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CDNA microarray analysis comparing transcription levels in the heads of control and hangAE10 mutants of D. melanogaster

ABSTRACT: To identify putative transcripts that might interact with Hang, we performed a cDNA microarray experiment in which we compared transcription levels in the heads of control and hangAE10 mutants. Experimental and control probes were simultaneously hybridized to custom-made glass cDNA microarrays (DGC Drosophila v1 6k array, GEO accession no. GPL22680) that contained 6024 PCR-amplified cDNAs (the DGC 1.0 collection of 5849 non-redundant cDNAs was kindly provided by the Berkeley Drosophila Genome Project) and analysed using a GenePix 4000A Microarray Scanner (Axon Instruments, Union City, CA). Values were further processed as log2-transformed ratios and analysed with Microsoft Excel, Cluster analysis (Eisen et al., 1998), and the Significance Analysis of Microarrays (SAM) software package (Tusher et al., 2001). The ratios were filtered to eliminate all values that did not produce signals above background in at least four out of the five replicate experiments. cDNA spots for which the expression between two hybridized samples of RNA with a log2 value > 0.8 differed in at least two experiments were retained for further analysis.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE91049 | GEO | 2016/12/09

SECONDARY ACCESSION(S): PRJNA356747

REPOSITORIES: GEO

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Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile pituitary gland gene expression during juvenile development (1 to 7 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia, and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in the pituitary gland during juvenile development using a reference design for the hybridization of total RNA from the pituitary gland. A reference RNA pool was made from an equal amount of high-quality total RNA extracted from all of the samples. Each of the microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the pituitary samples and Cy5-labled cDNA targets from the reference pituitary RNA pool. Log2-transformed fluorescence intensities were analyzed with a mixed model. Two-way ANOVA (SAS) of log2 ratios was used to detect significant (p<0.05) differences by line, age, and the line-by-age interaction. There were 1150 significantly different genes between the two lines, and 339 of these genes exhibited greater than 0.68-fold differences in their log2 ratios (highest group mean at least 160% of the lowest group mean). One thousand four hundred twenty nine genes were significantly different by age and of these, 583 exhibited fold changes greater than 0.68 in the log2 ratio. There were 145 genes that significantly differed in their line-by-age interaction, and 62 of these exhibited greater than 0.68-fold differences. There were 386 genes with significant differences by line or for line-by-age interaction with at least a 0.68-fold change in log2 ratio and n ≥ 2 for each experimental group.

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CDNA microarray analysis comparing transcription levels in the heads of control and hangAE10 mutants of D. melanogaster

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