This search option enables users to query the database with the same keyword as basic search but more specific criteria such as experimental type (i.e. ChIP-seq or ChIP-on-chip), species (i.e. human or mouse) and cell line.
Selection criteria were set to select several assay types (MeDIP and ChIP), several species (human and mouse) and cover several research fields.
We obtained analogous results for hundreds of GeneChip expression arrays of different specifications: chip generations, species (human, mouse, rat, drosophila, rice, arabidopsis etc).
ChIPs using species and isotype-matched immunoglobins directed against an unrelated protein (GST) were used to determine background levels analysed by qPCR as described above.
Analogously, for other types of assays, the rows of the matrix might correspond e.g., to binding regions (with ChIP-Seq), species of bacteria (with metagenomic datasets), or peptide sequences (with quantitative mass spectrometry).
While data sets are available for Affymetrix chip for some species, for other platforms, such as the custom cDNA microarrays, one would need to manually define the gene sets, which can delay procurement of downstream information or introduce errors.
Hybridisation to X species chip.
The chips for cod, hake, herring and sole could be available for commercial use within months, with chips for other species to be rolled out within a year.DNA is a sturdy molecule, so samples of fish taken anywhere along the trip from ocean to fork can be tested.
For the purpose of effectively maintaining genetic diversity, a marker density of around 500 SNPs/Morgan can be considered as the most cost effective density when developing SNP chips for new species.
Heterologous hybridizations are based on interrogation of a chip specifically designed for a species (primary species) with transcripts from a phylogenetically-related species (secondary species).
However, given that only ~2%% of the SNP in these cattle chips was segregating in buffaloes, a species specific SNP chip would be more informative.
