18 research outputs found

    List of discriminatory genes in components 1 and 2 with PLS-DA analysis.

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    The tool eggNOG-mapper was used for functional annotation based on precomputed orthology assignments. (XLSX)</p

    Exploratory analyses of each dataset.

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    After processing the raw data, we checked the distribution of raw counts and performed principal component analysis. (TIF)</p

    Sample clustering.

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    The quality of the expression matrix was evaluated by sample clustering based on the distance between different samples, measured as Spearman’s correlation. No outliers were detected. (TIF)</p

    <i>Klf5</i> but not <i>JunB</i> disturbs the LIF-dependent plasticity in early committed cells.

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    <p>Cells were depleted from LIF for 24 hours and either transfected with siControl (siCtrl) (A) siKlf5, or (B) siJunB and then induced with LIF for three days (d3). Graphs represent the average level of expression and SEM from 3 to 6 independent experiments. Paired sample t-test was performed to determine the significance of the difference in the expression levels observed with the non specific (siCtrl) versus specific siRNA: *p-value<0.05; **p-value<0.01, ***p-value<0.001; if not stated: not significant.</p

    Hypoxia maintains cell plasticity with a novel equilibrium of <i>Pluri</i> and <i>early Diff</i> genes.

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    <p>Cells grown under normoxia (N) or hypoxia (H) were depleted from LIF or induced with LIF after a period of LIF depletion as indicated. After 4 days, expression of the selected genes, (A) <i>Master</i>, (B) <i>Pluri</i>, (C) <i>Pluri Adhesion</i> and (D) <i>Diff</i> was analysed by RT-qPCR. Graphs represent the average level of expression and SEM as depicted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146281#pone.0146281.g002" target="_blank">Fig 2</a> (n = 4). One sample t-test was performed for the +LIF condition and paired sample t-test was performed for the other conditions to evaluate the significance of the difference in the expression levels observed in normoxia versus hypoxia: *p-value<0.05; **p-value<0.01, ***p-value<0.001; if not stated: not significant.</p

    PI3K does not regulate the LIF-dependent plasticity window but stimulates differentiation towards early mesoderm lineage while inhibiting ectoderm and endoderm differentiation processes.

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    <p>Cells were depleted from LIF or induced with LIF in the presence of LY, for the first 24 hours as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146281#pone.0146281.g001" target="_blank">Fig 1C</a>. After 5 days, expression of the selected genes (A) <i>Master</i> genes, (B) <i>Pluri</i> genes, (C) early <i>Diff</i> genes and (D) specific germ layer genes, was analyzed by RT-qPCR. Graphs represent the average level of expression and SEM from 4 independent experiments. Paired sample t-test was performed to evaluate the significance of the difference in the expression levels observed with or without LY: *p-value<0.05; **p-value<0.01, ***p-value<0.001; a: pvalue = 0.051; if not stated: not significant.</p

    LIF has differential effects on mESC-derived cells, after d1, d2 or d3 of LIF starvation.

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    <p>Cells were depleted from LIF or induced with LIF after a period of LIF depletion as indicated. After 4 days, expression of the selected genes (A) <i>Master</i> genes, (B) <i>Pluri</i> genes and (C) <i>Diff</i> genes was analyzed by RT-qPCR with <i>Hprt</i> used for normalization. Graphs represent the average level of expression and standard error of the mean (SEM) bars, calculated from 4 independent experiments. +LIF condition was arbitrarily set as 1. One sample t-test was performed for each condition versus the +LIF sample: *p-value<0.05; **p-value<0.01, ***p-value<0.001; a: p-value = 0.051; if not stated: not significant. (D) A representative experiment of flow cytometry, performed in the indicated conditions with the Ceacam-PE antibody, is presented: "off set graph" of the MFI of the total P1 gated cell population of each cell growth condition, with the Flo Jo software.</p
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