Prokaryotic RNA preparation methods useful for high density array analysis: Comparison of two approaches

Nucleic Acids Research

Volumn 29, Issue 22, 2020, Pages

  Rosenow, Carsten ^a   Saxena, Rini Mukherjee ^a   Durst, Mark ^b   Gingeras, Thomas R ^a  

^a Thermo Fisher Scientific   (United States)

^b Signature Bioscience   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; COMPLEMENTARY DNA; MESSENGER RNA; ADENOSINE 5' O (3 THIOTRIPHOSPHATE); ADENOSINE 5'-O-(3-THIOTRIPHOSPHATE); ADENOSINE TRIPHOSPHATE; BIOTIN; DIAGNOSTIC AGENT; DRUG DERIVATIVE; ISOPROPYL THIOGALACTOSIDE;

ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; CELL GROWTH; DNA SYNTHESIS; ESCHERICHIA COLI; GENE EXPRESSION LEVEL; GENE REPLICATION; GENE SEQUENCE; GENETIC TRANSCRIPTION; INTERMETHOD COMPARISON; NONHUMAN; OLIGONUCLEOTIDE PROBE; OPEN READING FRAME; PRIORITY JOURNAL; PROKARYOTIC CELL; REPRODUCIBILITY; RNA ANALYSIS; COMPARATIVE STUDY; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; LACTOSE OPERON; METABOLISM; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION;

ADENOSINE TRIPHOSPHATE; BIOTIN; DNA, COMPLEMENTARY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; ISOPROPYL THIOGALACTOSIDE; LAC OPERON; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, BACTERIAL;

MLCS; MLOWN;

EID: 0035891661     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/29.22.e112     Document Type: Article

References (15)

1. Xu, J., Stolk, J.A., Zhang, X., Silva, S.J., Houghton, R.L., Matsumura, M., Vedvick, T.S., Leslie, K.B., Badaro, R. and Reed, S.G. (2000) Identification of differentially expressed genes in human prostate cancer using subtraction and microarray. Cancer Res., 60, 1677-1682.
2. Coller, H.A., Grandori, C., Tamayo, P., Colbert, T., Lander, E.S., Eisenman, R.N. and Golub, T.R. (2000) Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling and adhesion. Proc. Natl Acad. Sci. USA, 97, 3260-3265.
3. Sudarsanam, P., Iyer, V.R., Brown, P.O. and Winston, F. (2000) Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 97, 3364-3369.
4. Bryant, Z., Subrahmanyan, L., Tworoger, M., La Tray, L., Liu, C.R., Li, M.J., van den Engh, G. and Ruohola-Baker, H. (1999) Characterization of differentially expressed genes in purified Drosophila follicle cells: toward a general strategy for cell type-specific developmental analysis. Proc. Natl Acad. Sci. USA, 96, 5559-5564.
5. Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H., Chu, A.M., Connelly, C., Davis, K., Dietrich, F., Dow, S.W., El Bakkoury, M., Foury, F., Friend, S.H., Gentalen, E., Giaever, G., Hegemann, J.H., Jones, T., Laub, M., Liao, H., Davis, R.W. et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285, 901-906.
6. Heller, R.A., Schena, M., Chai, A., Shalon, D., Bedilion, T., Gilmore, J., Woolley, D.E. and Davis, R.W. (1997) Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc. Natl Acad. Sci. USA, 94, 2150-2155.
7. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
8. Kaminski, N., Allard, J.D., Pittet, J.F., Zuo, F., Griffiths, M.J., Morris, D., Huang, X., Sheppard, D. and Heller, R.A. (2000) Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proc. Natl Acad. Sci. USA, 97, 1778-1783.
9. Richmond, C.S., Glasner, J.D., Mau, R., Jin, H. and Blattner, F.R. (1999) Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res., 27, 3821-3835.
10. Gingeras, T.R. and Rosenow, C. (2000) Studying microbial genomes with high-density oligonucleotide arrays. Am. Soc. Microbiol. News, 66, 463-469.
11. Nakazato, H., Venkatesan, S. and Edmonds, M. (1975) Polyadenylic acid sequences in E. coli messenger RNA. Nature, 256, 144-146.
12. Cao, G.J. and Sarkar, N. (1992) Identification of the gene for an Escherichia coli poly(A) polymerase. Proc. Natl Acad. Sci. USA, 89, 10380-10384.
13. Selinger, D.W., Cheung, K.J., Mei, R., Johansson, E.M., Richmond, C.S., Blattner, F.R., Lockhart, D.J. and Church, G.M. (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnol., 18, 1262-1268.
14. Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B. and Shao, Y. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
15. Guyer, M.S., Reed, R.R., Steitz, J.A. and Low, K.B. (1981) Identification of a sex-factor-affinity site in E. coli as gamma delta. Cold Spring Harbor Symp. Quant. Biol., 45, 135-140.