scholarly journals Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing

Cell Reports ◽  
2018 ◽  
Vol 24 (13) ◽  
pp. 3554-3567.e3 ◽  
Author(s):  
Ping Wang ◽  
Yidong Chen ◽  
Jun Yong ◽  
Yueli Cui ◽  
Rui Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Kidney Development ◽  
Fetal Kidney ◽  
Global Dynamic ◽  
Single Cell Rna Sequencing ◽  
Molecular Profiles ◽  
Human Fetal Kidney

scholarly journals Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development

PLoS Biology ◽  
2019 ◽  
Vol 17 (2) ◽  
pp. e3000152 ◽  
Author(s):  
Mazène Hochane ◽  
Patrick R. van den Berg ◽  
Xueying Fan ◽  
Noémie Bérenger-Currias ◽  
Esmée Adegeest ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Kidney Development ◽  
Fetal Kidney ◽  
Gene Expression Dynamics ◽  
Human Fetal Kidney

scholarly journals Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing

2020 ◽  
Vol 13 (8) ◽  
pp. 1178-1193 ◽  
Author(s):  
Zhixin Liu ◽  
Yaping Zhou ◽  
Jinggong Guo ◽  
Jiaoai Li ◽  
Zixia Tian ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Molecular Profiling ◽  
Cell Development ◽  
Global Dynamic ◽  
Single Cell Rna Sequencing ◽  
Stomatal Lineage

scholarly journals Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development

2020 ◽  
Vol 31 (10) ◽  
pp. 2278-2291 ◽  
Author(s):  
Yishay Wineberg ◽  
Tali Hana Bar-Lev ◽  
Anna Futorian ◽  
Nissim Ben-Haim ◽  
Leah Armon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Kidney Development ◽  
Transcript Length ◽  
Alternative Mrna Splicing ◽  
Single Cell Rna Sequencing ◽  
Splice Isoform ◽  
Isoform Switching

BackgroundDuring mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, Drop-seq single-cell RNA sequencing technology for measuring gene expression from thousands of individual cells identified the different cell types in the developing kidney. However, that analysis did not include the additional layer of heterogeneity that alternative mRNA splicing creates.MethodsFull transcript length single-cell RNA sequencing characterized the transcriptomes of 544 individual cells from mouse embryonic kidneys.ResultsGene expression levels measured with full transcript length single-cell RNA sequencing identified each cell type. Further analysis comprehensively characterized splice isoform switching during the transition between mesenchymal and epithelial cellular states, which is a key transitional process in kidney development. The study also identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2.ConclusionsDiscovery of the sets of genes that are alternatively spliced as the fetal kidney mesenchyme differentiates into tubular epithelium will improve our understanding of the molecular mechanisms that drive kidney development.

scholarly journals Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development

2019 ◽  
Author(s):  
Yishay Wineberg ◽  
Tali Hana Bar-Lev ◽  
Anna Futorian ◽  
Nissim Ben-Haim ◽  
Leah Armon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Kidney Development ◽  
Cell Types ◽  
Additional Layer ◽  
Single Cell Rna Sequencing ◽  
Splice Isoform ◽  
Isoform Switching

ABSTRACTDuring mammalian kidney development, nephron progenitors undergo a mesenchymal to epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, the different cell types in the developing kidney were characterized using the Dropseq single cell RNA sequencing technology for measuring gene expression from thousands of individual cells. However, many genes can also be alternatively spliced and this creates an additional layer of heterogeneity. We therefore used full transcript length single-cell RNA sequencing to obtain the transcriptomes of 544 individual cells from mouse embryonic kidneys. We first used gene expression levels to identify each cell type. Then, we comprehensively characterized the splice isoform switching that occurs during the transition between mesenchymal and epithelial cellular states and identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2. We anticipate that these results will improve our understanding of the molecular mechanisms involved in kidney development.

scholarly journals Single cell RNA sequencing uncovers cellular developmental sequences and novel potential intercellular communications in embryonic kidney

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Isao Matsui ◽  
Ayumi Matsumoto ◽  
Kazunori Inoue ◽  
Yusuke Katsuma ◽  
Seiichi Yasuda ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Kidney Development ◽  
Developmental Process ◽  
Mouse Kidney ◽  
Related Factors ◽  
Embryonic Mouse ◽  
Nephron Progenitors ◽  
Developmental Sequences ◽  
Single Cell Rna Sequencing

AbstractKidney development requires the coordinated growth and differentiation of multiple cells. Despite recent single cell profiles in nephrogenesis research, tools for data analysis are rapidly developing, and offer an opportunity to gain additional insight into kidney development. In this study, single-cell RNA sequencing data obtained from embryonic mouse kidney were re-analyzed. Manifold learning based on partition-based graph-abstraction coordinated cells, reflecting their expected lineage relationships. Consequently, the coordination in combination with ForceAtlas2 enabled the inference of parietal epithelial cells of Bowman’s capsule and the inference of cells involved in the developmental process from the S-shaped body to each nephron segment. RNA velocity suggested developmental sequences of proximal tubules and podocytes. In combination with a Markov chain algorithm, RNA velocity suggested the self-renewal processes of nephron progenitors. NicheNet analyses suggested that not only cells belonging to ureteric bud and stroma, but also endothelial cells, macrophages, and pericytes may contribute to the differentiation of cells from nephron progenitors. Organ culture of embryonic mouse kidney demonstrated that nerve growth factor, one of the nephrogenesis-related factors inferred by NicheNet, contributed to mitochondrial biogenesis in developing distal tubules. These approaches suggested previously unrecognized aspects of the underlying mechanisms for kidney development.

41-OR: Single Cell RNA-Sequencing Reveals the Developmental Heterogeneity of Brown Adipocytes

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 41-OR
Author(s):  
FARNAZ SHAMSI ◽  
MARY PIPER ◽  
LI-LUN HO ◽  
TIAN LIAN HUANG ◽  
YU-HUA TSENG
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Brown Adipocytes ◽  
Single Cell Rna Sequencing
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