Publications of the Month

Affymetrix Whole-Transcript Human Gene 1.0 ST Array is Highly Concordant with Standard 3' Expression Arrays
Sylvain Pradervand, Alexandra Paillusson, Jérôme Thomas, Johann Weber, Pratyaksha Wirapati, Otto Hagenbüchle, and Keith Harshman
BioTechniques^®  May 2008  Volume 44, Number 6: pp 759-762


ABSTRACT
The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3' based arrays: (i) it interrogates the entire mRNA transcript, and (ii) it uses DNA targets. To assess the impact of these differences on array performance, we performed a series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both RNA and DNA targets were hybridized on HG-U133 Plus 2.0 arrays. The results show that the overall reproducibility of the Gene 1.0 ST array is best. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. Agreements are best between the two labeling protocols using HG-U133 Plus 2.0 array. The Gene 1.0 ST array is most concordant with the HG-U133 array hybridized with cDNA targets. This may reflect the impact of the target type. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array.


Identification of New Genes in Sinorhizobium meliloti Using the Genome Sequencer FLX system
Chunhong Mao, Clive Evans, Roderick V Jensen and Bruno WS Sobral
BMC Microbiology, May 2008, 8:72doi:10.1186/1471-2180-8-72

ABSTRACT
Background
Sinorhizobium meliloti is an agriculturally important model symbiont.  There is an ongoing need to update and improve its genome annotation.  In this study, we used a high-throughput pyrosequencing approach to sequence the transcriptome of S. meliloti, and search for new bacterial genes missed in the previous genome annotation.  This is the first report of sequencing a bacterial transcriptome using the pyrosequencing technology.
Results
Our pilot sequencing run generated 19,005 reads with an average length of 136 nucleotides per read.  From these data, we identified 20 new genes.  These new gene transcripts were confirmed by RT-PCR and their possible functions were analyzed.
Conclusions
Our results indicate that high-throughput sequence analysis of bacterial transcriptomes is feasible and next-generation sequencing technologies will greatly facilitate the discovery of new genes and improve genome annotation. 


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