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. 2006 Mar 13:7:49.
doi: 10.1186/1471-2164-7-49.

Development of a chicken 5 K microarray targeted towards immune function

Jacqueline Smith  1 , David Speed, Paul M Hocking, Richard T Talbot, Winfried G J Degen, Virgil E J C Schijns, Elizabeth J Glass, David W Burt
Affiliations

Development of a chicken 5 K microarray targeted towards immune function

Jacqueline Smith et al. BMC Genomics. .

Abstract

Background: The development of microarray resources for the chicken is an important step in being able to profile gene expression changes occurring in birds in response to different challenges and stimuli. The creation of an immune-related array is highly valuable in determining the host immune response in relation to infection with a wide variety of bacterial and viral diseases.

Results: Here we report the development of chicken immune-related cDNA libraries and the subsequent construction of a microarray containing 5190 elements (in duplicate). Clones on the array originate from tissues known to contain high levels of cells related to the immune system, namely Bursa, Peyers patch, thymus and spleen. Represented on the array are genes that are known to cluster with existing chicken ESTs as well as genes that are unique to our libraries. Some of these genes have no known homologies and represent novel genes in the chicken collection. A series of reference genes (ie. genes of known immune function) are also present on the array. Functional annotation data is also provided for as many of the genes on the array as is possible.

Conclusion: Six new chicken immune cDNA libraries have been created and nearly 10,000 sequences submitted to GenBank [GenBank: AM063043-AM071350; AM071520-AM072286; AM075249-AM075607]. A 5 K immune-related array has been developed from these libraries. Individual clones and arrays are available from the ARK-Genomics resource centre.

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Figures

Figure 1
Figure 1
Scatter plots showing the variance between A). self/self hybridisation B). two biological replicates and C). a control sample compared with an activated sample. Very little spread is seen with the self/self hybridisation and between the two replicates, as would be expected. However, differences in gene expression can be seen between the activated and control samples.
Figure 2
Figure 2
Box plots showing the variance between self/self hybridisation, two biological replicates and a control sample compared with an activated sample. Boxes represent the interquartile range from 25–75%, with the median marked. Outliers to this range are also shown.
See this image and copyright information in PMC

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