Learning to use the NCBI Gene Expression Omnibus

As part of our workup for the toxin/antitoxin manuscript, I want to find expression data for the homologs of theHaemophilus influenzae toxin and antitoxin genes. The former post-doc recommends that I use NCBI's Gene Expression Omnibus ('GEO') for this.I'll need to learn how to search the GEO for specific accession data and data from specific taxa.I'll also need to find out the specific identifiers for the genes I'm interested in, in the species I'm interested in. I think I can use BLAST searches (queried with theH. influenzae sequences) to find the species and links to the DNA sequences of the homologs, and then I can look at the gene records to find the strain and gene identifiers.Then I need to check if anyone has reported doing gene-expression studies on this strain or species (ideally the same strain, but I think/hope the gene identifiers will be consistent across strains). These reports should contain the GEO accession numbers for the data.Then I can ask GEO for the data for this study. But I don't know what format the data will be in, nor how hard it will be to find the information about the genes I'm interested in.The best situation would be if GEO has done its own analysis on the data and made this available as a curated 'GEO Dataset' or a 'GEO Profile'. I could then search the GEO Profile to see their analysis of the particular genes I want to learn about.Here's a phylogenetic tree showing the relationships between the concatenated toxin/anti...
Source: RRResearch - Category: Molecular Biology Authors: Source Type: blogs