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      A Role for Two-Pore Channel Type 2 (TPC2)-Mediated Regulation of Membrane Contact Sites During Zebrafish Notochord Biogenesis?

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          Abstract

          We have previously shown that in the developing trunk of zebrafish embryos, two-pore channel type 2 (TPC2)-mediated Ca 2+ release from endolysosomes plays a role in the formation of the skeletal slow muscle. In addition, TPC2-mediated Ca 2+ signaling is required for axon extension and the establishment of synchronized activity in the primary motor neurons. Here, we report that TPC2 might also play a role in the development of the notochord of zebrafish embryos. For example, when tpcn2 was knocked down or out, increased numbers of small vacuoles were formed in the inner notochord cells, compared with the single large vacuole in the notochord of control embryos. This abnormal vacuolation was associated with embryos displaying attenuated body axis straightening. We also showed that TPC2 has a distinct pattern of localization in the notochord in embryos at ∼24 hpf. Finally, we conducted RNAseq to identify differentially expressed genes in tpcn2 mutants compared to wild-type controls, and found that those involved in actin filament severing, cellular component morphogenesis, Ca 2+ binding, and structural constituent of cytoskeleton were downregulated in the mutants. Together, our data suggest that TPC2 activity plays a key role in notochord biogenesis in zebrafish embryos.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

            A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.
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              Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

              R. Edgar (2002)
              The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.
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                Author and article information

                Journal
                Contact (Thousand Oaks)
                Contact (Thousand Oaks)
                CTC
                spctc
                Contact
                SAGE Publications (Sage CA: Los Angeles, CA )
                2515-2564
                7 November 2023
                Jan-Dec 2023
                : 6
                : 25152564231211409
                Affiliations
                [1 ]The Division of Life Science and Key State Laboratory for Molecular Neuroscience, Ringgold 58207, universityHKUST, Hong Kong; , People’s Republic of China
                Author notes
                [ # ]

                Joint first author.

                [ § ]

                Present address: Randall Centre of Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, Guy's Campus, King's College London, London, UK.

                [*]Sarah E. Webb, The Division of Life Science and Key State Laboratory for Molecular Neuroscience, HKUST, Clear Water Bay, Hong Kong, People’s Republic of China. Email: barnie@ 123456ust.hk
                Author information
                https://orcid.org/0000-0002-0108-6606
                Article
                10.1177_25152564231211409
                10.1177/25152564231211409
                10658360
                0e74b3a2-3347-4593-abd0-48bd43a8948a
                © The Author(s) 2023

                This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License ( https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access page ( https://us.sagepub.com/en-us/nam/open-access-at-sage).

                History
                : 27 June 2023
                : 09 October 2023
                : 16 October 2023
                Funding
                Funded by: The Hong Kong Research Grants Council General Research Fund;
                Award ID: 16100719
                Funded by: The Hong Kong Innovation and Technology Commission;
                Award ID: ITCPD/17-9
                Categories
                Membrane Contact Sites as Hubs for Ca 2+ Signaling
                Original Research
                Custom metadata
                ts19
                January-December 2023

                notochord development,endolysosomal vesicles,two-pore channel type 2,tpcn2 mutants and morphants,trans-ned19,zebrafish embryos

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