Data may be deposited with specialized service providers or institutional/subject repositories, preferably those that use the DataCite mechanism. Meta databases are databases of databases that collect data about data to generate new data. Journalists are encouraged to read the full version of any papers they wish to cover and are given the names and contact information of corresponding authors. Identity of third party provider: the identity of the third party data provider must be made known to the editors at time of submission and peer review. CAS Once given a database accession number, the data in primary databases are never changed: they form part of the scientific record. The journal reserves the right to ask authors to provide signed forms if necessary. Clusters are coloured by tissue (abdominal wall, diaphragm, oesophagus and tongue). Available online: Home Office. When data obtained from third parties cannot be made available, the restrictions should be clearly stated in the data availability statement. Clustering analysis was performed using ArchR by first identifying a robust set of peak regions followed by iterative latent semantic indexing (LSI) clustering. Search. In this regard, it is worth noting that the majority of reports of LGR5+ cells thus far have been in genetically engineered mouse models owing to the lack of specific tools and reagents to study other mammals25. Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinsons disease. Cells of the adult human heart. they should ensure the citation supports the statement made in their manuscript and should not misrepresent another work by citing it if it does not support the point the authors wish to make). No statistical methods were used to predetermine sample size. Feature If part of a contribution that an author wishes to submit to Scientific Reports has appeared or will appear elsewhere, the author must specify the details in the covering letter accompanying the submission. Monkeys were anaesthetized with an injection of ketamine hydrochloride (10mg per kg) and sodium pantabarbital (40mg per kg) before being euthanized by exsanguination. In the ovary, we identified a classical mesothelial population and two close PAX8+ (ref. dbDEMC (database of Differentially Expressed MiRNAs in human Cancers) is an integrated database that designed to store and display differentially expressed microRNAs (miRNAs) in cancers detected by high-throughput and low-throughput methods. For preliminary sorts that use 'cocktails' of antibodies to exclude certain cell populations, for example, lineage-minus (Lin-), the antibodies and fluorochromes that are contained in the 'cocktail' need to be specified for the 'dump' channel. 15, 14841506 (2020). PaGenBase has collected 143 quality microarray, NGS and tiling array datasets, as well as the literature, including 1,145,277 profiles. 2b, c and Supplementary Table 2eg). All raw data produced in this study (including NHPCA and mouse neocortex data) have been deposited to the CNGB Nucleotide Sequence Archive (accession code CNP0001469). Cell Biol. Stl, P., Marklund, S., Thornell, L. E., De Paul, R. & Eriksson, P. O. Fibre composition of human intrinsic tongue muscles. Structures of Small Molecules: Cambridge Structural Database (CSD) and PubChem. Integrated analysis of multimodal single-cell data. & Vento-Tormo, R. CellPhoneDB: inferring cellcell communication from combined expression of multi-subunit ligandreceptor complexes. n=1,144,706 individual cells/nuclei analysed. Cell 180, 764779 (2020). 'Text recycling'or re-use of parts of text from an authors previous research publication is a form of self-plagiarism. Eur. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Peripheral blood mononuclear cells (PBMCs) from heparinized venous blood and bone marrow cells were isolated using Lymphoprep medium (STEMCELL Technologies, 07851) according to a standard density gradient centrifugation protocol. Sequences were matched to all Homo sapiens motifs form JASPAR2018 using the matchMotifs function in motifmatchr (v1.8.0) with the default parameter. articles published under an open access Creative Common CC BY license, any part of the article may be reused without 41 and 42, and Supplementary Table 5b). We encourage authors to take advantage of this opportunity as proof of the rigorous process employed in publishing their research. 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. 1a and Supplementary Figs. Authors are encouraged to use the Microsoft Word template or LaTeX template to prepare their manuscript. Data available in a publicly accessible repository, Data available in a publicly accessible repository that does not issue DOIs, Data available on request due to restrictions eg privacy or ethical, Data is contained within the article or supplementary material. For embedded citations in the text with pagination, use both parentheses and brackets to indicate the reference number and page numbers; for example [5] (p. 10). Permission by email is acceptable. Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney. Authors should be prepared to supply Scientific Reports with original data on request, at the resolution collected, from which their images were generated. Publishers note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided. Most of these databases are cross-referenced with UniProt / UniProtKB so that identifiers can be mapped to each other.[13]. Neither conference presentations nor posting on recognised preprint servers constitute prior publication. In fact, Wnt factors are known to act predominantly on neighbouring cells24,42, and cells from the collecting duct and DCT are in closer physical proximity than other nephron structures (Supplementary Fig. whether individual de-identified participant data (including data dictionaries) will be shared (undecided is not an acceptable answer); whether additional, related documents will be available (e.g., study protocol, statistical analysis plan, etc. Cell 170, 11491163 (2017). 2f). Rev. We used a critical cut-off in this analysis: fold change>2 and adjusted P<0.01. The summary statistics file for each trait was downloaded from the UK Biobank database or published studies (Supplementary Table 6a). Rockx, B. et al. 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. 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. Corresponding and all submitting authors must register with Frontiers before submitting an article. Subcutaneous mature adipocytes and adipocyte progenitors were enriched for FOS expression. Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND, Drafting the work or revising it critically for important intellectual content; AND, Final approval of the version to be published; AND. c, UMAP visualization of specific markers used to identify type I (MYH7), type IIa (MYH2) and type IIb (GPD2) myonuclei, FAPs (LVRN), MTJ nuclei (NAV3 and COL22A1), NMJ nuclei (ETV5 and MUSK) and satellite cells (PAX7), as shown in b. For patents and patent applications, disclosure of the following information is requested: patent applicant (whether author or institution), name of inventor(s), application number, status of application, specific aspect of manuscript covered in patent application. Barker, N. et al. Code availability The mixture was then transferred to a clean 1-ml Dounce homogenizer to which 750l of buffer A containing 1% Igepal (Sigma, CA630) was added, and the tissue was further homogenized by 25 strokes of the tight pestle (pestle B). This policy does not extend to preprints available to the media or that are otherwise publicized outside the scientific community before or during the submission and consideration process at Scientific Reports. To guarantee impartial refereeing, the names of referees will be revealed only if the referees agree to do so, and after a paper has been accepted for publication. Cavalcanti, A. We confirm that neither the manuscript nor any parts of its content are currently under consideration or published in another journal. Author Corrections (formerly Corrigenda) are judged on their relevance to readers and their importance for the published record. Bakken, T. E. et al. Authors of randomized controlled trials should submit a completed CONSORT checklist, available at www.consort-statement.org. 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. Authors must make data available for purposes of peer review, if requested by reviewers, within the terms of a data use agreement and if compliant with ethical and legal requirements. In such cases, the cropping must be mentioned in the figure legend and the supplementary information must include original gels and blots, with gel/membrane edges visible. If previously unpublished de novo cell lines were used, including those gifted from another laboratory, details of institutional review board or ethics committee approval must be given, and confirmation of written informed consent must be provided if the line is of human origin. Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimers disease. Niehrs, C. The complex world of WNT receptor signalling. Advanced; Help; SRA - Now available on the cloud. Tosi, M. F. Innate immune responses to infection. if(elems[i].hasChildNodes()) SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. To cite:Pan JB, Hu SC, Shi D, Cai MC, Li YB, Zou Q, Ji ZL*. The total amount of data for all files must not exceed 120 MB. Scientific Reports will consider manuscripts reporting results from well-conducted clinical trials. Studies in whichconventional treatment is supplemented with a CAM technique are only valid if compared to the same conventional treatment supplemented with a placebo. Osmundsen, A. M., Keisler, J. L., Taketo, M. M. & Davis, S. W. Canonical WNT signaling regulates the pituitary organizer and pituitary gland formation. Accession numbers must be provided in the paper. References should be described as follows, depending on the type of work: In order to ensure the integrity and scientific validity of blots (including, but not limited to, Western blots) and the reporting of gel data, original, uncropped and unadjusted images should be uploaded as Supporting Information files at the time of initial submission. There is no additional cost for publishing full color graphics. During the submission process, please suggest three potential reviewers with the appropriate expertise to review the manuscript. Journal staff are not involved in the processing of their own work submitted to any MDPI journals. Microarray Data: GEO or ArrayExpress. a, Left, schematic representation of the monkey tissues analysed in this study. Alzheimers Res. MDPI data policies are informed by TOP Guidelines and FAIR Principles. Young, M. D. & Behjati, S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. Efremova, M., Vento-Tormo, M., Teichmann, S. A. If a study's design or the manuscript's structure or language has been inspired by previous works, these works must be explicitly cited. e, Heatmap showing DEGs among the skeletal muscle populations highlighted in d. f, Bubble plots showing DEGs for each of the myonucleus subtypes comparing different tissues. Authors should use the Table option of Microsoft Word to create tables. Because of their small proportions, the latter four populations are indicated by a red arrow. 38, 737746 (2020). Leung, C. et al. Scientific Reports follows the Nature Portfolio policies for the sharing of computer code and algorithm (read these policies in full). For more information on how to cite datasets in submitted manuscripts, please see our submission guidelines. Core Data Resource Data type; ArrayExpress: Functional Genomics Data from high-throughput functional genomics experiments. Editors reserve the right to ask for the checklist and to reject submissions that do not adhere to these guidelines, to reject submissions based on ethical or animal welfare concerns or if the procedure described does not appear to be justified by the value of the work presented. that they have not undergone peer review. Villiger, P. M. et al. Articles are published under a CC BY license (Creative Commons Attribution 4.0 International License). Adjustments should be applied to the entire image. Plagiarism is unacknowledged copying or an attempt to misattribute original authorship, whether of ideas or text. After this, the mixture was filtered through a 40-m strainer into a 1.5-ml tube and centrifuged at 500g for 5min at 4C to pellet the nuclei. 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. Nat. Datasets must be made freely available to readers from the date of publication and must be provided to Editorial Board Members and referees at submission, for the purposes of evaluating the manuscript. Translocation of viable gut microbiota to mesenteric adipose drives formation of creeping fat in humans. As proof of principle of the application for studying body-wide cellcell interactions, we examined the distribution of insulin and glucagon receptors throughout the 12 tissues (Supplementary Fig. Hoffmann, M. et al. Use of Research Data Support is optional and does not imply or guarantee that a manuscript will be accepted. CAS [metadatabase is a database model for metadata management, global query of For individual clustering, each tissue dataset was visualized using the Seurat package (v4.0.3)77 in the R environment (v4.0.2). Continue on to the final pages of this online tutorial for recommendations on what to learn next and to tell us what you thought of this tutorial. Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. 12, 2506 (2021). The editorial team will respect these requests so long as this does not interfere with the objective and thorough assessment of the submission. Authors are expected to fulfil the criteria below (adapted from McNutt et al., Proceedings of the National Academy of Sciences, Feb 2018, 201715374; DOI: 10.1073/pnas.1715374115; licensed under CC BY 4.0): Each author is expected to have made substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data; or the creation of new software used in the work; or have drafted the work or substantively revised it. Data from different replicates were integrated following a standard integration pipeline using Seurat. As with the GWAS, we observed a generally higher correlation of the expression in specific cell types between humans and monkeys than between either of these species and mice (Supplementary Fig. Endocrinology 158, 33393353 (2017). Data sharing policies concern the minimal dataset that supports the central findings of a published study. Ovarian Res. These results are consistent with markers described in previous reports16,17,18,19. We also generated a correlation map of specific mutant genes causing human diseases (Supplementary Fig. 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). Financial competing interests includeany of the following: Funding: Research support (including salaries, equipment, supplies, and other expenses) by organizations that may gain or lose financially through this publication. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Rep. 6, 28512 (2016). 101105). Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. 43b). The editors will not necessarily approach these referees. This could influence SARS-CoV-2 pathogenesis and may for example explain why drugs such as hydroxychloroquine, despite providing promising results in monkey cell lines in vitro, are not effective in humans64. In the interests of transparency and to help readers to form their own judgements of potential bias, authors must declare any competing financial and/or non-financial interests in relation to the work described. Submissions authored by editorial staff/editors will be assigned to at least two independent outside reviewers. Authors can disclose potential conflicts of interest via the online submission system during the submission process. JCI Insight 4, e131092 (2019). The DLD-1 cell line was obtained from Dr. XXXX. 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Two close PAX8+ ( ref 4.0 ) license, except where further licensing details are provided on... Also generated a correlation map of specific mutant genes causing human diseases Supplementary! Submitting authors must register with Frontiers before submitting an article 143 quality microarray, NGS and array... Team will respect these requests so long as this does not imply guarantee! Cell types ( Creative Commons attribution 4.0 International license ) optional and not. Was obtained from Dr. XXXX if necessary via the online submission system during the submission process, schematic representation the... Manuscripts, please suggest three potential reviewers with the default parameter importance for the published record in their! With Frontiers before submitting an article by a red arrow exceed 120.. From droplet-based single-cell RNA sequencing data summary statistics file for each trait was downloaded from the Biobank!, except where further licensing details are provided template to prepare their manuscript encouraged to use Table... Availability statement publishing full color graphics at www.consort-statement.org surrounding sequence information to provide signed forms if necessary Seurat! Made available, the data in primary databases are cross-referenced with UniProt UniProtKB! Publishing their research insights into the etiology of Parkinsons disease to generate data... In Alzheimers disease valid if compared to the same conventional treatment supplemented with a CAM are.
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