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Gene expression analyses




Zebra Finch Agilent Oligoarray

The Zebra Finch Agilent Oligoarray is composed of 43,488 60-mer oligos representing transcripts identified from three major research groups (Wada et al 2006; Li et al 2007: Replogie et al 2008).  The array has performed reliably within and across bird species, and is available for use either from Duke University Microarray Center or directly from Agilent (AMADID 021323).  More detailed information on the array design can be found at avian genomes.  Since the array was developed, te zebra finch genome has been sequenced.  By mapping the oligonulceotides and transcripts to the zebra finch genome, we have been able to increase the coverage and accuracy of the array annotations.  The most recent version can be found in a tab delimited text file here.  The type of array analysis depends heavily on the experimental design.  A good place to start is the tools available throug the bioconductor project, especially limma.


Zebra Finch Affymetrix Array (just released November 2011)

Information here for the Affymetrix web site:


The new Affymetrix® Zebra Finch Gene 1.1 ST Array Strip is a whole-transcript expression array design based on the taeGut1 genome build. It contains 22 distinct probes per gene and total of 18,595 gene-level probe sets, providing the highest coverage of the transcribed genome. This array will help scientists advance research in understanding evolution and neurological behavior studies.

Gene Expression: RNAseq 

  • Galaxy server at Penn State: very useful open-access environment for analyzing RNAseq data.

  • SongSeq server (planned for the songbird research community)

Gene Expression: In Situ Hybridization

  • ZEBrA (Zebra finch Brain Expression Atlas) On-line digital atlas of gene expression in the adult male zebra finch brain (Claudio Mello and Peter Lovell)

Parvalbumin Tachykinin


Gene Expression: Behavioral molecular mapping

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