d33bc0d10c0240997b56a8e8c4bc0fc0 270631.pdf 1d85d8713f43f87b051e4d37664dfad636d0ab68 270631.pdf a539e6fc5358456ec7e322a440e84e350e34c6da9a2f3d3e9a42e61af4d1f5a2 270631.pdf Title: Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses Subject: Nature Communications, doi:10.1038/s41467-022-29450-x Keywords: Author: Javier Rodríguez-Ubreva Creator: Springer Producer: iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) CreationDate: Mon Mar 28 17:12:32 2022 CEST ModDate: Tue Mar 29 07:08:09 2022 CEST Tagged: no UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 18 Encrypted: no Page size: 595.276 x 782.362 pts Page rot: 0 File size: 10322316 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- GLDCKM+AdvOTf23bb480+fb Type 1C Custom yes yes yes 1510 0 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edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR64' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR65' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR66' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR67' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR19' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR20' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR24' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR15' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR68' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR69' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR70' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR71' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR72' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR16' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR16' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR21' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR73' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR74' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR75' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR76' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR77' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR78' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR76' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR79' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR80' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR81' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR62' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR73' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR33' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR82' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR68' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR24' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR73' cannot be found Offset: 9741161 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'bm_CR83' cannot be found Offset: 9741161 MIMEtype: application/pdf PDFMetadata: Objects: 1642 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseOutlines Language: EN Outlines: Item: Title: Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-nobreakcell responses Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@eafc191 Children: Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612fc6eb Children: Item: Title: DNA methylation alterations in CVID in memory B-nobreakcell differentiation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1060b431 Item: Title: Heterogeneous DNA methylation alterations define key TFs in CVID Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612679d6 Item: Title: Chromatin accessibility changes in regulatory regions in CVID Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@11758f2a Item: Title: CVID epigenetic defects perturb transcription during B-nobreakcell activation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@e720b71 Item: Title: Alterations in immune cell communication in B-nobreakcell responses in CVID Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1b26f7b2 Item: Title: Epigenetic, transcriptional, and communication changes in a CVID cohort Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@491cc5c9 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@74ad1f1f Item: Title: Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6a1aab78 Children: Item: Title: Patients and ethics approval Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@462d5aee Item: Title: Sample collection and immune cell activation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@69b0fd6f Item: Title: Whole-genome sequencing analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@757942a1 Item: Title: KREC assay Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4a87761d Item: Title: Single-cell library preparations Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@66d1af89 Item: Title: Single-cell whole-genome bisulfite sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@8646db9 Item: Title: Imputation of DNA methylation signals Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@37374a5e Item: Title: DMR identification Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4671e53b Item: Title: Amplicon sequencing for DNA methylation analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2db7a79b Item: Title: Analysis of the different-omics datasets in relation with several biological features Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6950e31 Item: Title: Alignment, quantification, and quality control of scRNA-seq data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@b7dd107 Item: Title: Deconvolution of donors in pooled CITE-seq samples Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@42eca56e Item: Title: Doublet removal from scRNA-seq and CITE-seq data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@52f759d7 Item: Title: Denoising protein counts in CITE-seq data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7cbd213e Item: Title: Clustering and annotation of scRNA-seq data and CITE-seq data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@192d3247 Item: Title: Differential gene expression analysis in scRNA-seq Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3ecd23d9 Item: Title: Cell–nobreakcell communication analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@569cfc36 Item: Title: Alignment, quantification, and downstream analysis of single-cell ATAC-seq data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@43bd930a Item: Title: Statistical analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@33723e30 Item: Title: Reporting summary Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@64f6106c Item: Title: Data availability Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@553a3d88 Item: Title: Code availability Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a30d1e6 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5891e32e Item: Title: Acknowledgements Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@cb0ed20 Item: Title: Author contributions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@8e24743 Item: 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Clark Carlos de la Calle-Fabregat Luz Garcia-Alonso Louis-François Handfield Laura Ciudad Eduardo Andrés-León Felix Krueger Francesc Català-Moll Virginia C. Rodríguez-Cortez Krzysztof Polanski Lira Mamanova Stijn van Dongen Vladimir Yu. Kiselev María T. Martínez-Saavedra Holger Heyn Javier Martín Klaus Warnatz Eduardo López-Granados Carlos Rodríguez-Gallego Oliver Stegle Gavin Kelsey Roser Vento-Tormo Esteban Ballestar Springer US Nature Communications, doi:10.1038/s41467-022-29450-x Springer 2022-03-29T07:08:09+02:00 2022-03-28T20:42:32+05:30 2022-03-29T07:08:09+02:00 True iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) uuid:30eebfd0-eb4f-4fdf-8e54-351da2cfe298 uuid:828243f2-de8c-47b3-995f-5cf1eec1b6b7 default 1 converted uuid:c4c16afc-df32-466f-bcb9-425a5e9a80d9 converted to PDF/A-2b pdfToolbox 2022-03-28T20:44:13+05:30 2 B 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/pdfx/1.3/ pdfx Adobe Document Info PDF eXtension Schema 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 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. 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