Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture-5

<p><b>Copyright information:</b></p><p>Taken from "Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture"</p><p>http://www.biomedcentral.com/1471-2164/8/365</p><p>BMC Genomics 2007;8():365-365.</p><p>Published online 10 Oct 2007</p><p>PMCID:PMC2204012.</p><p></p>2 and KLF4 with Oct4 in sub-nuclear compartments (possibly nucleoli). Individual confocal images for OCT4, KLF2, KLF4, and DAPI are shown with the corresponding composite image. Scale bar 40 μm. () Electro-mobility gel shift assay showing changes in DNA binding activities at a conserved CACC box site in the p18-INK4c gene promoter. Nuclear extracts were generated from ES cells or EBs differentiated for four days in serum. Super-shifts were performed with specific antisera for SP1, SP3, KLF2, KLF3, and KLF4 (See Methods). There is strong binding of endogenous Sp1 to the CACC element in ES cells and EB cells. KLF2 DNA-binding activity is present in ES cells as determined by a specific inhibition of binding of the indicated DNA complex with a KLF2 antibody. This activity is lost upon differentiation into EBs. The identity of the CACC box binding activity in EBs denoted CAC-X, and the binding activity in ES cells denoted CAC-Y, was not definitively identified using this panel of antibodies

Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture-4

<p><b>Copyright information:</b></p><p>Taken from "Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture"</p><p>http://www.biomedcentral.com/1471-2164/8/365</p><p>BMC Genomics 2007;8():365-365.</p><p>Published online 10 Oct 2007</p><p>PMCID:PMC2204012.</p><p></p> serum-freeculture. Most of the genes are listed on the y-axis in order from their highest relative expression in ES cells. There is dramatic up regulation of only in serum following day 6 of differentiation. Plots representing (red), (red) and (green) are shown for comparison. and gene expression persists at high levels for 2–3 days after , and are down regulated. () Validation of changes in gene expression of six members of the KLF family by quantitative real time RT-PCR. Scheme as described for Figure 2B

Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture-7

<p><b>Copyright information:</b></p><p>Taken from "Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture"</p><p>http://www.biomedcentral.com/1471-2164/8/365</p><p>BMC Genomics 2007;8():365-365.</p><p>Published online 10 Oct 2007</p><p>PMCID:PMC2204012.</p><p></p>rentiated ES cells (0, grey bar) and in EBs collected for up to 16 days in serum (white bars) or defined media (black bars) from the same starting ES cell populations. Bars represent the means of three (serum) or two (serum-free) biological replicates. The Y-axis represents a log scale normalized relative to the housekeeping gene HPRT. Error bars indicate standard deviation

Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture-3

<p><b>Copyright information:</b></p><p>Taken from "Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture"</p><p>http://www.biomedcentral.com/1471-2164/8/365</p><p>BMC Genomics 2007;8():365-365.</p><p>Published online 10 Oct 2007</p><p>PMCID:PMC2204012.</p><p></p>nt of > 0.9). In sets 1–7, expression is higher in serum (black sets). In sets 8–9, expression is greater in serum-freeEB culture (red sets). Some sets have been named based on the similarity of overall gene function during differentiation pathways (see Table 3)

Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture-0

<p><b>Copyright information:</b></p><p>Taken from "Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture"</p><p>http://www.biomedcentral.com/1471-2164/8/365</p><p>BMC Genomics 2007;8():365-365.</p><p>Published online 10 Oct 2007</p><p>PMCID:PMC2204012.</p><p></p>rentiated ES cells (0, grey bar) and in EBs collected for up to 16 days in serum (white bars) or defined media (black bars) from the same starting ES cell populations. Bars represent the means of three (serum) or two (serum-free) biological replicates. The Y-axis represents a log scale normalized relative to the housekeeping gene HPRT. Error bars indicate standard deviation

Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture-2

<p><b>Copyright information:</b></p><p>Taken from "Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeculture"</p><p>http://www.biomedcentral.com/1471-2164/8/365</p><p>BMC Genomics 2007;8():365-365.</p><p>Published online 10 Oct 2007</p><p>PMCID:PMC2204012.</p><p></p>um or serum-freeculture. The up-regulation of genes between days 2–4 were similar under both conditions. () qRT-PCR analysis of Mixl, Lim1, Cdx4 and Riken clone 8430415E04Rik. The Y-axis represents expression relative to the housekeeping gene HPRT. Error bars indicate ± SD from three biological replicates. () 102 genes transiently up regulated during the first 4 days of ES cell differentiation were clustered using a tree algorithm and Pearson correlation of > 0.9. The '' group represents gene with very transient expression at day 3. () Coding region for 8430415E04Rik. The shaded areas represent the three Heat domains