CfDNA level in follicular fluid pools according to the embryo outcome at day 2 and 3.

<p><b>A</b>, Follicular Fluid cfDNA content according to the total number of embryos at day 2 (≤ 2 versus > 2, *p = 0.03). <b>B</b>, Follicular Fluid cfDNA content according to, left panel: the number of top quality (grade 1–2) embryos per patient (0 versus ≥ 1, *p = 0.002) at day 2, right panel: ratio between number of top quality embryos and total number of embryos (< 0.2 versus ≥ 0.2, *p = 0.04) at day 2. <b>C</b>, Follicular Fluid cfDNA content according to, left panel: number of top quality (grade 1–2) embryos per patient (0 versus ≥ 1, *p = 0.006) at day 3, right panel: ratio between number of top quality embryo and total number of embryos (< 0.2 versus ≥ 0.2, *p = 0.02) at day 3. <b>D</b>, Follicular Fluid cfDNA content according to, left panel: fragmentation rate at day 3 (<20% versus ≥ 20%, p = 0.18) and right panel: ratio between blastomere number and total embryo number at day 3 (<6 versus 6–8, *p = 0.02).</p

List of the 100 genes with the highest fold change in day 3 human embryos in comparison to TE samples.

<p>List of the 100 genes with the highest fold change in day 3 human embryos in comparison to TE samples.</p

Cell-free DNA level in follicular fluid pools according to the patients’ ovarian reserve status, ovarian reserve parameters and infertility length.

<p><b>A</b>, Follicular fluid cfDNA content in patients with normal ovarian reserve versus patients with ovarian reserve disorders (ovarian insufficiency and polycystic ovary syndrome); *p = 0.03. <b>B</b>, Follicular fluid cfDNA content according to the ovarian reserve parameters; left panel: AFC (<10 versus ≥ 10, *p = 0.04); right panel: AMH (≤ 1 versus > 1 ng/ml, *p = 0.06). <b>C</b>, Follicular fluid cfDNA levels according to the infertility length (1 versus ≥ 5 years, *p = 0.049).</p

Gene Ontology (GO) annotations of the day 3 embryo and TE molecular signatures.

<p>We compared the GO annotations of genes specifically over-expressed in day 3 embryos and in TE cells by using the Babelomics web tool (<a href="http://babelomics.bioinfo.cipf.es/" target="_blank">http://babelomics.bioinfo.cipf.es/</a>). Histograms show the percentage of genes with a specific GO annotation in day 3 embryos (white) or in TE samples (black). Only GO categories which differed significantly (<i>p</i> value <0.01) between the two groups are shown.</p

List of the 100 genes with the highest fold change in TE samples in comparison to day 3 embryos.

<p>List of the 100 genes with the highest fold change in TE samples in comparison to day 3 embryos.</p

Up-regulated genes that are related to the <i>NANOG</i> pathway, or to metabolic and epigenetic functions in day 3 human embryos and TE samples.

<p>(A) The interaction network was generated with the Ingenuity software and shows that many genes from the <i>NANOG</i> pathway are up-regulated (red) in day 3 embryos. (B) Top-ranked functional networks in which are involved transcription factors (<i>GATA2</i> and <i>GATA3</i>), or genes that regulate steroidogenesis (including <i>HSD1B3</i>), DNA repair (<i>TDG</i> and <i>BRCA1</i>) or epigenetic modifications (including <i>DNMT3L)</i> and that are up-regulated in TE samples. The color intensity indicates their degree of up-regulation. Uncolored genes were identified as not differentially expressed by our analysis, but were, nevertheless, integrated into the computationally generated networks on the basis of the evidence stored in the IPA knowledge memory indicating a relevance to this network. In each network, nodes indicate genes, a plain line indicates direct interaction, a dashed line indicates indirect interaction; a line without arrowhead indicates binding only; a line with an arrowhead indicates “acts on”.</p

Differential expression of apoptosis and stemness-related genes in day 3 embryos and TE samples.

<p>(A) Histograms show the microarray signal values for apoptosis-related genes in day 3 embryos (black) and TE samples (white). (B) The mean expression level of 48 stemness genes in six day 3 embryos and five TE samples was plotted on a logarithmic scale in a radar graph. Asterisks indicate a statistically significant difference (<i>P</i><0.05) between TE and day 3 embryos (Mann-Whitney test).</p