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ABSTRACT:
PROVIDER: PRJNA787070 | ENA |
REPOSITORIES: ENA
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Project description: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.
2013-10-01 | E-GEOD-48824 | biostudies-arrayexpress
Project description:To allow estimation of the complexity of the antennal transcriptome between sexes as well as in comparison with a non-antennal tissue, microarrays were designed based on an assembly of new 454 sequence data from the antenna and publicly available data including 454 data from the larval midgut. The microarrays were hybridized with samples generated from the repsecitve tissues from 3 (antenna) and 5 (midgut) animals per sample, with four independent samples per sex (antenna) and tissue (midgut). Sequence assembly of included Manduca antennal and gut ESTs (63) and all publicly available Genbank sequences was used with eArray (Agilent Technologies) for the design of 4 x 44K microarrays based on 60mer oligo probes. For sex-specific antennal microarray hybridizations, RNA of three individuals of one sex was pooled per preparation, and 5 larvae each were dissected for gut tissue isolation with four biological replicates per sex (antennae) and tissue (gut), 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.
2011-03-01 | E-GEOD-27470 | biostudies-arrayexpress
Project description: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.
2013-10-01 | GSE48824 | GEO
Project description:To allow estimation of the complexity of the antennal transcriptome between sexes as well as in comparison with a non-antennal tissue, microarrays were designed based on an assembly of new 454 sequence data from the antenna and publicly available data including 454 data from the larval midgut. The microarrays were hybridized with samples generated from the repsecitve tissues from 3 (antenna) and 5 (midgut) animals per sample, with four independent samples per sex (antenna) and tissue (midgut).
2011-03-01 | GSE27470 | GEO