scholarly journals A single-cell RNA-seq analysis of Brachyury-expressing cell clusters suggests a morphogenesis-associated signal center of oral ectoderm in sea urchin embryos

Author(s):  
Noriyuki Satoh ◽  
Kanako Hisata ◽  
Stephany Foster ◽  
Shumpei Morita ◽  
Koki Nishitsuji ◽  
...  
2019 ◽  
Author(s):  
Christina Huan Shi ◽  
Kevin Y. Yip

AbstractK-mer counting has many applications in sequencing data processing and analysis. However, sequencing errors can produce many false k-mers that substantially increase the memory requirement during counting. We propose a fast k-mer counting method, CQF-deNoise, which has a novel component for dynamically identifying and removing false k-mers while preserving counting accuracy. Compared with four state-of-the-art k-mer counting methods, CQF-deNoise consumed 49-76% less memory than the second best method, but still ran competitively fast. The k-mer counts from CQF-deNoise produced cell clusters from single-cell RNA-seq data highly consistent with CellRanger but required only 5% of the running time at the same memory consumption, suggesting that CQF-deNoise can be used for a preview of cell clusters for an early detection of potential data problems, before running a much more time-consuming full analysis pipeline.


2019 ◽  
Vol 86 (8) ◽  
pp. 931-934 ◽  
Author(s):  
Stephany Foster ◽  
Yee Voan Teo ◽  
Nicola Neretti ◽  
Nathalie Oulhen ◽  
Gary M. Wessel

1983 ◽  
Vol 80 (9) ◽  
pp. 2656-2660 ◽  
Author(s):  
D. A. Lynn ◽  
L. M. Angerer ◽  
A. M. Bruskin ◽  
W. H. Klein ◽  
R. C. Angerer

Open Biology ◽  
2016 ◽  
Vol 6 (6) ◽  
pp. 160062 ◽  
Author(s):  
Arseniy R. Morov ◽  
Tharcisse Ukizintambara ◽  
Rushan M. Sabirov ◽  
Kinya Yasui

Acquisition of dorsal structures, such as notochord and hollow nerve cord, is likely to have had a profound influence upon vertebrate evolution. Dorsal formation in chordate development thus has been intensively studied in vertebrates and ascidians. However, the present understanding does not explain how chordates acquired dorsal structures. Here we show that amphioxus retains a key clue to answer this question. In amphioxus embryos, maternal nodal mRNA distributes asymmetrically in accordance with the remodelling of the cortical cytoskeleton in the fertilized egg, and subsequently lefty is first expressed in a patch of blastomeres across the equator where wnt8 is expressed circularly and which will become the margin of the blastopore. The lefty domain co-expresses zygotic nodal by the initial gastrula stage on the one side of the blastopore margin and induces the expression of goosecoid , not-like, chordin and brachyury1 genes in this region, as in the oral ectoderm of sea urchin embryos, which provides a basis for the formation of the dorsal structures. The striking similarity in the gene regulations and their respective expression domains when comparing dorsal formation in amphioxus and the determination of the oral ectoderm in sea urchin embryos suggests that chordates derived from an ambulacrarian-type blastula with dorsoventral inversion.


2017 ◽  
Author(s):  
DT Severson ◽  
RP Owen ◽  
MJ White ◽  
X Lu ◽  
B Schuster-Böckler

ABSTRACTTechnical variance is a major confounding factor in single-cell RNA sequencing, not least because it is not possible to replicate measurements on the same cell. We present BEARscc, a tool that uses RNA spike-in controls to simulate experiment-specific technical replicates. We demonstrate that the tool improves the unsupervised classification of cells and facilitates the biological interpretation of single-cell RNA-seq experiments.


2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A753-A754
Author(s):  
Jingfei Chen ◽  
Jialei Duan ◽  
Alina Montalbano ◽  
Boxun Li ◽  
Gary Hon ◽  
...  

Abstract Single-cell RNA-seq of Mouse Decidual Leukocytes Reveals Intriguing Gestational Changes in the Immune Cell Landscape and Effects of SRC-1/-2 Double-DeficiencyOur previous findings suggest that the fetus signals the mother when it is ready to be born through secretion of surfactant components/immune modulators, surfactant protein A (SP-A) and platelet-activating factor (PAF) by the fetal lung into amniotic fluid (AF). This occurs with increased proinflammatory cytokine expression by fetal AF macrophages (Mϕ), increased myometrial NF-κB activation and contractile (CAP) gene expression. Steroid receptor coactivator (Src)-1 and Src-2 are critical for developmental induction SP-A and PAF by the fetal lung. The finding that pregnant wild-type (WT) mice carrying Src-1 and Src-2 double-deficient fetuses (Src-1/-2d/d) manifested a marked delay (~38h) in parturition, further suggests that signals for parturition arise from the fetus and that Src-1 and Src-2 serve a critical role. Infiltrating leukocytes at the maternal-fetal interface (MFI)/decidua are known to play a central role in pregnancy maintenance and parturition timing. However, there is limited knowledge regarding gestational changes in immune cell composition toward term. To analyze gestational changes in the composition of immune cells within decidua and effects of Src-1/-2d/d, we conducted single-cell RNA-seq of ~17,000 decidual leukocytes (CD45+) from pregnant mice at 15.5 and 18.5 dpc carrying WT or Src-1/-2d/d fetuses. Unsupervised clustering identified 22 distinct decidual immune cell clusters, comprised of Mϕ, B cells, natural killer cells, neutrophils, dendritic cells and monocytes. Significant differences in cell type composition and transcriptional profiles were found across study groups (WT @ 15.5 dpc vs. 18.5 dpc; Src-1/-2d/dvs. WT @15.5 dpc and 18.5 dpc). Interestingly, in deciduas of pregnant mice carrying WT fetuses, Mϕ and B cell clusters markedly increased between 15.5 and 18.5 dpc, whereas, neutrophils declined; however, these gestational changes did not occur in pregnant mice carrying Src-1/-2d/d fetuses. Differential gene expression and gene ontology enrichment analyses revealed specific gene expression patterns distinguishing these immune cell subtypes to uncover their putative functions. These findings highlight the complexity and dynamics of the decidual immune cell landscape during the transition from myometrial quiescence to contractility, and the fetal-maternal interactions leading to parturition. Support: NIH grants R01-HL050022 (CRM) and P01-HD087150 (CRM), Burroughs Wellcome Preterm Birth Grant #1019823 (CRM).


2003 ◽  
Vol 262 (1) ◽  
pp. 107-118 ◽  
Author(s):  
Vincenzo Cavalieri ◽  
Giovanni Spinelli ◽  
Maria Di Bernardo

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