Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis

Additional file 1:

Details of F-statistic analyses for time course microarray data. This document details the F-statistics and contrast matrix designs for identifying sex-differentially expressed genes and genes expressed in the male and female germlines using LIMMA. These analyses were conducted on the time course gene expression data. For this data, probes from wild type males, wild type females, tud progeny males, and tud progeny females were all separately hybridized against a common reference sample at five time points during metamorphosis (0, 24, 48, 72, and 96 hour APF).

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Additional file 2:

Numbers of genes identified in the time course experiment by F-statistic analyses implemented in LIMMA. This table reports the number of genes with significant differences in transcript abundance (q < 0.15), as identified using LIMMA contrasts analyses on the expression data from wild type or tud progeny males and females. For more details on contrast matrix designs, see Additional file 1.

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Additional file 3:

Genes with somatic, sex-differential expression across metamorphosis and at 0, 24, 48, 72, and 96 hour APF stages during metamorphosis. The first tab lists the genes identified as being sex-differentially expressed during metamorphosis as identified by F-statistic analyses implemented in LIMMA, using the time course microarray data. The second through sixth tabs lists the genes identified as sex-differentially expressed for each of the five time points examined (0, 24, 48, 72, and 96 hours APF). The genes in tabs two through six are all a subset of the genes listed in the first tab.

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Additional file 4:

Correlations of data from array experiments and number of genes identified in the microarray experiments. This first tab contains Pearson correlations between microarray replicates and the number of genes expressed for the time course microarray experiments. This second tab contains Pearson correlations between microarray replicates and the number of genes expressed when microarray comparisons between sex determination hierarchy mutants and wild type animals were performed.

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Additional file 5:

Gene lists of 38 clusters from time course microarray experiments. Lists of genes from each of the 38 clusters identified and presented in Figure 3 and Additional file 6. Clusters were generated using gene expression data from male and female tud progeny at five time points during metamorphosis (0, 24, 48, 72, and 96 hours APF). The gene list from each cluster is presented in the individual tabs.

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Additional file 6:

Average gene expression of the 38 clusters identified from the time course microarray experiments and presented in Figure 3. Clusters were generated using gene expression data from male and female tud progeny at five time points during metamorphosis. The wild type data is included, but has no weight in the cluster formation. For each cluster, the abscissa indicates the five time points during metamorphosis examined (0, 24, 48, 72, and 96 hour APF) and the ordinate indicates the average expression value for each genotype examined. Expression profiles for each cluster were generated by averaging the gene expression data at each time point for every gene in the cluster, in both sexes. Average expression values are represented by teal for wild type males, blue for wild type females, green for tud males, and red for tud females. Gene lists can be found in Additional file 5. Functional categories that were overrepresented among the genes in the cluster, as determined by the program DAVID (P < 0.05 [22]), are described in Additional file 7.

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Additional file 7:

DAVID analysis of 38 clusters from time course microarray experiments. Results of functional analysis from the program DAVID for each of the 38 clusters identified and presented in Figure 3 and Additional files 5 and 6. Clusters were generated using gene expression data from male and female tud progeny at five time points during metamorphosis (0, 24, 48, 72, and 96 hours APF). The DAVID functional analysis of each cluster is presented on individual tabs.

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Additional file 8:

Genes that are expressed in the male germline during metamorphosis. This table lists the genes identified as being expressed in or as a consequence of the male germline. Also included in the second tab are over-represented functional categories as determined by DAVID.

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Additional file 9:

Genes that are expressed in the female germline during metamorphosis. This table lists the genes identified as being expressed in or as a consequence of the female germline. Also included in the second tab are over-represented functional categories as determined by DAVID.

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Additional file 10:

Genes that show somatic, sex-differential expression at 48 hour APF, and genes expressed downstream of tra and dsx at 48 hour APF. The first tab lists genes with somatic, sex-differential transcript abundance differences at 48 hour APF during metamorphosis, the second tab lists genes with somatic sex differential transcript abundance downstream of tra at 48 hour APF during metamorphosis, and the third tab lists genes with somatic, sex-differential transcript abundance downstream of dsx at 48 hour APF during metamorphosis.

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Additional file 11:

Oligonucleotide sequences used as controls on the microarrays for genes in the Drosophila sex determination hierarchy. This table includes the sequence information for the control microarray spots for genes in the sex determination hierarchy. Included are control spots for Sex lethal (Sxl), transformer (tra), the female-specific region of doublesex transcripts (dsx^F), the male-specific region of doublesex transcripts (dsx^M), the PI-transcript of fruitless (fru P1), the A, B and C DNA binding domain of fruitless (fru^A, fru^B, fru^C).

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