Gene Expression Profiling: Metatranscriptomics

Methods in Molecular Biology

Volumn 733, Issue , 2011, Pages 195-205

  Gilbert, Jack A ^a   Hughes, Margaret ^b  

^a PLYMOUTH MARINE LABORATORY   (United Kingdom)

^b NONE

Author keywords

Expression; Marine; Metatranscriptomics; Soil

Indexed keywords

MESSENGER RNA; SEA WATER;

ARTICLE; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETICS; ISOLATION AND PURIFICATION; METAGENOMICS; METHODOLOGY; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; SEDIMENT;

BASE SEQUENCE; GENE EXPRESSION PROFILING; GEOLOGIC SEDIMENTS; METAGENOMICS; RNA, MESSENGER; SEAWATER; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

EID: 79960045904     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-089-8_14     Document Type: Chapter

References (13)

1. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, et al. (2006) Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311, 496 –503.
2. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5, 398 – 431
3. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 5, 432– 466.
4. Handelsman J, Tiedje J, Alvarez-Cohen L, Ashburner M, Cann IKO, et al. (2007) The New Science of metagenomics: revealing the secrets of our microbial planet, Washington, DC: The National Academies Press.
5. Parro V, Moreno-Paz M, Gonzalez-Toril E (2007) Analysis of environmental transcriptomes by DNA microarrays. Environ. Microbiol. 9, 453– 464.
6. Poretsky RS, Bano N, Buchan A, LeCleir G, Kleikemper J, et al. (2005) Analysis of microbial gene transcripts in environmental samples. Appl. Environ. Microbiol. 71, 4121– 4126.
7. Leininger S, Urich T, Schloter M, Schwark L, Qi J, et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806 – 809.
8. Urich T, Lanzén A, Qi J, Huson DH, Schleper C, et al. (2008) Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome. PLoS ONE 3: e2527. doi:10.1371/journal.pone.0002527
9. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, et al. (2008) Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. USA 105, 3805 –10.
10. Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities. PLoS ONE 3(8): e3042. doi:10.1371/jour-nal.pone.0003042
11. Poretsky R.S., Hewson I, Sun S, Allen A. E., Zehr J.P. and Moran, M.A. 2009a. Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ. Microbiol. 11, 1358 –1375.
12. Poretsky R.S., Gifford S., Rinta-Kanto J., Vila-Costa M., Moran M.A. 2009b. Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics. JoVE. 24. http://www.jove. com/index/Details.stp?ID=1086, doi: 10.3791/1086
13. Li W & Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658 –1659.