6478f95106329f399bf33c09f8a93408 pmc_29783948.pdf de07228eb199271eec1cb241f2311617a312bd75 pmc_29783948.pdf e09efdd7fc33b575fe0a6d92d10fb211d0f118fab5494716f38d8ca8239347d0 pmc_29783948.pdf Title: Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation Subject: BMC Genomics, 2018, doi:10.1186/s12864-018-4716-8 Keywords: SOS response,DNA repair,Transcriptome,ncRNA,nrdA,nrdB Author: Evelyne Krin Creator: Arbortext Advanced Print Publisher 9.1.440/W Unicode Producer: Acrobat Distiller 10.1.5 (Windows); modified using iText® 5.3.5 ©2000-2012 1T3XT BVBA (AGPL-version) CreationDate: Fri May 18 03:52:27 2018 CEST ModDate: Mon May 21 14:24:27 2018 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 18 Encrypted: no Page size: 595.276 x 790.866 pts Page rot: 0 File size: 1823480 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ 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destination - referenced object 'link_CR49' cannot be found Offset: 1569698 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'link_CR50' cannot be found Offset: 1569698 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'link_CR14' cannot be found Offset: 1569698 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'link_CR51' cannot be found Offset: 1569698 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'link_CR52' cannot be found Offset: 1569698 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'link_CR53' cannot be found Offset: 1569698 ID: PDF-HUL-122 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Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4eb7f003 Item: Title: Background Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@eafc191 Item: Title: Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612fc6eb Children: Item: Title: Bacterial strains and growth conditions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1060b431 Item: Title: RNA preparation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612679d6 Item: Title: 5’end-RNA-seq library Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@11758f2a Item: Title: Directional RNA-Seq library Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@e720b71 Item: Title: Library sequencing Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1b26f7b2 Item: Title: Statistical analysis of SOS RNA-Seq Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@491cc5c9 Item: Title: SOS operons RT-PCR Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@74ad1f1f Item: Title: nrd operon RT-PCR Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6a1aab78 Item: Title: Electrophoresis mobility shift assays (EMSA) with LexA protein Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@462d5aee Item: Title: Determination of mitomycin C susceptibility Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@69b0fd6f Item: Title: UV survival tests Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@757942a1 Item: Title: Plac-cep insertion inside specific Tn7 site in N16961 V. cholerae genome Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4a87761d Item: Title: ncRNA and TSS content comparisons Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@66d1af89 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@8646db9 Children: Item: Title: Transcriptional start sites determination Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@37374a5e Item: Title: The set of non-coding RNAs in V. cholerae Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4671e53b Item: Title: Transcriptional profiling of V. cholerae during mitomycin C treatment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2db7a79b Item: Title: Extending the SOS regulon of V. cholerae Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6950e31 Item: Title: Two major pathways are induced by mitomycin C beyond the SOS regulon Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@b7dd107 Item: Title: The set of ncRNAs induced by mitomycin C Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@42eca56e Item: Title: Phenotypic characterization of new members of the SOS regulon and the most highly induced genes and ncRNAs by MMC treatment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@52f759d7 Item: Title: Comparative analyses with previously published ncRNA/TSS screens Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7cbd213e Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@192d3247 Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3ecd23d9 Item: Title: Additional files Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@569cfc36 Item: Title: Abbreviations Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@43bd930a Item: Title: Acknowledgments Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@33723e30 Item: Title: Funding Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@64f6106c Item: Title: Availability of data and materials Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@553a3d88 Item: Title: Authors’ contributions Destination: 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