A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes

Nature Protocols

Volumn 11, Issue 8, 2016, Pages 1477-1491

  Avraham, Roi ^a,e   Haseley, Nathan ^a   Fan, Amy ^a   Bloom Ackermann, Zohar ^a   Livny, Jonathan ^a,b   Hung, Deborah T ^a,c,d  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME; BACTERIAL RNA;

ANIMAL CELL; ARTICLE; BACTERIOLYSIS; CONTROLLED STUDY; CYTOLYSIS; GENE EXPRESSION; GENE LIBRARY; GENETIC TRANSCRIPTION; HOST CELL; HOST PATHOGEN INTERACTION; NONHUMAN; PRIORITY JOURNAL; RNA PROCESSING; RNA SEQUENCE; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; ANIMAL; BONE MARROW CELL; CYTOLOGY; GENE EXPRESSION PROFILING; GENETICS; LIMIT OF DETECTION; MACROPHAGE; METABOLISM; MICROBIOLOGY; MOUSE; PHYSIOLOGY; PROCEDURES; SALMONELLA; TIME FACTOR;

ANIMALS; BONE MARROW CELLS; GENE EXPRESSION PROFILING; HOST-PATHOGEN INTERACTIONS; LIMIT OF DETECTION; MACROPHAGES; MICE; RNA, BACTERIAL; SALMONELLA; SEQUENCE ANALYSIS, RNA; TIME FACTORS;

EID: 84979901414     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2016.090     Document Type: Article

References (30)

1. Galan, J.E., & Wolf-Watz, H. Protein delivery into eukaryotic cells by type III secretion machines. Nature 444, 567-573 (2006
2. Medzhitov, R. TLR-mediated innate immune recognition. Semin. Immunol. 19, 1-2 (2007
3. Eriksson, S., Lucchini, S., Thompson, A., Rhen, M., & Hinton, J.C. Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol. Microbiol. 47, 103-118 (2003
4. Berry M.P., et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466, 973-977 (2010
5. Westermann, A.J., Gorski, S.A., & Vogel, J. Dual RNA-seq of pathogen and host. Nat. Rev. Microbiol. 10, 618-630 (2012
6. Baddal B., et al. Dual RNA-seq of nontypeable Haemophilus influenzae and host cell transcriptomes reveals novel insights into host-pathogen cross talk. mBio 6, e01765-e01715 (2015
7. Humphrys M.S., et al. Simultaneous transcriptional profiling of bacteria and their host cells. PloS One 8, e80597 (2013
8. Mavromatis C.H., et al. The co-Transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions. Cell Microbiol. 17, 730-746 (2015
9. Avraham R., et al. Pathogen cell-To-cell variability drives heterogeneity in host immune responses. Cell 162, 1309-1321 (2015
10. Shishkin A.A., et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat. Methods 12, 323-325 (2015
11. Dillon L.A., et al. Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions. BMC Genomics 16, 1108 (2015
12. Schulze, S., Henkel, S.G., Driesch, D., Guthke, R., & Linde, J. Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. Front. Microbiol. 6, 65 (2015
13. Tierney L., et al. An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front. Microbiol. 3, 85 (2012
14. Kawahara Y., et al. Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PloS One 7, e49423 (2012
15. Yazawa, T., Kawahigashi, H., Matsumoto, T., & Mizuno, H. Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PloS One 8, e62460 (2013
16. Bischler, T., Tan, H.S., Nieselt, K., & Sharma, C.M. Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori. Methods 86, 89-101 (2015
17. Westermann A.J., et al. Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions. Nature 529, 496-501 (2016
18. Losick, V.P., & Isberg, R.R. NF-kappaB translocation prevents host cell death after low-dose challenge by Legionella pneumophila. J. Exp. Med. 203, 2177-2189 (2006
19. Beattie L., et al. Apintu transcriptomic network identified in uninfected macrophages responding to inflammation controls intracellular pathogen survival. Cell Host Microbe. 14, 357-368 (2013
20. Risso, D., Ngai, J., Speed, T.P., & Dudoit, S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32, 896-902 (2014
21. Giannoukos G., et al. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol. 13, R23 (2012
22. Li, H., & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009
23. Langmead, B., Trapnell, C., Pop, M., & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009
24. Liao, Y., Smyth, G.K., & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930 (2014
25. Haas, B.J., Chin, M., Nusbaum, C., Birren, B.W., & Livny, J. How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? BMC Genomics 13, 734 (2012
26. Ashburner M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 (2000
27. Kanehisa, M., & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000
28. Love, M.I., Huber, W., & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014
29. Soneson, C., & Delorenzi, M. Apintu comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 14, 91 (2013
30. Subramanian A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005