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Manduca sexta differential gene expression, male & female antenna, larval midgut

ABSTRACT: 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.

ORGANISM(S): Manduca sexta

SUBMITTER: Heiko Vogel

PROVIDER: E-GEOD-27470 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Manduca sexta differential gene expression, male & female antenna, larval midgut

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

Caste-specific expression patterns of olfactory related genes in the leaf-cutting ant, Atta vollenweideri

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 manufacturerÂ´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

Caste-specific expression patterns of olfactory related genes in the leaf-cutting ant, Atta vollenweideri

2013-10-01 | GSE48824 | GEO

Microarray analysis of stalk-eyed fly lines selected for divergent eyespan

Project description:Eye-stalks of some flies exhibit extreme sexual dimorphism, but little is known about the genetic mechanisms producing variation in these ornamental traits. Therefore, we constructed an EST database of genes expressed in the developing eye-antennal imaginal disc of the highly dimorphic species, Teleopsis dalmanni, and used this set of genes to construct high density oligoarrays and compare patterns of gene expression between lines of flies selected for divergent eyespan. Microarray experiments using eye-antennal disc tissue identified over 350 genes with significant differential expression between male flies from lines selected for high and low relative eyespan but did not reveal any primary biological process or pathway that is driving the expression differences. Custom 4x44K Agilent arrays were designed for approximately 3600 unique genes. Each gene was represented by three 60 bp oligo probes and each probe was printed in triplicate on each array. Each oligoarray was hybridized with two biological samples labeled either with cy3 or cy5. Each sample came from 25 sets of eye-antennal imaginal discs that were dissected from gut-purged male larvae. Samples were from lines of flies that had been under directional selection on males to either increase or decrease relative eyespan for 65 generations. Dye labeling was switched between lines for every other array. Ratios of median intensities were averaged across probes for each gene and then analyzed by SAM to identify genes with differential expression between lines.

2010-06-24 | E-GEOD-15444 | biostudies-arrayexpress

Large scale transcript analysis of PI compensatory effects in the midgut and caeca of Locusta migratoria

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2016-04-07 | E-GEOD-79995 | biostudies-arrayexpress

Abrupt scrib- vs. Abrupt and RasV12 (RasACT) scrib-, NotchICD (NACT) scrib- +/- JNK (Bsk) expression profiles

Project description:Drosophila mosaic eye-antennal discs from the listed genotypes generated using the MARCM system were dissected from 3rd instar larvae at day 5 after egg deposition. 20 pairs of discs for the Abrupt and scrib- + Abrupt samples and 50 pairs from FRT control, NACT scrib- +/- BskDN and RasACT scrib- +/- BskDN were used to prepare RNA. Samples were prepared in triplicate, and the RNA isolated using TRIZOL, before being column purified (Qiagen). Probes were hybridized to GeneChip Drosophila 2.0 Genome Arrays (Affymetrix). To compare the expression profile of Abrupt when overexpressed in the eye-antennal discs with tumours formed by Abrupt overexpression in scrib- clones, and to reveal JNK responsive genes in RasV12 (RasACT) scrib- versus NotchICD (NACT) scrib- eye-antennal mosaic discs

2013-08-15 | E-GEOD-42938 | biostudies-arrayexpress

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2008-06-14 | E-GEOD-6300 | biostudies-arrayexpress

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2012-10-03 | E-GEOD-26678 | biostudies-arrayexpress

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2014-02-14 | E-MTAB-1500 | biostudies-arrayexpress

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