Raw intensity values for all microarray data and microarray platform information have been deposited in the NCBI Gene Expression Omnibus database (Series accession no. GSE14607 (SKF) and GSE14610 (LY)) under MIAME compliance.
However, the major barrier against using genomic approaches to improve Ae. variabilis is that the genome sequence, cDNA libraries, EST databases, and microarray platform information are not available [ 14].
Microarray platform information and data for the DSM 17938 strains are deposited at the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO GSE54324; http://www.ncbi.nlm.nih.gov/geo/, last accessed July 2 , 2014.
ExpressionSets were packaged as the curatedOvarianData R library, which provides a reference manual including descriptions of the syntax template and summaries of the annotations, citation, microarray platform and other information for each study.
All protocols related to this microarray platform, which include information on probe sequences and synthesis, labeling, hybridization and scan protocols, and microarray data have been submitted to NCBI's Gene Expression Omnibus database at http://www.ncbi.nlm.nih.gov/geo/ with GEO accession number GSE42597.
For each study, the transcriptomic data stored in the database is comprised of individual probeset values for each patient sample (in some cases multiple samples from each patient are profiled), and annotation information further describing the experiment (e, g. trial information, microarray platform identifier, normalization method, gene descriptions).
Detailed information about the microarray platform (accession number: GPL2581) and the array data from this study (accession number: GSE46601) are accessible on the Gene Expression Omnibus database, http://www.ncbi.nlm.nih.gov/geo/.nih.gov/geo/
Table 2 gives an overview of the 16 studied data sets with information on outcome, microarray platform and number of included samples and genes.
Today, a large portion of microarray platform providers make all probe sequence information available; in addition, MIAME guidelines require submission of probe sequences for each spot on a microarray [ http://www. mged.org/Workgroups/MIAME/miame.html].
All information on SLA-RI/NRSP8-13 microarray platform has been submitted to the Gene Expression Omnibus (GEO) repository and the accession number is GPL7151.
Human microarray platform, GPL1528; human HCC microarray data, GSE1898; mouse microarray platform, GPL1529; mouse HCC microarray data, GSE1897.
