EST-based microarrays: 1. A set of unique Locusta ESTs (from LocustDB and the CNS database), 2. Schistocerca ESTs having no homolog in the unique Locusta set.
The microarray platform contains probes representing (i) all EST sequences retrieved from LocustDB [1], (ii) all EST sequences retrieved from the L. migratoria central nervous system deep-sequencing project [2] that did not appear to be represented in LocustDB and (iii) all S. gregaria EST sequences [3] having no ortholog in the L. migratoria set (blastn hits producing E < 1E-10 were considered orthologs). The locust microarrays were designed by means of the eArray system (Agilent Technologies). Probes were designed according to the following eArray criteria: (i) probe length: 60 nucleotides, (ii) two probes per target sequence (best probe methodology) and (iii) probe orientation: sense. Other parameters were set at default settings. The locust microarray platform was assayed by means of self-self hybridizations of pooled brain and midgut samples of 5th larval locusts in three different feeding conditions, i.e., normal fed, fed a diet supplemented with protease inhibitors, and starved. The aim of these gene expression studies was (i) to determine the genes that appear to be expressed in the tissues under study, and (ii) for each of these gene targets, to select the best-performing corresponding probe for platform optimization for future studies. For detailed information, we refer to the article corresponding to the associated data Series.
[1] Ma ZY, Yu J, Kang L (2006) LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria). BMC Genomics 7: 11. [2] Zhang Z, Peng ZY, Yi K, Cheng Y, Xia Y (2012) Identification of representative genes of the central nervous system of the locust, Locusta migratoria manilensis by deep sequencing. Journal of Insect Science 12: 86. [3] Badisco L, Huybrechts J, Simonet G, Verlinden H, Marchal E et al. (2011) Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database. PLoS One 6: e17274.
Arrays of this design have barcodes that begin with 16034971 or 2534971.
Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the Agilent Feature Extraction feature number.
Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
