Transcriptome data on maternal RNA of 24 individual zebrafish eggs from five sibling mothers

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 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. Keywords: Zebrafish, Danio rerio, Egg transcriptome, Single eg

Additional file 13: of Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

First two principal components of the intensity matrix of the expressed Ensembl genes. The variance explained by the components is indicated between brackets as percentages. Each embryo is colored by spawn as indicated. (PDF 26 kb

Subtle mother-specific maternal gene-expression.

<p>Overall low-variable maternal genes are almost all mother-specific differentially expressed. (A) Representation of the first four principal components of a PCA on the 11,118 expressed genes. (color code see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147151#pone.0147151.g001" target="_blank">Fig 1A</a>). The contribution to the total variability is given as a percentage at the axes. (B) Scatterplots of the per gene average clutch expression value of the first clutch against the four other clutches. Red dots represent the 2,224 genes that show an absolute distinct mother-specific expression level; green dots represent all other expressed genes. Dashed lines represent a fold change of 2 between the two clutches (also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147151#pone.0147151.s017" target="_blank">S14 File</a>). Labels on the Y-axes represent ‘Clutch 1’. (C) Illustrative examples of four mother-specific differentially-expressed genes that do not have an absolute distinct mother-specific expression. Labels on the X-axes represent ‘Mother (clutch)’, labels on the Y-axes represent log2 Intensity.</p

Obvious mother-specific maternal gene-expression.

<p>Maternal genes expressed at mother-specific distinct levels. (A) Heatmap showing 17 clusters of genes containing at least 25 genes that are expressed at a mother-specific or group-of-mothers specific level (see main text paragraph 3.4). The first 10 clusters are numbered by their relative gene-expression level between mothers as indicated by a 5-digit code (1 = high; 2 = low). In these 17 clusters only two levels were present because clusters with more than two levels contain less than 25 genes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147151#pone.0147151.s009" target="_blank">S6 File</a>) (B) Raw intensity data of three probes that query the transcript (ENSDART00000132835, pax1b-001) at positions: 985, 1268 and 1472 (color code: see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147151#pone.0147151.g001" target="_blank">Fig 1A</a>). Labels on the X-axes represent ‘Mother (clutch)’, labels on the Y-axes represent log2 Intensity. (C) Illustrative examples of genes with mother-specific gene expression of the 16 clusters from A that have an inverse counterpart (color code see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147151#pone.0147151.g001" target="_blank">Fig 1A</a>). Labels on the X-axes represent ‘Mother (clutch)’, labels on the Y-axes represent log2 Intensity.</p

Maternal gene expression in <i>zebrafish</i> eggs.

<p>(A) Experiment design: the transcriptomes of 24 individual <i>zebrafish</i> eggs was determined in five clutches. (B) Gene-expression distribution of the 11,118 expressed (red) and 11,353 non-expressed (green) unique Ensembl-defined genes. (C) Top 15 over-represented KEGG pathways associated with the maternally non-expressed genes. (D) Top 15 over-represented KEGG pathways associated with the maternally-expressed genes.</p

Differential gene expression in the maternal transcriptome.

<p>Variability of the maternal transcriptome. (A) Distribution of maximum fold changes (mFCs) in gene expression per gene between individual eggs (black, B left panel) and per gene within clutches (grey, B right panel). (B) Left panel, the maximum fold change (mFC) in gene expression between individual eggs, calculated as the difference per gene of the log intensity of the highest gene expression in any egg and the lowest log intensity of any other egg; Right panel, the maximum fold change within clutches was calculated per gene as the largest of the differences of the highest log intensity in any clutch (≈ mother) and the lowest log intensity in the same clutch (≈ mother). The red dashed line represents an absolute gene-expression mFC of 2. (C) Four illustrative examples of similar gene-expression in clutches from different mothers (color code see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147151#pone.0147151.g001" target="_blank">Fig 1A</a>). Labels on the X-axes represent ‘Mother (clutch)’.</p