Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines

Genome Research

Volumn 17, Issue 1, 2007, Pages 108-116

  Khattra, Jaswinder ^a   Delaney, Allen D ^a   Zhao, Yongjun ^a   Siddiqui, Asim ^a   Asano, Jennifer ^a   McDonald, Helen ^a   Pandoh, Pawan ^a   Dhalla, Noreen ^a   Prabhu, Anna Liisa ^a   Kevin, Ma ^a   Lee, Stephanie ^a   Ally, Adrian ^a   Tam, Angela ^a   Sa, Danne ^a   Rogers, Sean ^a   Charest, David ^b   Stott, Jeff ^a   Zuyderduyn, Scott ^a   Varhol, Richard ^a   Eaves, Connie ^c   Jones, Steven ^a   Holt, Robert ^a   Hirst, Martin ^a   Hoodless, Pamela A ^c   Marra, Marco A ^a   more..

^a BRITISH COLUMBIA CANCER RESEARCH CENTRE   (Canada)

^b Genome British Columbia   (Canada)

^c BRITISH COLUMBIA CANCER AGENCY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BASE PAIRING; BIOINFORMATICS; CELL LINE; CLINICAL PROTOCOL; CONTROLLED STUDY; DNA LIBRARY; DNA SEQUENCE; GENE DUPLICATION; GENE MAPPING; GENETIC VARIABILITY; MICRODISSECTION; MOLECULAR CLONING; MOUSE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA ISOLATION; RNA PURIFICATION; SERIAL ANALYSIS OF GENE EXPRESSION;

ANIMALS; CAENORHABDITIS ELEGANS; CELL LINE; CELL SEPARATION; DATABASES, NUCLEIC ACID; EMBRYONIC STEM CELLS; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOME; HUMANS; MICE; MICRODISSECTION; SEQUENCE ANALYSIS, DNA; SOFTWARE; ZEBRAFISH;

EID: 33846000624     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5488207     Document Type: Article

References (35)

1. Akmaev, V.R. and Wang, C.J. 2004. Correction of sequence-based artifacts in serial analysis of gene expression. Bioinformatics 20: 1254-1263.
2. Angelastro, J.M., Klimaschewski, L.P., and Vitolo, O.V. 2000. Improved NlaIII digestion of PAGE-purified 102 bp ditags by addition of a single purification step in both the SAGE and microSAGE protocols. Nucleic Acids Res. 28: E62.
3. Beissbarth, T., Hyde, L., Smyth, G.K., Job, C., Boon, W.M., Tan, S.S., Scott, H.S., and Speed, T.P. 2004. Statistical modeling of sequencing errors in SAGE libraries. Bioinformatics 20: I31-I39.
4. Bennett, S.T., Barnes, C., Cox, A., Davies, L., and Brown, C. 2005. Toward the $1000 human genome. Pharmacogenomics 6: 373-382.
5. Chen, J. and Sadowski, I. 2005. Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements. Proc. Natl. Acad. Sci. 102: 4813-4818.
6. Colinge, J. and Feger, G. 2001. Detecting the impact of sequencing errors on SAGE data. Bioinformatics 17: 840-842.
7. Dinel, S., Bolduc, C., Belleau, P., Boivin, A., Yoshioka, M., Calvo, E., Piedboeuf, B., Snyder, E.E., Labrie, F., and St-Amand, J. 2005. Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome. Nucleic Acids Res. 33: e26.
8. Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
9. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
10. Gowda, M., Jantasuriyarat, C., Dean, R.A., and Wang, G.L. 2004. Robust-LongSAGE (RL-SAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol. 134: 890-897.
11. Halaschek-Wiener, J., Khattra, J.S., McKay, S., Pouzyrev, A., Stott, J.M., Yang, G.S., Holt, R.A., Jones, S.J., Marra, M.A., Brooks-Wilson, A.R., et al. 2005. Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res. 15: 603-615.
12. Heidenblut, A.M., Luttges, J., Buchholz, M., Heinitz, C., Emmersen, J., Nielsen, K.L., Schreiter, P., Souquet, M., Nowacki, S., Herbrand, U., et al. 2004. aRNA-longSAGE: A new approach to generate SAGE libraries from microdissected cells. Nucleic Acids Res. 32: e131.
13. Impey, S., McCorkle, S.R., Cha-Molstad, H., Dwyer, J.M., Yochum, G.S., Boss, J.M., McWeeney, S., Dunn, J.J., Mandel, G., and Goodman, R.H. 2004. Defining the CREB regulon: A genome-wide analysis of transcription factor regulatory regions. Cell 119: 1041-1054.
14. Kenzelmann, M. and Muhlemann, K. 1999. Substantially enhanced cloning efficiency of SAGE (Serial Analysis of Gene Expression) by adding a heating step to the original protocol. Nucleic Acids Res. 27: 917-918.
15. Kim, J., Bhinge, A.A., Morgan, X.C., and Iyer, V.R. 2005. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nat. Methods 2: 47-53.
16. Kirschman, J.A. and Cramer, J.H. 1988. Two new tools: Multi-purpose cloning vectors that carry kanamycin or spectinomycin/streptomycin resistance markers. Gene 68: 163-165.
17. Kodzius, R., Kojima, M., Nishiyori, H., Nakamura, M., Fukuda, S., Tagami, M., Sasaki, D., Imamura, K., Kai, C., Harbers, M., et al. 2006. CAGE: Cap analysis of gene expression. Nat. Methods 3: 211-222.
18. Loh, Y.H., Wu, Q., Chew, J.L., Vega, V.B., Zhang, W., Chen, X., Bourque, G., George, J., Leong, B., Liu, J., et al. 2006. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 38: 431-440.
19. Margulies, E.H., Kardia, S.L., and Innis, J.W. 2001. Identification and prevention of a GC content bias in SAGE libraries. Nucleic Acids Res. 29: e60.
20. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
21. Matsumura, H., Reich, S., Ito, A., Saitoh, H., Kamoun, S., Winter, P., Kahl, G., Reuter, M., Kruger, D.H., and Terauchi, R. 2003. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc. Natl. Acad. Sci. 100: 15718-15723.
22. McKay, S.J., Johnsen, R., Khattra, J., Asano, J., Baillie, D.L., Chan, S., Dube, N., Fang, L., Goszczynski, B., Ha, E., et al. 2003. Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans. Cold Spring Harb. Symp. Quant. Biol. 68: 159-169.
23. Neilson, L., Andalibi, A., Kang, D., Coutifaris, C., Strauss III, J.F., Stanton, J.A., and Green, D.P. 2000. Molecular phenotype of the human oocyte by PCR-SAGE. Genomics 63: 13-24.
24. Peters, D.G., Kassam, A.B., Yonas, H., O'Hare, E.H., Ferrell, R.E., and Brufsky, A.M. 1999. Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite. Nucleic Acids Res. 27: e39.
25. Powell, J. 1998. Enhanced concatemer cloning-a modification to the SAGE (Serial Analysis of Gene Expression) technique. Nucleic Acids Res. 26: 3445-3446.
26. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
27. Saha, S., Sparks, A.B., Rago, C., Akmaev, V., Wang, C.J., Vogelstein, B., Kinzler, K.W., and Velculescu, V.E. 2002. Using the transcriptome to annotate the genome. Nat. Biotechnol. 20: 508-512.
28. Schroeder, A., Mueller, O., Stocker, S., Salowsky, R., Leiber, M., Gassmann, M., Lightfoot, S., Menzel, W., Granzow, M., and Ragg, T. 2006. The RIN: An RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol. 7: 3.
29. Shendure, J., Mitra, R.D., Varma, C., and Church, G.M. 2004. Advanced sequencing technologies: Methods and goals. Nat. Rev. Genet. 5: 335-344.
30. Siddiqui, A.S., Khattra, J., Delaney, A.D., Zhao, Y., Astell, C., Asano, J., Babakaiff, R., Barber, S., Beland, J., Bohacec, S., et al. 2005. A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc. Natl. Acad. Sci. 102: 18485-18490.
31. Smailus, D.E., Marziali, A., Dextras, P., Marra, M.A., and Holt, R.A. 2005. Simple, robust methods for high-throughput nanoliter-scale DNA sequencing. Genome Res. 15: 1447-1450.
32. Velculescu, V.E., Zhang, L., Vogelstein, B., and Kinzler, K.W. 1995. Serial analysis of gene expression. Science 270: 484-487.
33. Wei, C.L., Ng, P., Chiu, K.P., Wong, C.H., Ang, C.C., Lipovich, L., Liu, E.T., and Ruan, Y. 2004. 5′ Long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation. Proc. Natl. Acad. Sci. 101: 11701-11706.
34. Wei, C.L., Wu, Q., Vega, V.B., Chiu, K.P., Ng, P., Zhang, T., Shahab, A., Yong, H.C., Fu, Y., Weng, Z., et al. 2006. A global map of p53 transcription-factor binding sites in the human genome. Cell 124: 207-219.
35. Yang, G.S., Stott, J.M., Smailus, D., Barber, S.A., Balasundaram, M., Marra, M.A., and Holt, R.A. 2005. High-throughput sequencing: A failure mode analysis. BMC Genomics 6: 2.