dc.contributor.author | Avraham, Roi | |
dc.contributor.author | Haseley, Nathan | |
dc.contributor.author | Fan, Amy | |
dc.contributor.author | Bloom-Ackermann, Zohar | |
dc.contributor.author | Livny, Jonathan | |
dc.contributor.author | Hung, Deborah Tan | |
dc.date.accessioned | 2017-08-16T18:44:09Z | |
dc.date.issued | 2016 | |
dc.identifier | Quick submit: 2016-04-01T15:52:22-0400 | |
dc.identifier.citation | Avraham, Roi, Nathan Haseley, Amy Fan, Zohar Bloom-Ackermann, Jonathan Livny, and Deborah T Hung. 2016. “A Highly Multiplexed and Sensitive RNA-Seq Protocol for Simultaneous Analysis of Host and Pathogen Transcriptomes.” Nature Protocols 11 (8) (July 21): 1477–1491. doi:10.1038/nprot.2016.090. | en_US |
dc.identifier.issn | 1754-2189 | en_US |
dc.identifier.uri | http://nrs.harvard.edu/urn-3:HUL.InstRepos:33766540 | |
dc.description.abstract | The ability to simultaneously characterize the bacterial and host expression programs during infection would facilitate a comprehensive understanding of pathogen-host interactions. While RNA-Seq has greatly advanced our ability to study the transcriptomes of prokaryote and eukaryotes separately, limitations in existing protocols for generating and analyzing RNA-Seq data have hindered simultaneous profiling of host and bacterial pathogen transcripts from the same sample. Here we provide a detailed protocol for simultaneous analysis of host and bacterial transcripts by RNA-Seq. Importantly, this protocol details the steps required for efficient host and bacteria lysis, barcoding of samples, technical advances in sample preparation for low yield sample inputs and a computational pipeline to analyze both mammalian and microbial reads from mixed hostpathogen RNA-Seq data. Sample preparation takes 3 d from cultured cells to pooled libraries. Data analysis takes an additional day. Compared with previous methods, the protocol detailed here provides a sensitive, facile and generalizable approach, suitable for large-scale studies, which will enable the field to obtain in-depth analysis of hostpathogen interactions in infection models. | en_US |
dc.language.iso | en_US | en_US |
dc.publisher | Springer Nature | en_US |
dc.relation.isversionof | doi:10.1038/nprot.2016.090 | en_US |
dash.license | LAA | |
dc.title | A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes | en_US |
dc.type | Journal Article | en_US |
dc.date.updated | 2016-04-01T19:52:26Z | |
dc.description.version | Accepted Manuscript | en_US |
dc.relation.journal | Nature Protocols | en_US |
dash.depositing.author | Hung, Deborah Tan | |
dash.waiver | 2016-04-01 | |
dc.date.available | 2016 | |
dc.date.available | 2017-08-16T18:44:09Z | |
dash.funder.name | NIH | en_US |
dash.funder.award | HG002295 | en_US |
dc.identifier.doi | 10.1038/nprot.2016.090 | * |
dash.contributor.affiliated | Avraham, Roi | |
dash.contributor.affiliated | Livny, Jonathan | |
dash.contributor.affiliated | Hung, Deborah | |