E-GEOD-48824 - Caste-specific expression patterns of olfactory related genes in the leaf-cutting ant, Atta vollenweideri
Released on 1 October 2013, last updated on 3 June 2014
To allow estimation of the complexity and gene expression differences of the antennal transcriptome between sexes as well as between castes, microarrays were designed based on an assembly of A. vollenweideri antennal sequence data from all sexes and castes. The microarrays were hybridized with samples generated from the respecitve antennal tissues, with four independent sample pools per sex and caste. Custom 2x105 k Agilent microarrays (Agilent Technologies, Palo Alto, CA) were designed based on the antennal transcriptome data of A.vollenweideri. For all contigs with an identified ORF by automatic annotation, two 60mer oligo probes were designed, with two additional 60mer oligo probes for opposite reading direction for those with unknown ORF, thus resulting in 4 oligo probes per contig. Additionally, we added three 60mer oligo probes for each identified and revised OR coding gene, resulting in a total of 5 oligo probes per OR coding contig. For design and arrangement of the Agilent microarrays, the eArray software (Agilent Technologies, Palo Alto, CA) was used. For sex- and caste-specific antennal microarray hybridizations, RNA from antennae of 50 (Males) to 300 (Tiny Workers) individuals was pooled per preparation, and four pools (replicates) each were dissected per sex and caste, respectively. Double purified total RNA was added to Agilent Technologies spike-in RNA and labeld using QuickAmp Amplification kit (Agilent Technologies) and the Kreatech ULS Fluorescent Labeling Kit with cyanine 3-CTP dye following the manufacturer´s instructions. Amplified cRNA samples were used for microarray hybridization, scanned with the Agilent Microarray Scanner and data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Raw data output files were analyzed using the GeneSpring GX11 and GeneSifter microarray analysis softwares.
transcription profiling by array
Cristoph Kleineidam, Ewald Grosse-Wilde, Heiko Vogel, Sarah Koch