Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from Serinus canaria HVC, RA and Entopallium

ABSTRACT: Within the overall project, we performed a set of microarrays to validate RNAseq data (submitted to EBI: PRJEB4463). In this data set, we compare the expression data of song nuclei to the optical tectrum dissected from adult canaries housed at long day cycles to identify nuclei specific genes. 18 total S. canaria samples were analyzed, 6 HVC samples, 5 RA samles and 7 Entopallium samples. The differential expression was analyzed using the group-wise exhaustive analysis with False Discovery Rate set to zero and 10-significant probe minimum coverage, HVc/RA compared to entopallium samples. ChipInspector carries out significance analysis on the single probe level (directly generated from the CEL files). Thus, normalized probe set level data for individual Sample records are not available. Processed data files containing transcripts and the fold changes are available on Series record.

ORGANISM(S): Serinus canaria

SUBMITTER: Carolina Frankl-Vilches

PROVIDER: E-GEOD-50070 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Photoperiod and hormonal cues drive dramatic seasonal changes in structure and function of the avian song control system. Little is known, however, about the patterns of gene expression associated with seasonal changes. Here we address this issue by exposing GambelM-bM-^@M-^Ys white-crowned sparrows to season-appropriate cues and extracting RNA from the telencephalic song control nuclei HVC and RA across multiple time points that capture different stages of growth and regression. We chose HVC and RA because while both nuclei change in volume across seasons, the cellular mechanisms underlying these changes differ. We thus hypothesized that different genes would be expressed between HVC and RA. We tested this by using the extracted RNA to perform a cDNA microarray hybridization developed by the SoNG initiative. We then validated these results using qRT-PCR. Supporting our hypothesis, only 59 of the 363 genes of interest were found to vary by more than |1.5| fold in expression in both nuclei, while 132 gene expression changes were HVC specific and 172 genes were RA specific. We then assigned many of these genes to functional categories relevant to the different mechanisms underlying seasonal change in HVC and RA, including neurogenesis, apoptosis, cell growth, dendrite arborization and axonal growth, angiogenesis, endocrinology, growth factors, and electrophysiology. This revealed categorical differences in the kinds of genes regulated in HVC and RA. These results show that different molecular programs underlie seasonal changes in HVC and RA, and that gene expression is time specific across different reproductive conditions. Our results provide insights into the complex molecular pathways that underlie adult neural plasticity. Experimental groups: long-term Short Day (SD); Long Day (LD) with Testosterone (T) for 3, 7, and 21 days (3LD+T, 7LD+T, 21LD+T respectively); SD and removal of T at 1 and 2 days (1SD-T, 2SD-T); two tissues (HVC, RA) collected separately from each individual animal; one experimental sample and one universal SoNG reference sample per array; dye balanced within groups. Six biological replicates per group, five biological replicates in 3LD+T.HVC group.

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Expression data from Serinus canaria HVC, RA and Entopallium

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