## Description

This track shows expression data from the Zon Lab at Children's Hospital Boston using the Affymetrix Zebrafish GeneChip Genome Array. The chip type or strain medians associated with replicate experiments (Chip ID display) or the average of this data across all strains for each developmental stage (Tissue Averages display) can be displayed by selecting the appropriate option from the Experiment Display menu on the track description page. For more information, see the Track Configuration section.

## Methods

For detailed information about the experimental methods, see Weber et al. (2005) below. This expression data is for five strains of wild type zebrafish whole embryos at different developmental stages. Alignments displayed on the track correspond to the target sequences used by Affymetrix to choose probes.

Microarray data were preprocessed using MAS background correction, MAS probe specific correction, and Loess normalization. Bioconductor's affy package was used to perform this processing. CEL files were normalized as a single group. The track color denotes the signal ratio for a specific developmental stage and strain on a log base 2 scale. The ratio is the expression value for a probeset divided by the median of expression values for that probeset across all experiments. Over-expressed genes are colored red; under-expressed genes are show in green. Black indicates that a gene is neither over- nor under-expressed in the tissue. Uncolored boxes (white on most browsers) represent missing data.

Each row on the track or details page shows gene expression data for a single developmental stage and a single strain (see Strains and Stages table below) from wild type, whole embryo zebrafish. Data was collected by the Children’s Hospital Boston Zebrafish Genome Initiative.

## Track Configuration

This track may be configured to vary the type of experiment information shown. It is possible to display all arrays, arrays grouped by replicate means, or arrays grouped by replicate medians. Choose the desired set of arrays from the Combine arrays list above. To display all arrays for each strain and developmental stage, select All Arrays from the list. The default display shows the Replicate Medians.

## Strains and Stages Table

Key: TL = Tuebingen longfin; TU = Tuebingen; hpf. = hours post-fertilization.

Strain | Stage | Replicates
--- | --- | ---
AB | 14 Somites | 6
AB | 36 hpf. | 9
golden | 14 somites | 1
TL | 14 somites | 2
TL | 36 hpf. | 7
TU | 14 somites | 2
TU | 15 somites | 3
TU | 36 hpf. | 3
WIK | 14 somites | 1

## Credits

Thanks to the Zon Lab for kindly providing this data as part of the following NIH grants: PO1 DK 055381 - Characterization of the Zebrafish Genome, UO1 DK 63328 - SCGAP, and P30 DK49216 - Center Grant Core. Data collection and curation was performed by Gerhard Weber, Yi Zhou, Anhua Song and Tony DiBiase.

## References

Weber GJ, Choe SE, Dooley KA, Paffett-Lugassy NN, Zhou Y, Zon LI. Mutant-specific gene programs in the zebrafish. Blood. 2005 Jul;106(2):521-30.