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Open Access Highly Accessed Research article

Gene expression changes in aging Zebrafish (Danio rerio) brains are sexually dimorphic

Ayca Arslan-Ergul12 and Michelle M Adams13*

Author Affiliations

1 BilGen Genetics and Biotechnology Center, Bilkent University, Ankara, Turkey

2 Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey

3 Department of Psychology, Bilkent University 06800 Bilkent Ankara, Turkey

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BMC Neuroscience 2014, 15:29  doi:10.1186/1471-2202-15-29

Published: 18 February 2014

Additional files

Additional file 1:

In Sheet 1 (Data) 15,617 probes are given with their annotations obtained through BioMart (http://www.biomart.org/biomart/martview webcite) with the current Zebrafish Genome Built (Danio rerioZv9). Probe Set Ids are found in column A, columns B and C display fold change ratios in log2 base of Female/Male and Young/Old, respectively. Columns D, E, and F show the corresponding p values for Female vs. Male, Young vs. Old, and Age by Gender interaction. In the following columns, annotation information and GO ontology information are given. Sheet 2 (FvsM) gives the list of 909 probesets that are significantly different between female and male, sheet 3 (YvsO) gives the list of 1543 probesets that are different between young and old. Sheet 4 (AbyG) shows the 495 probesets that have a significant difference in age by gender analysis. Intersection sheet shows the list of 210 genes that are common to FvsM and YvsO lists.

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Open Data

Additional file 2:

Representative image of Go Analysis results. Page 1; Female vs. Male, Page 2; Young vs. Old, Page 3; Color legend. In this picture colors more toward yellow mean relatively lower p-values, and colors more toward orange mean the highest p-values.

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Additional file 3:

A complete list of the Gene Ontology analysis. For female vs. male comparison, 189 descriptions, their p-values, and the genes that were included in the description are given. For young vs. old comparison. 299 descriptions, their p-values, and the genes that were included in the description are given.

Format: XLSX Size: 151KB Download file

Open Data

Additional file 4:

Box plot representation of selected genes. Expression values from microarray data in log2 base are given on y-axis. On the x-axis the genes are provided. Expression variation of all samples are summarized in one box for each gene. The horizontal lines in the boxes indicate the mean values. Actin values were the most stable among other genes.

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Additional file 5:

Individual expression values for samples from microarray analysis. Expression values are actual linear values from microarray experiment. FO; female old, FY; female young, MO; male old, MY; male young. Expression values on Y-axis are displayed in units of hundreds (i.e. 80 represents 8000).

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Additional file 6:

SPSS statistical test report sheets for microarray and qPCR expressions of the selected genes. On the first page, the first column indicates animal sex and age. The second and third columns indicate a number assignment as to the age or gender in order to perform the SPSS analysis. Columns four through eleven list the 2^-(target-actin) values for the PCR table, and log2-based expression values for the array table. Following sheets show the SPSS output files from multivariate analysis for the microarray and qPCR results, univariate analysis and the relevant post-hoc tests for the microarray and qPCR results, respectively.

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Additional file 7:

Genes selected for real-Time PCR experiments along with their corresponding RefSeq ID numbers used for microarray experiments and for primer design. Primer sequences are given for each gene, left primer (top) and right primer (bottom). Amplicon lengths are given as nucleotide numbers and melting temperatures used for PCR are provided. UPL; universal probe library, Tm; melting temperature, nt; nucleotides.

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