7dd89922bbe74afcc46fd8c1dadc26ac 89_Burgos_et_al_MSB_25_.pdf dabc69db151f1909072cd1167538f99efceb3ddb 89_Burgos_et_al_MSB_25_.pdf 67b878d08aef021a0e9ad71d34d70437e087e83c7e1d5172934ddcc9a4bc9ece 89_Burgos_et_al_MSB_25_.pdf Title: A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation Subject: Molecular Systems Biology 0.0:1-27 Keywords: Spermatogenesis; Zebrafish; Epigenetics; Single-cell Multiomics; DNA Methylation Author: Ana María Burgos-Ruiz Creator: Springer Producer: iText 4.2.0 by 1T3XT CreationDate: Fri Oct 10 02:25:15 2025 CEST ModDate: Wed Oct 15 07:51:09 2025 CEST Custom Metadata: yes Metadata Stream: yes Tagged: no UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 27 Encrypted: no Page size: 595.276 x 790.866 pts Page rot: 0 File size: 14221447 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- 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14221447 Format: PDF Version: 1.4 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 0 FreeObjects: 2 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseOutlines Language: EN Outlines: Item: Title: A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation Destination: title_link Children: Item: Title: Introduction Destination: A1 Item: Title: Results Destination: A2 Children: Item: Title: Cell-type resolved transcriptomes of the zebrafish testis Destination: B1 Item: Title: Localised DNA methylation changes characterise spermatocyte formation Destination: B2 Item: Title: Global and local dynamics of chromatin accessibility during spermatogenesis Destination: B3 Item: Title: Open chromatin peaks coincide with sites of multivalent chromatin in sperm Destination: B4 Item: Title: Discussion Destination: A3 Item: Title: Methods Destination: A4 Children: Item: Title: Zebrafish husbandry and ethics Destination: B5 Item: Title: Zebrafish procedures Destination: B6 Item: Title: scRNA-seq and scATAC-seq library construction and sequencing Destination: B7 Item: Title: Single-cell RNA-Seq read alignment and quantification Destination: B8 Item: Title: Pre-processing, quality filtering, batch integration, and dimensional reduction scRNA-seq Destination: B9 Item: Title: Cell classification and marker identification Destination: B10 Item: Title: Gene set enrichment analysis Destination: B11 Item: Title: scRNA-seq trajectory analysis Destination: B12 Item: Title: RNA velocity analysis Destination: B13 Item: Title: Double fluorescent in situ hybridisation (FISH) on zebrafish testis cryostat sections Destination: B14 Item: Title: Single-cell ATAC pre-processing and quality control Destination: B15 Item: Title: Single-cell ATAC analysis Destination: B16 Item: Title: Flow cytometry and cell enrichment analysis Destination: B17 Item: Title: WGBS sample collection and library construction Destination: B18 Item: Title: WGBS analysis Destination: B19 Item: Title: Data availability Destination: A5 Item: Title: References Destination: A6 Children: Item: Title: Acknowledgements Destination: B20 Item: Title: ACKNOWLEDGMENTS Destination: M1 Children: Item: Title: Author contributions Destination: B21 Item: Title: ACKNOWLEDGMENTS Destination: M1 Filters: FilterPipeline: FlateDecode FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 1100 ImageHeight: 90 ColorSpace: black is zero BitsPerSample: 1 BitsPerSampleUnit: integer Filter: FlateDecode Image: NisoImageMetadata: FormatName: image/png ImageWidth: 22 ImageHeight: 4 ColorSpace: CMYK BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Image: NisoImageMetadata: FormatName: image/png ImageWidth: 10 ImageHeight: 3 ColorSpace: CMYK BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Image: NisoImageMetadata: FormatName: 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LastChar: 1 FontDescriptor: FontName: FCBLLH+AdvOT1ef757c0+22 Flags: Symbolic FontBBox: -135, -166, 697, 916 FontFile3: true EncodingDictionary: Differences: true ToUnicode: true Font: BaseFont: FCAONP+AdvOTb65e897d.B FontSubset: true FirstChar: 41 LastChar: 41 FontDescriptor: FontName: FCAONP+AdvOTb65e897d.B Flags: Nonsymbolic FontBBox: -20, -250, 968, 854 FontFile3: true Encoding: WinAnsiEncoding XMP: application/pdf doi:10.1038/s44320-025-00157-7 A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation Ana María Burgos-Ruiz Fan-Suo Geng Gala Pujol Estefanía Sanabria Thirsa Brethouwer María Almuedo-Castillo Aurora Ruiz-Herrera Juan J Tena Ozren Bogdanovic Springer US Spermatogenesis Zebrafish Epigenetics Single-cell Multiomics DNA Methylation Molecular Systems Biology, doi:10.1038/s44320-025-00157-7 10.1038/s44320-025-00157-7 http://dx.doi.org/10.1038/s44320-025-00157-7 journal Molecular Systems Biology © 2025, The Author(s) 1744-4292 10.1038/s44320-025-00157-7 springer.com springerlink.com 2010-04-23 True 10.1038/s44320-025-00157-7 springer.com springerlink.com Springer 2025-10-14T22:51:09-07:00 2025-10-10T05:55:15+05:30 2025-10-14T22:51:09-07:00 True Spermatogenesis; Zebrafish; Epigenetics; Single-cell Multiomics; DNA Methylation VoR uuid:c7ac6e34-1efc-4f79-8075-6881643be101 uuid:fda4e6cc-95e1-4fd3-8fb6-46d60c53a80d default 1 converted uuid:840a8237-538a-472c-8012-f09e67e58d15 converted to PDF/A-2b pdfToolbox 2025-10-10T05:56:52+05:30 2 B Ana María Burgos-Ruiz http://orcid.org/0009-0006-3095-8668 Gala Pujol http://orcid.org/0000-0002-3915-4766 Thirsa Brethouwer http://orcid.org/0009-0009-0522-9799 Aurora Ruiz-Herrera http://orcid.org/0000-0003-3868-6151 Juan J Tena http://orcid.org/0000-0001-8165-7984 Ozren Bogdanovic http://orcid.org/0000-0001-5680-0056 http://ns.adobe.com/xap/1.0/mm/ xmpMM XMP Media Management Schema internal UUID based identifier for specific incarnation of a document InstanceID URI internal The common identifier for all versions and renditions of a document. OriginalDocumentID URI internal A reference to the original document from which this one is derived. It is a minimal reference; missing components can be assumed to be unchanged. For example, a new version might only need to specify the instance ID and version number of the previous version, or a rendition might only need to specify the instance ID and rendition class of the original. DerivedFrom ResourceRef internal An unordered array of references to resources that were incorporated, by inclusion or reference, into this document. Ingredients Bag ResourceRef Identifies a portion of a document. This can be a position at which the document has been changed since the most recent event history (stEvt:changed). For a resource within an xmpMM:Ingredients list, the ResourceRef uses this type to identify both the portion of the containing document that refers to the resource, and the portion of the referenced resource that is referenced. http://ns.adobe.com/xap/1.0/sType/Part# stPart Part http://ns.adobe.com/pdf/1.3/ pdf Adobe PDF Schema internal A name object indicating whether the document has been modified to include trapping information Trapped Text http://ns.adobe.com/xap/1.0/t/pg/ xmpTPg XMP Paged-Text internal XMP08 Spec: An ordered array of plate names that are needed to print the document (including any in contained documents). PlateNames Seq Text internal A structure containing the characteristics of a font used in a document Fonts Bag Font A structure containing the characteristics of a font used in a document. http://ns.adobe.com/xap/1.0/sType/Font# stFnt Font http://ns.adobe.com/pdfx/1.3/ pdfx pdfx internal ID of PDF/X standard GTS_PDFXVersion Text internal Conformance level of PDF/X standard GTS_PDFXConformance Text internal Company creating the PDF Company Text internal Date when document was last modified SourceModified Text external Mirrors crossmark:CrosMarkDomains CrossMarkDomains Seq Text internal Mirrors crossmark:DOI doi Text http://crossref.org/crossmark/1.0/ crossmark crossmark internal CrossMarkDomains CrossMarkDomains Seq Text internal CrossmarkDomainExclusive CrossmarkDomainExclusive Text internal Usual same as prism:doi DOI Text external The date when a publication was published. MajorVersionDate Text http://prismstandard.org/namespaces/basic/2.0/ prism Prism external The aggregation type specifies the unit of aggregation for a content collection. Comment PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. Note: PRISM recommends against the use of the #other value currently allowed in this controlled vocabulary. In lieu of using #other please reach out to the PRISM group at info@prismstandard.org to request addition of your term to the Aggregation Type Controlled Vocabulary. aggregationType Text external Copyright copyright Text external The Digital Object Identifier for the article. The DOI may also be used as the dc:identifier. If used as a dc:identifier, the URI form should be captured, and the bare identifier should also be captured using prism:doi. If an alternate unique identifier is used as the required dc:identifier, then the DOI should be specified as a bare identifier within prism:doi only. If the URL associated with a DOI is to be specified, then prism:url may be used in conjunction with prism:doi in order to provide the service endpoint (i.e. the URL). doi Text external ISSN for an electronic version of the issue in which the resource occurs. Permits publishers to include a second ISSN, identifying an electronic version of the issue in which the resource occurs (therefore e(lectronic)Issn. If used, prism:eIssn MUST contain the ISSN of the electronic version. See prism:issn. issn Text external Title of the magazine, or other publication, in which a resource was/will be published. Typically this will be used to provide the name of the magazine an article appeared in as metadata for the article, along with information such as the article title, the publisher, volume, number, and cover date. Note: Publication name can be used to differentiate between a print magazine and the online version if the names are different such as “magazine” and “magazine.com.” publicationName Text external This element provides the url for an article or unit of content. The attribute platform is optionally allowed for situations in which multiple URLs must be specified. PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary. url Text http://www.niso.org/schemas/jav/1.0/ jav NISO external Values for Journal Article Version are one of the following: AO = Author’s Original SMUR = Submitted Manuscript Under Review AM = Accepted Manuscript P = Proof VoR = Version of Record CVoR = Corrected Version of Record EVoR = Enhanced Version of Record journal_article_version Closed Choice of Text http://www.aiim.org/pdfa/ns/id/ pdfaid PDF/A ID Schema internal Part of PDF/A standard part Integer internal Amendment of PDF/A standard amd Text internal Conformance level of PDF/A standard conformance Text http://springernature.com/ns/xmpExtensions/2.0/ sn Springer Nature ORCID Schema external Author information: contains the name of each author and his/her ORCID (ORCiD: Open Researcher and Contributor ID). An ORCID is a persistent identifier (a non-proprietary alphanumeric code) to uniquely identify scientific and other academic authors. authorInfo Bag AuthorInformation Specifies the types of author information: name and ORCID of an author. http://springernature.com/ns/xmpExtensions/2.0/authorInfo/ author AuthorInformation Gives the ORCID of an author. orcid URI Gives the name of an author. name Text iText 4.2.0 by 1T3XT Pages: Page: Label: 1 Annotations: Annotation: Subtype: Link Rect: 337, 728, 382, 760 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 337, 733, 392, 765 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 391, 733, 392, 743 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 391, 733, 392, 743 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 156, 581, 158, 593 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 156, 581, 158, 593 Flags: Print AppearanceDictionary: 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