JCI Insight 4, e131092 (2019). Moreover, DEGs specific to this LGR5+ population in comparison with other pituitary cells were enriched in GO terms related to development (Supplementary Fig. In other analyses, we used the FindMarkers or FindAllMarkers function in Seurat. We confirm that neither the manuscript nor any parts of its content are currently under consideration or published in another journal. For example, "AB and CD wrote the main manuscript text and EF prepared figures 13. Editorial and publishing policies. However, just as financial interests need not invalidate the conclusions of an article, nor do they automatically disqualify an individual from evaluating it. The BeadChip data set was downloaded as a processed normalized matrix from ArrayExpress (E-TABM-633 (ref. You are using a browser version with limited support for CSS. Authors should use the terms sex (biological attribute) and gender (shaped by social and cultural circumstances) carefully in order to avoid confusing both terms. 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. Editors reserve the rights to reject any submission that does not meet these requirements. According to The International Committee of Medical Journal Editors, Authors should avoid entering into agreements with study sponsors, both for-profit and non-profit, that interfere with authors access to all of the studys data or that interfere with their ability to analyze and interpret the data and to prepare and publish manuscripts independently when and where they choose.. Transcriptional response modules characterize IL-1 and IL-6 activity in COVID-19. 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. Multiple exposures should be presented in Supplementary Information if high contrast is unavoidable. Single-cell transcriptomic atlas of primate ovarian aging. ADS The statement should reflect all the collected potential conflict of interest disclosures in the form. NSW Department of Primary Industries and Animal Research Review Panel. g, UMAP visualization of mesothelial(meso) cells from selected tissues (adrenal gland, bladder, diaphragm, fallopian tube, ovary and visceral adipose tissue). Med. Vankelecom, H. Non-hormonal cell types in the pituitary candidating for stem cell. 25b). Next, we examined the genes encoding Wnt factors and the R-spondin family (RSPO1RSPO4) of ligands for LGR proteins25 in a panel of monkey tissues containing cells with high LGR5 and LGR6 (Supplementary Figs. For related terms, see Glossary of evolutionary biology. Of note, RSPO2 expression was high in inhibitory neurons from the neocortex (Supplementary Fig. All submissions of translations must conform with our, If errors and inaccuracies are found by the authors after publication of their paper, they need to be promptly communicated to the editors of this journal so that appropriate actions can be taken. Advanced; Help; SRA - Now available on the cloud. Processing (such as changing brightness and contrast) is appropriate only when it is applied equally across the entire image and is applied equally to controls. Niehrs, C. The complex world of WNT receptor signalling. d, Stacked bar plots representing the proportions of skeletal muscle nuclei (myonucleus subtypes type I, type IIa and type IIb, MTJ and NMJ nuclei, and satellite cells and FAPs) in the indicated tissues. Notably, we have also shown that the distribution of ACE2 and TMPRSS2 expression across different cell types is not identical between monkeys and humans. Adipocyte progenitors were composed of two populations for visceral tissue (WT1+ITLN1+ and CFDhighWT1lowITLN1), three populations for subcutaneous tissue (ESR1+, CXCL14+APOD+ and DPP4+) and one population shared by both tissues (NOX4+). To address this, we have generated the first version of a large-scale cell transcriptomic atlas for an NHP widely used in research studies, M.fascicularis, and an open, expandable and interactive NHPCA database to facilitate its exploration. Editorial Board Members are welcome to submit papers to the journal. All authors reviewed the manuscript.". Authors of randomized controlled trials should submit a completed CONSORT checklist, available at www.consort-statement.org. New Engl. Sometimes used interchangeably with nucleobase or simply base. The transcription start site enrichment score and fragment number for each nucleus were calculated using ArchR83. For each submitted manuscript supporting genetic information and origin must be provided. We further analysed Wnt receptors and other co-receptors43 as well as the TCF family of transcription factors bound by -catenin44 as a resource for exploration (Supplementary Figs. Cross-species single-cell analysis reveals divergence of the primate microglia program. For research involving human participants, authors must identify the committee that approvedthe research, confirm that all research was performed in accordance with relevant guidelines/regulations, and include in their manuscript a statement confirming that informed consent was obtained from all participants and/or their legal guardians. We encourage our authors to follow the Sex and Gender Equity in Research SAGER guidelines and to include sex and gender considerations where relevant. Moreover, type I and type IIa tongue myonuclei clustered in close proximity, which may be related to the tongue being a highly innervated muscle. It is only necessary to submit to one database as data are exchanged between DDBJ, EMBL and GenBank on a daily basis. Authors should not cite sources that they have not read. Mol. Cells from lymph node and spleen were obtained from fresh tissue by mechanical dissociation. Secondary databases are:[clarification needed]. Delorey, T. M. et al. In global visualization of cell clustering using uniform manifold approximation and projection (UMAP), each tissue tended to cluster separately, with those from the same system generally clustering more closely to each other (Fig. Neurosci. Immunostaining for CD44 and single-molecule fluorescence in situ hybridization (smFISH) for LGR5 confirmed their coexpression in a subset of monkey surface epithelial cells (Supplementary Fig. Huch, M. et al. Molecular Omics publishes high-quality research from across the -omics sciences.. Europe PMC is an archive of life sciences journal literature. 35a, b and 3639). The editorial team will respect these requests so long as this does not interfere with the objective and thorough assessment of the submission. The lymph node was profiled using both scRNA-seq and snRNA-seq for comparison. Likewise, the number of detected main cell types was roughly comparable in the three species (111 in monkeys, 110 in mice and 106 in humans), but with differences in the proportions. MDPI requires a completed CONSORT 2010 checklist and flow diagram as a condition of submission when reporting the results of a randomized trial. This is in agreement with the emerging concept that structural cells have immune properties8,11 and the known immunomodulatory role of the visceral adipose tissue in responses to gut bacteria20. Likewise, the expression of LGR5 in skeletal slow-twitch myofibres and LGR6 in the pituitary gland and heart is intriguing. through the use of a biased choice of threshold settings), is inappropriate, as is emphasizing experimental data relative to the control. ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. Depending on the data described in the manuscript, data availability statements commonly take one of the following forms, or can be a composite of the statements below: The datasets generated during and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS]. 48, D682D688 (2020). We reserve the right to request confirmation that all authors meet the authorship conditions. interesting to authors, or important in this field. 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). Lake, B. After acceptance, the proof is sent to the corresponding author, who deals with Scientific Reports on the behalf of all co-authors; Scientific Reports will not necessarily correct errors after publication if they result from errors that were present on a proof that was not shown to co-authors before publication. Nature 562, 367372 (2018). As with all research involving humans, ethical approval from an appropriate ethics committee must be obtained prior to conducting the study. Please include all the parameters used to run software/programs analyses. We isolated cells/nuclei for 45 different tissue samples from five male and three female 6-year-old monkeys (Fig. 20a). For instance, spinocerebellar ataxia caused by mutations in PLEKHG4 (ref. Generated data should be publicly available and cited in accordance with journal guidelines. Likewise, blood-related traits such as mean sphered cell volume and red blood cell distribution width were enriched in erythroid cells. You may not submit your manuscript elsewhere while it is under consideration at Scientific Reports. Search. In such circumstances, advice will usually be sought simultaneously with the technical peer-review process. Scientific Reports follows the Nature Portfolio policies for the sharing of computer code and algorithm (read these policies in full). 25c). The other well known alternative to GEO is ArrayExpress. MDPI operates Preprints, a preprint server to which submitted papers can be uploaded directly after completing journal submission. BMC Infect. Scientific Reports keeps all details about a submitted manuscript confidential and does not comment to any outside organization about manuscripts that are either under consideration or that have been rejected. Wang, S. et al. It is intended as introductory material for novices; for more specific and technical detail, see the article corresponding to each term iRAP: RNA-seq analysis tool A flexible pipeline for RNA-seq analysis that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. Meta databases are databases of databases that collect data about data to generate new data. For interspecies cell atlas analysis, data were retrieved from the HCL8 and MCA7. Genome Biol. e, Left, ArchR track visualization of aggregated scATAC-seq signal at the ACE2 locus in each of the annotated kidney cell types. You may suggest reviewers from among the authors that you frequently cite in your paper. Notably, migraine had a higher score in human and monkey excitatory neurons than in mice but was more highly enriched in kidney intercalated cells of these two species. Additionally, when studies describe groups by race, ethnicity, gender, disability, disease, etc., explanation regarding why such categorization was needed must be clearly stated in the article. Cell-typespecific receptorligand interactions between cell types were identified on the basis of specific expression of a receptor by one cell type and a ligand by another cell type. The journal requires that clinical trials are prospectively registered in a publicly accessible database and clinical trial registration numbers should be included in all papers that report their results. Bell, L. C. K. et al. To demonstrate the utility of the atlas, we have reconstructed the cellcell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. PubMed Central They should include details of the populations sampled on the site of collection (GPS coordinates), date of collection, and document the part(s) used in the study where appropriate. The lack of enrichment in satellite cells is unsurprising given that we did not apply any injury before obtaining the skeletal muscle tissues. Seurat clusters were then annotated into different cell types using cell-type-specific markers defined in this paper. ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. Available online: American Association for Laboratory Animal Science. Four different clusters of mesothelial cells belonging to the visceral adipose tissue are indicated by the dashed red line. 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. No judgment on the potential impact of the work will be made at this stage. Material in a paper submitted to Scientific Reports may also have been published as part of a PhD or other academic thesis. DCTC,distal convoluted tubule cell;Endo, endothelial cell; LOH, loop of Henle; Myofibro, myofibroblast. Merrick, D. et al. MAGE-ML is the standard format for storing both Affymetrix and cDNA microarray data at the ArrayExpress repository. Biomed. 101105). In brief, nuclei were extracted from tissue using the same protocol as describe above. We encourage authors to ensure that their datasets are either deposited in publicly available repositories (where available and appropriate) or presented in the main manuscript or additional supporting files whenever possible. 33d, e). [2] Omics Discovery Index can be used to browse and search several biological databases. A single-blind review is applied, where authors' identities are known to reviewers. We suggest that our authors consult the full guidelines before submission. Manuscripts submitted to an open Guest Edited Collection may be considered unsuitable for inclusion,particularlyif they fall outside the scope of the Collection. If national legislation requires it, studies involving vertebrates or higher invertebrates must only be carried out after obtaining approval from the appropriate ethics committee. If ethical approval is not required, authors must either provide an exemption from the ethics committee or are encouraged to cite the local or national legislation that indicates ethics approval is not required for this type of study. High levels ofWNT9B in these cells may be responsible for inducing LGR5 (a Wnt pathway target) in monkey DCTCs. Article Nat. Diao, B. et al. Addenda are published when the in-house editors decide that the addendum is crucial to the reader's understanding of a significant part of the published contribution. Use the query builder below to create your search At minimum, your article should report the content addressed by each item of the checklist. This responsibility includes, but is not limited to: (1) ensuring that original data upon which the submission is based is preserved and retrievable for reanalysis; (2) approving data presentation as representative of the original data; and (3) foreseeing and minimizing obstacles to the sharing of data, materials, s or reagents described in the work. We computed Pi,j,k as the fraction of cells in tissue i expressing gene j in cell population k. A given cell-type-specific gene j in tissue i (SCSGi) was defined using the following cut-off: log2(fold change)>2, adjusted P<0.01 and (Pi,j,c1Pi,j,c2)/Pi,j,c1>0.8 (where c1 represents a given cell type in tissue i and c2 represents other cell types in tissue i). ADS Also five-prime untranslated region and leader sequence. g:Convert enables to convert between various gene, protein, microarray probe and numerous other types of namespaces. Chavali, M. et al. Tosi, M. F. Innate immune responses to infection. The editors of this journal enforce a rigorous peer-review process together with strict ethical policies and standards to ensure to add high quality scientific works to the field of scholarly publication. Scientific Reports in-house editors reserve the right to assume responsibility for the management of a Collection at any stage. Deposition of Sequences and Expression Data. Barker, N. et al. You might try searching there. If further clarification is required, please contact the press office by email. Rep. 6, 28512 (2016). 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. & Vento-Tormo, R. CellPhoneDB: inferring cellcell communication from combined expression of multi-subunit ligandreceptor complexes. MIAME-compliant microarray data: deposit in GEO or ArrayExpress upon submission to Scientific Reports. Data relating to individual participants must be described in detail, but private information identifying participants need not be included unless the identifiable materials are of relevance to the research (for example, photographs of participants faces that show a particular symptom). The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request. Code availability Semin. 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. Author B has received a speaker honorarium from Company X and owns stocks in Company Y. 26, 681687 (2020). 31a, b). permission provided that the original article is clearly cited. 20b). Unpublished materials intended for publication: Unpublished materials not intended for publication: File for Figures and Schemes must be provided during submission in a single zip archive and at a sufficiently high resolution (minimum 1000 pixels width/height, or a resolution of 300 dpi or higher). Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. In brief, single-nucleus/cell suspensions were used for droplet generation, emulsion breakage, bead collection, reverse transcription and cDNA amplification to generate barcoded libraries. For the purposes of this policy, competing interests are defined as financial and non-financial interests that could directly undermine, or be perceived to undermine, the objectivity, integrity and value of a publication, through a potential influence on the judgements and actions of authors with regard to objective data presentation, analysis and interpretation. Methods 14, 979982 (2017). In line with community guidelines, a study typically contains metadata such as detailed sample annotations, protocols, processed data and raw data. In case of any doubt, authors should seek advice from the Editorial Board Member handling their contribution. Data should be MIAME compliant. For any co-author who would like their name on the article abstract page and PDF to be linked to a Frontiers profile on the Loop network, please register before the final publication of the paper. Denoted in shorthand with the somatic number 2n. Apart from these analyses and comparisons, our NHPCA website provides a platform for interactive comparisons with manually uploaded datasets. Conflicts of Interest: Author A has received research grants from Company A. Authors should list all image acquisition tools and image processing software packages used. surveys, questionnaires, social media research), all participants must be fully informed if the anonymity is assured, why the research is being conducted, how their data will be used and if there are any risks associated. Libraries were sequenced on a DNBSEQ-T1 or DNBSEQ-T7 sequencer at the China National GeneBank (Shenzhen, China) with the following sequencing strategy: 41-bp read length for read 1 and 100-bp read length for read 2. scATAC-seq libraries were prepared using the DNBelab C Series Single-Cell ATAC Library Prep Set70 (MGI, 1000021878). Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model. and L.L. Topics include, but are not limited to: omics studies to gain mechanistic insight into biological processes for example, determining the mode of action of a drug or the basis of a particular phenotype, such as drought tolerance ; omics studies for clinical applications with experimental validation, such Sequences were matched to all Homo sapiens motifs form JASPAR2018 using the matchMotifs function in motifmatchr (v1.8.0) with the default parameter. Tse, K. H. & Herrup, K. DNA damage in the oligodendrocyte lineage and its role in brain aging. If necessary, individual authors can be listed in both the main author list and as a member of a consortium. Data should be MIAME compliant. A total of 113 cell clusters were identified in the dataset. Aside from wholesale verbatim re-use of text, due care must be taken to ensure appropriate attribution and citation when paraphrasing and summarising the work of others. Please see the joint statement by journal editors. Citations and References in Supplementary files are permitted provided that they also appear in the main text and in the reference list. A written informed consent for publication must be obtained from participating patients. PaGenBase has collected 143 quality microarray, NGS and tiling array datasets, as well as the Similar patterns were seen in liver in the two species, whereas more distinct patterns were observed in the gallbladder, kidney and lung (Fig. Peer reviewer reports are available. Cell numbers as well as gene and UMI capture rates were higher in NHPCA for all 12 tissues. We also advise that researchers approached by reporters in response to a preprint make it clear that the paper has not yet undergone peer review, and that the content is provisional. 37c). 21) epithelial-like populations (one mature and one progenitor-like) of mesothelial origin (Fig. Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature. Ideally, authors should cite sources that have undergone peer review where possible. Yu, Y. et al. The summary statistics file for each trait was downloaded from the UK Biobank database or published studies (Supplementary Table 6a). Identification of stem cells in small intestine and colon by marker gene Lgr5. The potential for mining this information to make new discoveries is vast. This is also reflective in our multi-national and inclusive workplace. Dataset title; Data repository or archive; Version (if any); Persistent identifier (e.g., DOI). 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. ArrayExpress: Crystallographic data for small molecules: Cambridge Structural Database: Where a widely established research community expectation for data archiving in public repositories exists, submission to a community-endorsed, public repository is mandatory. 343, 1616-1620; 2000). J. Immunotoxicol. c, Integrated kidney snRNA-seq and scATAC-seq data. If plagiarism is detected during the peer review process, the manuscript may be rejected. He also has consulted for C and received compensation. For the purposes of publishing in MDPI journals, a consent, permission, or release form should include unlimited permission for publication in all formats (including print, electronic, and online), in sublicensed and reprinted versions (including translations and derived works), and in other works and products under open access license. 3g), whereas LGR6 was higher in cardiomyocytes and smooth muscle cells (aorta, ovary, carotid and vagina) (Supplementary Fig. Change the whole style of database. We have also provided the NHPCA website (https://db.cngb.org/nhpca/), an open and interactive database for exploration. If the manuscript includes personal communications, please provide a written statement of permission from any person who is quoted. These transcription factors are targets of tissue-protective and innate immune responses mediated by interleukin (IL)-6, IL-1 and interferons53. For tissues sequenced with scRNA-seq, reads were aligned to the exons of mRNA as normal. 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Authors and reviewers must use the ARRIVE guidelines as a checklist, which can be found at https://arriveguidelines.org/sites/arrive/files/documents/ARRIVE%20Compliance%20Questionnaire.pdf. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. We did not detect substantial proliferation in any of the progenitor populations on the basis of expression of the pan-cycling marker MKI67 (Supplementary Fig. MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Declarations regarding conflicts of interest can also be collected via the MDPI disclosure form. Publishers note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. was supported by a Changbai Mountain Scholar award (419020201252), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502), a Chinese Academy of SciencesJapan Society for the Promotion of Science joint research project (GJHZ2093), the National Natural Science Foundation of China (92068106, U20A2015) and the Guangdong Basic and Applied Basic Research Foundation (2021B1515120075). Progenitor-like ovarian epithelial cells have previously been reported22. Data availability statements should include information on where data supporting the results reported in the article can be found including, where applicable, hyperlinks to publicly archived datasets analysed or generated during the study. 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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. Concentrations were measured with a Qubit ssDNA Assay Kit (Thermo FisherScientific, Q10212). Biotechnol. Scope . Editorial Board Members may not be best qualified to make such judgments unassisted, and so we reserve the right to take expert advice in cases where we believe that concerns may arise. Yates, A. D. et al. The editors will not necessarily approach these referees. Authors should ensure that data shared are in accordance with consent provided by participants on the use of confidential data. Google Scholar. Collection Guest Editors are involved in soliciting papers, and in writing an introductory Editorial. 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