Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with... Show moreMaternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize technical interference, we used mature, unfertilized eggs from siblings. About half of the number of analyzed genes was found to be expressed as maternal RNA. The expressed and non-expressed genes showed that maternal mRNA accumulation is a non-random process, as it is related to specific biological pathways and processes relevant in early embryogenesis. Moreover, it turned out that overall the composition of the maternal transcriptome is tightly regulated as about half of the expressed genes display a less than twofold expression range between the observed minimum and maximum expression values of a gene in the experiment. Even more, the maximum gene-expression difference within clutches is for 88% of the expressed genes lower than twofold. This means that expression differences observed in maternally expressed genes are primarily caused by differences between mothers, with only limited variability between eggs from the same mother. This was underlined by the fact that 99% of the expressed genes were found to be differentially expressed between any of the mothers in an ANOVA test. Furthermore, linking chromosome location, transcription factor binding sites, and miRNA target sites of the genes in clusters of distinct and unique mother-specific gene-expression, suggest biological relevance of the mother-specific signatures in the maternal transcriptome composition. Altogether, the maternal transcriptome composition of mature zebrafish oocytes seems to be tightly regulated with a distinct mother-specific signature. Show less
Maternal mRNA that is present in the mature oocyte plays an important role in the proper development of the early embryo. To elucidate the role of the maternal transcriptome we recently reported a... Show moreMaternal mRNA that is present in the mature oocyte plays an important role in the proper development of the early embryo. To elucidate the role of the maternal transcriptome we recently reported a microarray study on individual zebrafish eggs from five different clutches from sibling mothers and showed differences in maternal RNA abundance between and within clutches, "Mother-specific signature in the maternal transcriptome composition of mature, unfertilized Eggs" [1]. Here we provide in detail the applied preprocessing method as well as the R-code to identify expressed and non-expressed genes in the associated transcriptome dataset. Additionally, we provide a website that allows a researcher to search for the expression of their gene of interest in this experiment. Show less
