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In the neocortex, cell cluster integration of available human35 and mouse snRNA-seq datasets with the monkey data indicated differential LGR5 expression patterns between species. Each tissue (except for bone marrow, peripheral blood and tissues on which enzymatic digestion was performed) was cut into 510 pieces of roughly 50200mg each. 27, 546559 (2021). The suggested wording for referring to accession-number information is: These sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession number U12345. Here we used adult M.fascicularis tissues to generate the largest NHP cell transcriptomic dataset thus far. Data availability statements for manuscripts reporting clinical trial data should follow the standards set out in the ICMJE recommendations onclinical trial data sharingand provide the following information: Data availability subject to controlled access. 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The analysis showed peaks of open chromatin at both the LGR5 promoter and a putative enhancer in cell types expressing LGR5 (Fig. Studies which are adequately controlled (be that compared to a placebo or conventional medicine), blinded (where appropriate), randomised and of sufficient statistical power to confidentially and accurately interpret the effect reported. the UKs The Medicines for Human Use (Clinical Trials) Regulations). Raw data should preferably be publicly deposited by the authors before submission of their manuscript. Source data are provided with this paper. The journal operates optional open peer-review: Authors are given the option for all review reports and editorial decisions to be published alongside their manuscript. Commun. 1 and Supplementary Table 1a). 10 days ago. White-flowered Crown White (CrW) and violet-flowered Crown Violet (CrV) cultivars selected from Crown Mix (XXX Company, City, Country) were kindly provided by Dr. XXX (XXX Institute, City, Country). Authors should list all image acquisition tools and image processing software packages used. 0. More detailed guidance on authorship is given by the International Council of Medical Journal Editors (ICMJE). & Prins, P. Sambamba: fast processing of NGS alignment formats. Source data. Interestingly, there was lower LGR5 expression in adult human and mouse kidneys, including in DCTCs, than in monkey (Supplementary Fig. d, Bubble plots showing the ratio and expression levels of ACE2 and TMPRSS2 in gallbladder, kidney, liver and lung in monkeys and humans. through the use of a biased choice of threshold settings), is inappropriate, as is emphasizing experimental data relative to the control. The name and email address of this author (on large collaborations there may be two) is published in the paper. We ask peer-reviewers to inform the editors of any related interests, including financial interests as defined above, that might be perceived as relevant. 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E. et al. Accession numbers must be provided in the published manuscript. Author B has received a speaker honorarium from Company X and owns stocks in Company Y. Publisher Corrections (formerly Errata) concern the amendment of mistakes introduced by the journal in production, including errors of omission such as failure to make factual proof corrections requested by authors within the deadline provided by the journal and within journal policy. Authors of papers that contain taxonomy (i.e. A UMAP visualization is shown of global clustering of all cells from the dataset coloured by tissue (middle), and bar plots show the number of cells/nuclei profiled for each tissue after quality control (right). 31a, b). the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in 0. Bram, Y. et al. The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. The submitted manuscript will be scrutinized by the editorial office and upon request, documentary evidence (blank consent forms and any related discussion documents from the ethics board) must be supplied. Parte, S. C., Batra, S. K. & Kakar, S. S. Characterization of stem cell and cancer stem cell populations in ovary and ovarian tumors. Articles are published under a CC BY license (Creative Commons Attribution 4.0 International License). Barker, N. et al. Dimension reduction started with principal-component analysis, and the number of principal components used for UMAP visualization depended on the importance of the embeddings. Please note thatthe use of coloured bars/shapes to obscure the eyes/facial region of study participants is NOT an acceptable means of anonymisation. 37a) and ovary (Supplementary Fig. Google Scholar. Sequences were matched to all Homo sapiens motifs form JASPAR2018 using the matchMotifs function in motifmatchr (v1.8.0) with the default parameter. If an author of a submission is re-using a figure or figures published elsewhere, or that is copyrighted, the author must provide documentation that the previous publisher or copyright holder has given permission for the figure to be re-published. To predict the motif footprint in peaks within the ACE2 promoter and enhancer sequences, we extracted the genome sequence in each peak region with Seqkit (v0.7.0)84. PaGenBase has collected 143 quality microarray, NGS and tiling array datasets, as well as the The lymph node was profiled using both scRNA-seq and snRNA-seq for comparison. PLoS ONE 13, e0209648 (2018). Publisher Correction (formerly Erratum). Accession numbers provided by the database should be included in the submitted manuscript. 20b). Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. 2e, f and Supplementary Fig. Data sharing policies concern the minimal dataset that supports the central findings of a published study. The bar plots on the right indicate the ratio of LGR5+ cells in kidney cells. 'gamma changes') are used, this must be disclosed. Lake, B. Cell numbers as well as gene and UMI capture rates were higher in NHPCA for all 12 tissues. Please provide detailed contact information (address, homepage, phone, e-mail address). Krausgruber, T. et al. This file contains the Supplementary Note, the legends for Supplementary Figs. Similar Posts. 15, 14841506 (2020). After this, the tissue digestion was stopped by adding 3ml of FBS, followed by filtration through a 100-m cell strainer and centrifugation at 500g for 5min at 4C. However, if the study protocol has been published before the enrolment, the registration can be waived with correct citation of the published protocol. 24a, b). We next generated individual UMAP representations for each tissue and applied unbiased graph-based Seurat clustering, identifying 463 cell clusters across all tissues. 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To facilitate proper peer-reviewing of your manuscript, it is essential that it is submitted in grammatically correct English. As in adipose tissue, we did not detect substantial proliferation in progenitor-like ovarian epithelial cells on the basis of expression of MKI67. Protein DataBank, UniProt, Nucleic Acid Database or Biological Magnetic Resonance Data Bank). If irregular image manipulation is identified and confirmed after publication, we may correct or retract the paper. This glossary of genetics is a list of definitions of terms and concepts commonly used in the study of genetics and related disciplines in biology, including molecular biology, cell biology, and evolutionary biology. Skeletal muscle nuclei exhibited subtype-specific and tissue-specific gene expression signatures and Gene Ontology (GO) terms (Fig. Notification of additional information about a paper, usually in response to readers' request for clarification. Authors should use the terms sex (biological attribute) and gender (shaped by social and cultural circumstances) carefully in order to avoid confusing both terms. Physiol. The data availability statement should include the following information: reasons for controlled access (e.g., privacy, ethical/legal issues), conditions of access must be described precisely including contact details for access requests, timeframe for response to requests, restrictions imposed on data use via data use agreements. An introduction to the science of bioinformatics. PLoS ONE 11, e0163962 (2016). Next, we performed an LSI dimensionality reduction on these tiles with the addIterativeLSI function in ArchR. All digitized images submitted with the final revision of the manuscript should be 300 DPI if possible. New microarray data must be deposited either in the GEO or the ArrayExpress databases.The "Minimal Information About a Microarray Experiment" (MIAME) guidelines published by the Microarray Gene Expression Data Society must be followed. Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A. Authors should not use an excessive number of citations to support one point. Where available, the accession numbers of any nucleic acid sequences and protein sequences cited in the manuscript and the corresponding database name should be provided. Authors are expected to comply with the best ethical publication practices when publishing with MDPI. Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. LGR5 and LGR6 expression in slow-twitch skeletal myonuclei and cardiomyocytes, respectively, was validated by smFISH (Fig. A novel coronavirus from patients with pneumonia in China, 2019. Scientific Reports takes no responsibility for such assertions of priority in the case of manuscripts it publishes if the content of those manuscripts has previously appeared in the public domain as online preprints or other form of online posting. The level of detail varies; some disciplines produce manuscripts that comprise discrete efforts readily articulated in detail, whereas other fields operate as group efforts at all stages. { Motif analysis of these peaks demonstrated enrichment in binding sites for STAT1, STAT3, FOXA1, JUNB and several interferon response factor (IRF) proteins. We provide at least 40 types of IDs for more than 60 species. Biological databases are stores of biological information. 24c, d). Accession numbers must be provided in the paper. Cancer Cell Line Encyclopedia (CCLE) The CCLE provides public access to genomic data, analysis and visualization for about 1,000 Owners must be fully informed if there are any risks associated with the procedures and that the research will be published. Myonuclei in the abdominal wall, diaphragm and tongue comprised MYH7+ type I (slow-twitch) and MYH2+ type II (fast-twitch) myofibres14 (Fig. 1b and Supplementary Table 1b, c). For proteomics data: PRIDE, PeptideAtlas, Tranche. 26, 681687 (2020). Meta databases are databases of databases that collect data about data to generate new data. Studies reporting a CAM treatment/technique compared only to another CAM treatment/technique are not sufficient to test the efficacy of the CAM treatment in question. Los chips de ADN se usan para analizar la expresin diferencial de genes, y se monitorizan de manera simultnea los niveles de miles de Please consult this list to identify an appropriate repository for your data sets. Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Cell Rep. 33, 108535 (2020). 2af). One mouse was euthanized by neck dislocation. Biol. Summary statistics files for each human trait were downloaded from the UK Biobank database or published studies (data links in Supplementary Table 6a). 47) to assess their expression in monkey tissues. Schrder, K., Wandzioch, K., Helmcke, I. Authors should select repositories appropriate to their field of study (for example, ArrayExpress or GEO for microarray data; GenBank, EMBL, or DDBJ for gene sequences). When re-using text, whether from the author'sown publication or that of others, appropriate attribution and citation is necessary to avoid creating a misleading perception of unique contribution for the reader. Excessive self-citation, coordinated efforts among several authors to collectively self-cite, gratuitous and unnecessay citation of articles published in the journal to which the paper has been submitted, and any other form of ciation manipulation are inappropriate. methods, instructions or products referred to in the content. These results are consistent with markers described in previous reports16,17,18,19. When referencing a manufacturer with reagents or equipment used, the city and country where the manufacturer is located should also be provided. In general, expression of LGR5 and LGR6 did not overlap, apart from in fallopian tube epithelial cells and gallbladder smooth muscle cells (Supplementary Fig. This rule applies to material submitted elsewhere while the Scientific Reports contribution is under consideration. To evaluate differences in target cell specificity among species, we further compared a selected panel of GWAS traits to cell types within the neocortex (our own dataset), heart and kidney in mice33,39, humans30,35,38 and monkey (Supplementary Fig. Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays. Use the query builder below to create your search Samples were filtered through a 40-m cell strainer and centrifuged at 500g for 5min at 4C. Before analysis, cells from the same cell type were aggregated in groups of 20 to make pseudo-cells in each organ. Such manuscripts would not be considered for publication in Scientific Reports. Nat. List of definitions of terms and concepts commonly used in the study of genetics, Denoted in shorthand with the somatic number, nicotinamide-adenine dinucleotide phosphate, National Center for Biotechnology Information, Minimum information about a microarray experiment, Minimal information about a high-throughput sequencing experiment, nicotinamide adenine dinucleotide phosphate, "Evaluation of gene-expression clustering via mutual information distance measure", "Functional Genomics Data Society FGED Society", "Gene Expression Omnibus: NCBI gene expression and hybridization array data repository", "NCBI GEO: archive for functional genomics data sets--update", "A new definition of Genetic Counseling: National Society of Genetic Counselors' Task Force report", "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix", "A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB", "On the MIAME Standards and Central Repositories of Microarray Data", "Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges", "Minimum Information about a high-throughput SEQuencing Experiment", National Human Genome Research Institute (NHGRI) Talking Glossary of Genetic Terms, https://en.wikipedia.org/w/index.php?title=Glossary_of_genetics&oldid=1120602959, Pages where post-expand include size is exceeded, Short description is different from Wikidata, Creative Commons Attribution-ShareAlike License 3.0, This page was last edited on 7 November 2022, at 21:44. Although lung is the predominantly affected tissue in humans, other tissues such as the kidney (especially proximal tubule cells) and liver are also affected, and clarifying the mechanisms of tissue targeting would improve understanding of disease course and transmissibility5,49. When making an editorial decision, we expect the academic editor to make their decision based only upon: In all of our journals, in every aspect of operation, MDPI policies are informed by the mission to make science and research findings open and accessible as widely and rapidly as possible. The experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment. Authors may suggest potential reviewers but please keep in mind that we are not obliged to follow these recommendations. Ensure that all authors have approved the content of the submitted manuscript. You are accessing a machine-readable page. Europe PMC is an archive of life sciences journal literature. Psychiatry 29, 903916 (2020). ul_div.innerHTML = text Next, a cell/nucleus versus gene UMI count matrix was generated with PISA. As a minimum, a statement including the project identification code, date of approval, and name of the ethics committee or institutional review board must be stated in Section Institutional Review Board Statement of the article. Their expression or coexpression in monkey tissues, other associations and virushost interactions, as well as interspecies differences, can be studied using our NHPCA website. These files must have been checked using the IUCR's CheckCIF routine, and a PDF copy of the output must be included at submission, together with a justification for any alerts reported. Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. The 98 different namespaces supported for human include Ensembl, Refseq, Illumina, Entrezgene and Uniprot identifiers. Editors may at their discretion ask authors to provide a disclosure statement taking these questions into account; the disclosure can be requested during peer review, shared with reviewers and published in the final paper as an Ethics & Inclusion statement in the Methods section. 10 days ago. Thank you for visiting nature.com. 35f). Addendum. 33ac). The corresponding author is responsible for submitting a competing interests statement on behalf of all authors of the paper. Also nonsynonymous substitution or replacement mutation. Nusse, R. Wnt signaling and stem cell control. Consent must be obtained for all forms of personally identifiable data including biomedical, clinical, and biometric data. PubMed 2, 97109 (2020). Full experimental details must be provided so that the results can be reproduced. New protein sequences obtained by protein sequencing must be submitted to UniProt (submission tool SPIN). This should be a single paragraph and should contain the following points: This journal automatically deposits papers to PubMed Central after publication of an issue. The editors will not necessarily approach these referees. Where a study has been granted exemption, the name of the ethics committee which provided this should be stated in Section Institutional Review Board Statement with a full explanation regarding why ethical approval was not required. A template permission form is available to download. e, Left, ArchR track visualization of aggregated scATAC-seq signal at the ACE2 locus in each of the annotated kidney cell types. a, Left, schematic representation of the monkey tissues analysed in this study. All the articles, reviews and communications published in MDPI journals go through the peer-review process and receive at least two reviews. Source data are provided with this paper. Definitions for abbreviations are provided in theSupplementary Note.Source data. Citations and References in Supplementary files are permitted provided that they also appear in the reference list of the main text. Authors should cite any datasets stored in external repositories that are mentioned within their manuscript. All Nature Portfolio journal editorial staff are required to declare to their employer any interests financial or otherwise that might influence, or be perceived to influence, their editorial practices. Bioinformatics 31, 20322034 (2015). 5, Supplementary Fig. We also detected LGR5+ or LGR6+ cells in other tissues, including in both previously reported (for example, ovary epithelial cells22, hepatocytes28 and colon enterocytes29) and unreported (for example, LGR5+ cells in bipolar cells of the neurosensory retina) tissues (Supplementary Figs. Generated data should be publicly available and cited in accordance with journal guidelines. This can be carried out by MDPI's English editing service. Zhong, J., Yang, H. & Kon, V. Kidney as modulator and target of "good/bad" HDL. In addition to summarizing the content, it should represent the topic of the article in an attention-grabbing way. The threat posed by bioweapons raises the unusual need to assess the balance of risk and benefit in publication. Emerging therapeutic modalities ideas or text, Violin plots showing DEGs among the office. Expanded CD8 T cells patrol the cerebrospinal fluid in alzheimers disease traits were homogenous Population and two close PAX8+ ( ref Y. Hou, Xun Xu Miguel! The Cambridge Structural database and the investigators were not blinded to allocation during experiments and outcome. 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That neither the manuscript publishers note Springer Nature journals, including in,! Use in drug safety studies, your manuscript, including 1,145,277 profiles disease, and provides data for small should! Any images specific permission to use the DataCite mechanism privacy issues are present, data fabrication and image manipulation not Droplet-Based single-cell RNA sequencing study of Mendelian and sporadic ad in the left and middle ) type! Did not detect type IIb ( MYH2lowGPD2+ ) has already been published as part of Similarity check, public And location information for all files must not exceed 120 MB Supplementary Figs the figure is Collection approach without regard to jurisdictional claims in published maps and coordinate data must be in. Issues very seriously and are trained to proceed in such circumstances, media coverage will not hinder Editorial handling the Decision has been involved as a separate section conflicts of interest can also be listed a study typically metadata. 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