BBSRC and UD clones were shipped to the FHCRC core genomics lab. Information on the libraries joined to produce this collection is available at individual web sites and previous publications. Microarrays were constructed using modified protocols of those discussed by De Risi et al. Individual PCR products were verified as unique via gel electrophoresis and purified using the Millipore Multiscreen-PCR filtration system. Purified PCR products were mechanically "spotted" in 3X SSC (1X = 150 mM sodium chloride, 15 mM sodium citrate, pH 7.0) onto poly-lysine coated microscope slides using a GeneMachines OmniGrid high-precision robotic gridder (Genomics Solutions, Ann Arbor, MI). The array layout consists of 32 blocks in a 4 × 8 configuration and each PCR product is represented once on the array. In addition, each array sub-grid (i.e., "block") contains spots representing 4 different Arabidopsis genes (negative controls) and 1 spot consisting of sheared chicken (white leghorn) genomic DNA.
Description
Background The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes.
Results We have produced cDNA arrays using chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. From a total of 363,838 chicken ESTs representing 24 different adult or embryonic tissues, a set of 11,447 non-redundant ESTs were selected and added to an existing collection of clones (4,162) from immune tissues and a chicken bursal cell line (DT40). Quality control analysis indicates there are 13,007 useable features on the array, including 160 control spots. The array provides broad coverage of mRNAs expressed in many tissues; in addition, clones with expression unique to various tissues can be detected.
Conclusions A chicken multi-tissue cDNA microarray with 13,007 features is now available to academic researchers from genomics@fhcrc.org. Sequence information for all features on the array is in GenBank, and clones can be readily obtained. Targeted users include researchers in comparative and developmental biology, immunology, vaccine and agricultural technology. These arrays will be an important resource for the entire research community using the chicken as a model.
Differential gene expression in the bone marrow of layer and broiler chickens
Data table header descriptions
ID
Source
a designation of the group or institution that provided the
Source Clone Name
an identifier for the corresponding clone, issued by the clone's source.
PCR Amp Code
the PCR amplification code for each clone, determined by agarose gel electrophoresis of its resultant PCR product: 'M' indicates the presence of multiple bands; 'N' indicates no band detected; A blank in this column means that an acceptable single band was observed.
Source Assigned Annotation
annotation provided by the clone's source. Not all sources provided this information, so not all rows will have values in this column. 'NA' indicates none available.
TIGR: GB Accession
the GenBank accession number associated with this clone in the Gallus gallus Gene Index (GgGI) maintained by the Institute for Genomic Research (TIGR). Not all clones are recorded in GgGI, so not all rows will have values in this column. 'NA' indicates none available.
TIGR: EST Id
the EST Id recorded for this clone in the EST Annotation table in TIGR's GgGI. 'NA' indicates none available.
TIGR: TC
an identifier for the tentative consensus (TC) if TIGR has constructed a consensus sequence that includes this clone. Further information on how TIGR constructs TCs is provided below, in Section VI. 'NA' indicates none available.
TIGR: Annotation
an annotation derived by TIGR for the TC representing this clone. TIGR's method of acquiring annotation for their TCs is described below, in section VI. 'NA' indicates none available.
BLAST Annotation
in those cases where a clone was not associated with a TC in TIGR's GgGI, an annotation was derived locally by performing a blast with those sequences against GgGI. The procedure by which blast results were selected for inclusion in the chicken13k_anno_v1.0.txt file is described below, in section VII. 'NA' indicates none available.
GB_ACC
GenBank Accession
CLONE_ID
SPOT_ID
Comment
an additional remark pertaining to data in the row; the word 'none' appears if no remarks are required.
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