Enabling coupled quantitative genomics and proteomics analyses from rat spinal cord samples

Molecular and Cellular Proteomics

Volumn 6, Issue 9, 2007, Pages 1574-1588

  Butt, R Hussain ^a   Pfeifer, Tom A ^b,c   Delaney, Allen ^d   Griliatti, Thomas A ^b   Tetzlaff, Wolfram G ^c   Coorssen, Jens R ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c Intl Collaboration Repair D   (Canada)

^d CANADA'S MICHAEL SMITH GENOME SCIENCES CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ANIMAL TISSUE; ARTICLE; AUTOMATION; CONTROLLED STUDY; CORRELATION ANALYSIS; DIGITAL IMAGING; FROZEN SECTION; GENE IDENTIFICATION; GENOMICS; MALE; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEOMICS; QUANTITATIVE ANALYSIS; QUANTITATIVE GENETICS; RAT; RNA ANALYSIS; RNA EXTRACTION; RNA ISOLATION; SPINAL CORD; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ANIMALS; AUTOMATION; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENOMICS; GUANIDINES; MALE; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOLS; PROTEIN BIOSYNTHESIS; PROTEOME; PROTEOMICS; RATS; RATS, SPRAGUE-DAWLEY; RNA; SPINAL CORD;

RATTUS;

EID: 34848860170     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700083-MCP200     Document Type: Article

References (37)

1. Madabusi, L. V., Latham, G. J., and Andruss, B. F. (2006) RNA extraction for arrays. Methods Enzymol. 411, 1-14
2. Heber, S., and Sick, B. (2006) Quality assessment of Affymetrix GeneChip data. Omics 10, 358-368
3. Bowtell, D. D. (1999) Options available - from start to finish - for obtaining expression data by microarray. Nat. Genet. 21, 25-32
4. Dash, P. K., Kobori, N., and Moore, A. N. (2004) A molecular description of brain trauma pathophysiology using microarray technology: an overview. Neurochem. Res. 29, 1275-1286
5. Gorg, A., Obermaier, C., Boguth, G., Harder, A., Scheibe, B., Wildgruber, R., and Weiss, W. (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21, 1037-1053
6. Schuhmann, M. U., Heine, G., Skardelly, M., Jaeger, M., and Selle, H. (2005) Brain injury and proteomics/peptidomics: is it relevant? An overview. Acta Neurochir. Suppl. 95, 465-470
7. Baggerman, G., Vierstraete, E., De, L. A., and Schoofs, L. (2005) Gel-based versus gel-free proteomics: a review. Comb. Chem. High Throughput Screen. 8, 669-677
8. Butt, R. H., Lee, M. W., Pirshahid, S. A., Backlund, P.S., Wood, S., and Coorssen, J. R. (2006) An initial proteomic analysis of human preterm labor: placental membranes. J. Proteome Res. 5, 3161-3172
9. Righetti, P. G., Castagna, A., Antonucci, F., Piubelli, C., Cecconi, D., Campostrini, N., Antonioli, P., Astner, H., and Hamdan, M. (2004) Critical survey of quantitative proteomics in two-dimensional electrophoretic approaches. J. Chromatogr. A 1051, 3-17
10. MacIntyre, D. A., Smith, R., and Chan, E. C. (2006) Differential enrichment of high- and low-molecular weight proteins and concurrent RNA extraction. Anal. Biochem. 359, 274-276
11. Soverchia, L., Ubaldi, M., Leonardi-Essmann, F., Ciccocioppo, R., and Hardiman, G. (2005) Microarrays - the challenge of preparing brain tissue samples. Addict. Biol. 10, 5-13
12. Morse, S. M., Shaw, G., and Larner, S. F. (2006) Concurrent mRNA and protein extraction from the same experimental sample using a commercially available column-based RNA preparation kit. BioTechniques 40, 54, 56, 58-
13. Berglund, S. R., Schwietert, C. W., Jones, A. A., Stern, R. L., Lehmann, J., and Goldberg, Z. (2007) Optimized methodology for sequential extraction of RNA and protein from small human skin biopsies. J. Investig. Dermatol. 127, 349-353
14. Chadderton, T., Wilson, C., Bewick, M., and Gluck, S. (1997) Evaluation of three rapid RNA extraction reagents: relevance for use in RT-PCR's and measurement of low level gene expression in clinical samples. Cell. Mol. Biol. (Noisy-le-grand) 43, 1227-1234
15. Yang, F., Stenoien, D. L., Strittmatter, E. F., Wang, J., Ding, L., Lipton, M. S., Monroe, M. E., Nicora, C. D., Gristenko, M. A., Tang, K., Fang, R., Adkins, J. N., Camp, D. G., Chen, D. J., and Smith, R. D. (2006) Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation. J. Proteome Res. 5, 1252-1260
16. Mastro, R., and Hall, M. (1999) Protein delipidation and precipitation by tri-n -butylphosphate, acetone, and methanol treatment for isoelectric focusing and two-dimensional gel electrophoresis. Anal. Biochem. 273, 313-315
17. Aivaliotis, M., Corvey, C., Tsirogianni, I., Karas, M., and Tsiotis, G. (2004) Membrane proteome analysis of the green-sulfur bacterium Chlorobium tepidum. Electrophoresis 25, 3468-3474
18. Butt, R. H., and Coorssen, J. R. (2006) Pre-extraction sample handling by automated frozen disruption significantly improves subsequent proteomic analyses. J. Proteome Res. 5, 437-448
19. Chan, V. T., Fleming, K. A., and McGee, J. O. (1988) Simultaneous extraction from clinical biopsies of high-molecular-weight DNA and RNA: comparative characterization by biotinylated and 32P-labeled probes on Southern and Northern blots. Anal. Biochem. 168, 16-24
20. Krieg, P., Amtmann, E., and Sauer, G. (1983) The simultaneous extraction of high-molecular-weight DNA and of RNA from solid tumors. Anal. Biochem. 134, 288-294
21. Serizawa, S., Ito, M., Hamanaka, S., and Otsuka, F. (1993) Bound lipids liberated by alkaline hydrolysis after exhaustive extraction of pulverized clavus. Arch. Dermatol. Res. 284, 472-475
22. Lo, I. K., Boorman, R., Marchuk, L., Hollinshead, R., Hart, D. A., and Frank, C.B. (2005) Matrix molecule mRNA levels in the bursa and rotator cuff of patients with full-thickness rotator cuff tears. Arthroscopy 21, 645-651
23. Peters, G. J., Laurensse, E. J., Leyva, A., and Pinedo, H. M. (1986) Tissue homogenization using a micro-dismembrator for the measurement of enzyme activities. Clin. Chim. Acta 158, 193-198
24. Righetti, P. G., Castagna, A., Antonioli, P., and Boschetti, E. (2005) Prefractionation techniques in proteome analysis: the mining tools of the third millennium. Electrophoresis 26, 297-319
25. Butt, R. H., and Coorssen, J. R. (2005) Postfractionation for enhanced proteomic analyses: routine electrophoretic methods increase the resolution of standard 2D-PAGE. J Proteome Res. 4, 982-991
26. 2+ sensitivity. J. Cell Biol. 143, 1845-1857
27. Cannon-Carlson, S., and Tang, J. (1997) Modification of the Laemmli sodium dodecyl sulfate-polyacrylamide gel electrophoresis procedure to eliminate artifacts on reducing and nonreducing gels. Anal. Biochem. 246, 146-148
28. Benjamini, Y., Drai, D., Elmer, G., Kafkafi, N., and Golani, I. (2001) Controlling the false discovery rate in behavior genetics research. Behav. Brain Res. 125, 279-284
29. Churchward, M. A., Butt, R. H., Lang, J. C., Hsu, K. K., and Coorssen, J. R. (2005) Enhanced detergent extraction for analysis of membrane proteomes by two-dimensional gel electrophoresis. Proteome Sci. 3, 5-12
30. Lognonne, J. L. (1994) 2D-page analysis: a practical guide to principle critical parameters. Cell. Mol. Biol. (Noisy-le-grand) 40, 41-55
31. Harris, L. R., Churchward, M. A., Butt, R. H., and Coorssen, J. R. (2007) Assessing. detection methods for gel-based proteomic analyses. J. Proteome Res. 6, 1418-1425
32. Herbert, B., and Righetti, P. G. (2000) A turning point in proteome analysis: sample prefractionation via multicompartment electrolyzers with isoelectric membranes. Electrophoresis 21, 3639-3648
33. de Hassonville, H. S., Chiap, P., Liegeois, J. F., Evrard, B., Delattre, L., Crommen, J., Piel, G., and Hubert, P. (2004) Development and validation of a high-performance liquid chromatographic method for the determination of cyproterone acetate in human skin. J. Pharm. Biomed. Anal. 36, 133-143
34. Smejkal, G. B., Li, C., Robinson, M. H., Lazarev, A. V., Lawrence, N. P., and Chernokalskaya, E. (2006) Simultaneous reduction and alkylation of protein disulfides in a centrifugal ultrafiltration device prior to two-dimensional gel electrophoresis. J Proteome Res. 5, 983-987
35. Kane, L. A., Yung, C. K., Agnetti, G., Neverova, I., and Van Eyk, J. E. (2006) Optimization of paper bridge loading for 2-DE analysis in the basic pH region: application to the mitochondrial subproteome. Proteomics 6, 5683-5687
36. Stanley, B. A., Neverova, I., Brown, H. A., and Van Eyk, J. E. (2003) Optimizing protein solubility for two-dimensional gel electrophoresis analysis of human myocardium. Proteomics 3, 815-820
37. Taylor, C. M., and Pfeiffer, S. E. (2003) Enhanced resolution of glycosyl phosphatidylinositol-anchored and transmembrane proteins from the lipid-rich myelin membrane by two-dimensional gel electrophoresis. Proteomics 3, 1303-1312