Figure 2. Microarray analysis of Parhyale embryos.

Labelled RNA pools from transcriptionally inactive embryos (1- to 4-cell stage) and RNA pools from transcriptionally active embryos (germ band and limb bud stages) were hybridized together in a two-colour microarray experiment. (A) The MA plot uses the logarithmic fold-change value “M” as the y-axis and the logarithmic average expression value “A” as the x-axis, where: M = log2(zyg/mat), A = 1/2(log2(mat)+log2(zyg)), mat = signal intensity for transcriptionally inactive embryos, zyg = signal intensity for transcriptionally active embryos. The red data points represent the 690 unique maternally enriched RNAs, which constitute more than 10% of all unique gene sequences on the microarray. (B, C) The 8-cell embryo consists of four macromeres and four micromeres, each of them invariantly contributing to only one of the germ layers or the germ line. The three blue-coloured blastomeres give rise to ectoderm, the green-coloured blastomeres establish mesoderm, the yellow-coloured micromere is the progenitor of endoderm and the red-coloured cell contributes to the germ line. Blastomeres of the 8-cell stage were separated from each other by dissection and used for preparation of labelled cRNA for a two-coloured microarray experiment. The comparison between RNA from mesoderm progenitors and the rest of the 8-cell stage embryo (progenitors for ectoderm, endoderm and germline) resulted in the identification of a total of 129 asymmetrically localized RNAs. In the first experiment we found 35 RNAs overrepresented in the mesoderm progenitors transcript pool and 40 RNAs that were underrepresented. The second experiment approach revealed 33 transcripts enriched in ectoderm progenitors and 31 others that were predominantly found in the RNA pool from mesoderm, endoderm and germline progenitors. The four groups of asymmetrically localized RNAs from the two experiments add up to 139 because 10 of the RNAs were found in both experiments (see Table S4).