8-by-15-K DNA microarray chips covering the whole genome were implemented under the Agilent platform.
The overall transcriptional profile was similar to the previous study of infected B. abortus strain 2308 [ 6], although we used different microarray chips covering more than 30,000 genes.
Toward identifying such target genes, we carried out a ChIP (chromatin immunoprecipitation -on-chip analysimmunoprecipitation -on-chip a set of mimmunoprecipitation -on-chip kb region flanalysisach putative profothe of 17000 Xenopus tropintestinenes to look for genes byusingy TR (unpublished observation).
In order to uncover the regulome of HrpX transcription regulator by profiling the wild-type and the hrpX mutant strains transcriptome, we had designed a microarray chip covering the whole genome under Agilent platform in our previous study [ 33].
All samples were processed using Affymetrix Drosophila (DrosophilaGenome2) chips covering nearly the whole fly coding genome.
In this study, we have designed custom microarray chips with probes covering majority of annotated genes from the MSU database.
Labelling of samples and hybridisation to the Affymetrix Human HG-U133 Plus 2.0 oligonucleotide microarray chips (Santa Clara, CA, USA), covering over 47 000 human transcripts and variants, were performed following the manufacturer's protocols.
The microarray chips we used contained 46,657 probes each, covering almost all known protein-encoding genes.
Yet in recent years, attempts to probe the genomic diversity of conifers have seen the development of such genomic resources as expressed sequence tag (EST) databases, cDNA microarray chips, and bacterial artificial chromosome (BAC) libraries, covering a handful of conifer species, notably loblolly pine (Pinus taeda) and white spruce (Picea glauca).
For the analysis of expression at different stages of differentiation, data were obtained for 43 mouse samples in StemBase (Sandie et al., 2009), originating from 16 studies with Affymetrix MOE430A microarray chips, as used in an Oct4 expression profiling study (Campbell et al., 2007) covering murine ESCs, embryonal carcinoma cell lines, and several early differentiated lineages.
Our 4-plex Nimblegen Inc. microarray chip consisted of 72,000 features, covering the complete Nematostella genome with three replicate oligonucleotide probes per gene.
