Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Weiberg, Arne ^a   Pöhler, Dirk ^a   Morgenstern, Burkhard ^a   Karlovsky, Petr ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA FRAGMENT; RESTRICTION ENDONUCLEASE; PRIMER DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARABIDOPSIS; ARTICLE; CATALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA DETERMINATION; DNA FRAGMENTATION; DNA SEQUENCE; HUMAN; MOUSE; NONHUMAN; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SIMULATION; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY;

ARABIDOPSIS THALIANA; MUS;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANIMALS; ARABIDOPSIS; COMPUTER SIMULATION; DNA PRIMERS; DNA RESTRICTION ENZYMES; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; HUMANS; MICE; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; SOFTWARE;

EID: 55349108922     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-480     Document Type: Article

References (23)

1. Liang P Pardee A Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction Science 1992, 257:967-971. 1354393 1354393 10.1126/science.1354393
2. Vos P Hogers R Bleeker M Reijans M Lee van de T Hornes M Frijters A Pot J Peleman J Kuiper M Zabeau M AFLP: A new technique for DNA fingerprinting Nucleic Acids Res 1995, 23:4407-4414. 307397 7501463 10.1093/nar/23.21.4407
3. Bachem CWB Hoeven van der RS de Bruijn SM Vreugdenhil D Zabeau M Visser RGF Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: Analysis of gene expression during potato tuber development Plant Journal 1996, 9:745-753. 10.1046/ j.1365-313X.1996.9050745.x 8653120
4. Vuylsteke M Peleman JD van Eijk MJT AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis Nature Protocols 2007, 2:1399-1413. 10.1038/nprot.2007.174 17545977
5. Breyne P Dreesen R Cannoot B Rombaut D Vandepoele K Rombauts S Vanderhaeghen R Inzé D Zabeau M Quantitative cDNA-AFLP analysis for genome-wide expression studies Mol Gen Genomics 2003, 269:173-179. 12756529
6. Metsis A Andersson U Baurén G Ernfors P Lönnerberg P Montelius A Oldin M Pihlak A Linnersson S Whole-genome expression profiling through fragment display and combinatorial gene identification Nucleic Acids Res 2004, 32:e127. 519127 15356287 10.1093/nar/gnh126
7. Reineke A Karlovsky P Simplified AFLP protocol: Replacement of primer labeling by the incorporation of alpha-labeled nucleotides during PCR BioTechniques 2000, 28:622-623. 10769736
8. Kadota K Araki R Nakai Y Abe M GOGOT: A method for the identification of differentially expressed fragments from cDNA-AFLP data Algorithms for Molecular Biology 2007, 2:5. 1904450 17535446 10.1186/1748-7188-2-5
9. Qin L Prins P Jones JT Popeijus H Smant G Bakker J Helder J GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP Nucleic Acids Res 2001, 29:1616-1622. 11266565 11266565 31277 10.1093/nar/29.7.1616
10. The GenEST homepage http://thebird.nl/download/genest/
11. Kivioja T Arvas M Saloheimo M Penttilä M Ukkonen E Optimization of cDNA-AFLP experiments using genomic sequence data Bioinformatics 2005, 21:2573-2579. 10.1093/bioinformatics/bti393 15774551
12. Rombauts S Peer Van De Y Rouzé P AFLPinSilico, simulating AFLP fingerprints Bioinformatics 2003, 19:776-777. 10.1093/bioinformatics/ btg090 12691992
13. The AFLP in Silico v2 homepage http://bioinformatics.psb.ugent.be/ webtools/aflpinsilico/
14. Bikandi J San Millán R Rementeria A Garaizar J In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction Bioinformatics 2004, 20:798-799. 10.1093/bioinformatics/ btg491 14752001
15. The In Silico AFLP-PCR amplification homepage http://www.in-silico.com/ sAFLP/
16. San Millán R Garaizar J Bikandi J In silico simulation of fingerprinting techniques based on double endonuclease digestion of genomic DNA In Silico Biology 2005, 5:341-346. 16153186 16153186
17. The In silico simulation of molecular biology experiments homepage http://insilico.ehu.es/
18. Fukumura R Takahashi H Saito T Tsutsumi Y Fujimori A Sato S Tatsumi K Araki R Abe M A sensitive transcriptome analysis method that can detect unknown transcripts Nucleic Acids Res 2003, 31:e94. 12907746 12907746 169986 10.1093/nar/gng094
19. Feron R Mariani C Vriezen WH Application of the mRNA Capture Kit in cDNA-AFLP Biochemica 2004, 3:23-24.
20. Venkatesh B Hettwer U Koopmann B Karlovsky P Conversion of cDNA differential display results (DDRT-PCR) into quantitative transcription profiles BMC Genomics 2003, 6:51. 15807902 10.1186/1471-2164-6-51
21. Wheeler DL Church DM Federhen S Lash AE Madden LT Pontius JU Schuler GD Schriml LM Sequeria E Tatusova TA Wagner L Database resources of the National Center for Biotechnology Nucleic Acids Res 2003, 31:28-33. 165480 12519941 10.1093/nar/gkg033
22. Pruitt KD Tatusova T Maglott DR NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res 2005, 33:D501-D504. 15608248 15608248 539979 10.1093/nar/gki025
23. Roberts R Vincze T Posfai J Macelis D REBASE - restriction enzymes and methyltransferases Nucleic Acids Res 2003, 31:418-420. 12520038 12520038 165516 10.1093/nar/gkg069