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| Status |
Public on May 31, 2012 |
| Title |
The impact of experience-dependent and independent factors on gene expression in songbird brain [e09] |
| Organism |
Taeniopygia guttata |
| Experiment type |
Expression profiling by array
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| Summary |
Songbirds provide rich natural models for studying the relationships of brain anatomy, behavioral function, environmental signals and gene expression. Under the Songbird Neurogenomics Initiative, investigators from more than a dozen laboratories collected brain samples from six species of songbird under a range of experimental conditions, and 488 of these samples were analyzed systematically for gene expression by microarray. ANOVA was used to test 32 planned contrasts in the data, revealing the relative impact of different factors. The brain region from which tissue was taken had the greatest influence on gene expression profile, affecting the majority of signals measured by the 18,848 non-redundant cDNAs spotted on the microarray. Social and environmental manipulations had highly variable impact, ranging from nil in some cases to robust in others. Several specific genes were identified as points of interest in the evolution of mechanisms by which environmental signals influence behavior. The data were also analyzed using Weighted Gene Co-expression Network Analysis (WGCNA) followed by Gene Ontology (GO) analysis. This revealed modules of co-regulated genes that are also enriched for specific functional annotations such as “ribosome” (expressed more highly in juvenile brain) and “dopamine metabolic process” (expressed more highly in striatal song control nucleus Area X). These results underscore the complexity of influences on neural gene expression and provide a resource for studying how these influences are integrated during natural experience.
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| Overall design |
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e09: Comparison of HVC and shelf regions from adult male zebra finches, 6 biological replicates per group. Each sample was hybridized against the SoNG universal reference RNA pool.
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| Contributor(s) |
Drnevich J, Replogle K, Arnold AP, Ball GF, Brenowitz E, Hahn TP, Johnson F, London S, Lovell P, Mast TG, Mello C, Mukai M, Strand C, Wade J, Wingfield JC, Clayton DF |
| Citation(s) |
23045667 |
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| Submission date |
Mar 23, 2012 |
| Last update date |
Nov 05, 2012 |
| Contact name |
Kirstin Replogle |
| E-mail(s) |
replogle@igb.uiuc.edu
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| Organization name |
University of Illinois
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| Street address |
1206 W Gregory Drive
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| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
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| Platforms (1) |
| GPL9554 |
Songbird Neurogenomics Initiative 20K Array |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE36748 |
The impact of experience-dependent and independent factors on gene expression in songbird brain |
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| Relations |
| BioProject |
PRJNA155431 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE36738_RAW.tar |
21.7 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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