ◽  
Pascal Barbry ◽  
Rainer Waldmann
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Rna Splicing ◽  
Transcriptome Profiling ◽  
Cell Isolation ◽  
Sequence Information ◽  
Isolation System ◽  
Single Cell Isolation ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

ABSTRACTDroplet-based high throughput single cell isolation techniques tremendously boosted the throughput of single cell transcriptome profiling experiments. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. We introduce an approach that combines Oxford Nanopore sequencing with unique molecular identifiers to obtain error corrected full length sequence information with the 10×Genomics single cell isolation system. This allows to examine differential RNA splicing and RNA editing at a single cell level.

scholarly journals SARS-CoV-2 Neurotropism and Single Cell Responses in Brain Organoids Containing Innately Developing Microglia

2021 ◽  
Author(s):  
Samudyata ◽  
Ana Osorio Oliveira ◽  
Susmita Malwade ◽  
Nuno Rufino de Sousa ◽  
Sravan K Goparaju ◽  
...  
Keyword(s):  
Single Cell ◽  
Neuronal Cell Death ◽  
Neuronal Cell ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Cellular Responses ◽  
Cellular Respiration ◽  
Neuropsychiatric Manifestations ◽  
Altered Blood ◽  
Cell Transcriptome

Neuropsychiatric manifestations are common in both acute and post-acute phase of SARS-CoV-2 infection, but the mechanism of these effects is unknown. Here, we derive human brain organoids with innately developing microglia to investigate the cellular responses to SARS-CoV-2 infection on a single cell level. We find evidence of limited tropism to SARS-CoV-2 for all major cell types and observe extensive neuronal cell death that also include non-infected cells. Single cell transcriptome profiling reveals distinct responses in microglia and astrocytes that share features with cellular states observed in neurodegenerative diseases, includes upregulation of genes with relevance for synaptic stripping, and suggests altered blood brain barrier integrity. Across all cell types, we observe a global translational shut-down as well as altered carbohydrate metabolism and cellular respiration. Together, our findings provide insights into cellular responses of the resident brain immune cells to SARS-CoV-2 and pinpoint mechanisms that may be of relevance for the neuropathological changes observed in COVID-19 patients.

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