70-mer oligonucleotide probes  (Operon Biotech)

Journal: Genome Biology

Article Title: Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy

doi: 10.1186/gb-2008-9-7-r115

Figure Lengend Snippet: Validation of DNA microarray expression data by qRT-PCR. The mean log10 ratios of selected genes from microarray expression data (grey bars) are compared to qRT-PCR data (black bars) for (a) L. infantum MTX20.5 and (b) L. major MTX60.4. The microarray data are the average of four biological replicates (with two dye swaps), while the qRT-PCR data are the average of three biological replicates repeated two times each. The asterisk indicates that the related gene transcript was not detected by qRT-PCR. The upper panel shows the expression of orthologous genes where the expression changes in the two species; the middle panel shows the modulation in the expression of FBT genes; the lower panel shows the expression of individual genes specific for each mutant.

Article Snippet: Completion of the L. major genome has allowed the generation of arrays containing 60-mer oligonucleotide probes designed by NimbleGen Systems [ , ] and in this work, we present the generation of a full genome DNA microarray composed of 70-mer oligonucleotide probes suitable for both L. major and L. infantum analysis (see Materials and methods for a full description of the arrays).

Techniques: Microarray, Expressing, Quantitative RT-PCR, Mutagenesis

Journal: Genome Biology

Article Title: Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy

doi: 10.1186/gb-2008-9-7-r115

Figure Lengend Snippet: Extrachromosomal circular amplification of a genomic region of Leishmania chromosome 6 that includes the DHFR-TS locus. (a) Genomic organization of the DHFR-TS locus in both L. infantum MTX20.5 and L. major MTX60.4. Relative gene expression data (RNA) were determined using DNA microarrays and relative hybridization data were obtained by comparative genomic hybridization (DNA). Asterisks indicate that the microarray data of these genes were not found to be reliable. Direct repeats are shown with thick arrows and the approximate position of primers 6a and 6b are indicated with half arrows. (b) Chromosome size blot of Leishmania cells hybridized to a DHFR-TS probe. Sizes were determined using a yeast molecular weight marker (Biorad. Hercules, CA, USA). (c) Model for the formation of the extrachromosomal DHFR-TS circular DNA generated through homologous recombination between direct repeats (Figure S1 in Additional data file 2). (d) PCR with primers 6a and 6b to support the model shown in (c). Lane 1, L. infantum wild-type cells; lane 2, L. infantum MTX 20.5; lane 3, L. major wild-type cells; lane 4, L. major MTX60.4.

Article Snippet: Completion of the L. major genome has allowed the generation of arrays containing 60-mer oligonucleotide probes designed by NimbleGen Systems [ , ] and in this work, we present the generation of a full genome DNA microarray composed of 70-mer oligonucleotide probes suitable for both L. major and L. infantum analysis (see Materials and methods for a full description of the arrays).

Techniques: Amplification, Expressing, Hybridization, Microarray, Molecular Weight, Marker, Generated, Homologous Recombination