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Abstract
Three distinct cell types are present within the 64-cell stage mouse blastocyst. We
have investigated cellular development up to this stage using single-cell expression
analysis of more than 500 cells. The 48 genes analyzed were selected in part based
on a whole-embryo analysis of more than 800 transcription factors. We show that in
the morula, blastomeres coexpress transcription factors specific to different lineages,
but by the 64-cell stage three cell types can be clearly distinguished according to
their quantitative expression profiles. We identify Id2 and Sox2 as the earliest markers
of outer and inner cells, respectively. This is followed by an inverse correlation
in expression for the receptor-ligand pair Fgfr2/Fgf4 in the early inner cell mass.
Position and signaling events appear to precede the maturation of the transcriptional
program. These results illustrate the power of single-cell expression analysis to
provide insight into developmental mechanisms. The technique should be widely applicable
to other biological systems.
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