Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE).
BACKGROUND
Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries relies on the identification of ditags from sequencing files; however, the software used to examine SAGE libraries cannot distinguish between authentic versus false ditags ("quasi-ditags").


RESULTS
We provide examples of quasi-ditags that originate from cloning and sequencing artifacts (i.e. genomic contamination or random combinations of nucleotides) that are included in SAGE libraries. We have employed a mathematical model to predict the frequency of quasi-ditags in random nucleotide sequences, and our data show that clones containing less than or equal to 2 ditags (which include chromosomal cloning artifacts) should be excluded from the analysis of SAGE catalogs.


CONCLUSIONS
Cloning and sequencing artifacts contaminating SAGE libraries could be eliminated using simple pre-screening procedure to increase the reliability of the data.
Anisimov
Sergey V
SV
Section for Neuronal Survival, Wallenberg Neuroscience Center, Lund University, 221 84 Lund, Sweden. Sergey.Anisimov@mphy.lu.se
Sharov
Alexei A
AA
D000818:Animals; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D044708:DNA, Concatenated / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D048168:Escherichia coli K12 / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics; D015723:Gene Library; D016680:Genome, Bacterial; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D051379:Mice; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics
D017931:DNA Primers; D004269:DNA, Bacterial; D044708:DNA, Concatenated; D004271:DNA, Fungal