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-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-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

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

Overlap of FANTOM CRITICA Predictions with Genome-Based Gene Predictions Made by Six Methods

<p>Only the 16,900 maximal-length isoforms of the FANTOM CRITICA predictions were considered; these were compared to each genome-based method in turn as follows. Each CRITICA prediction was compared to the genome-based gene prediction that overlapped it by the greatest number of nucleotides, and the degree of overlap was quantified using the performance coefficient: the number of nucleotides in the intersection of the two predictions divided by the number of nucleotides in the union of the predictions [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020052#pgen-0020052-b045" target="_blank">45</a>]. These are box-and-whisker plots: the centre lines indicate the medians, the top and bottom of the boxes indicate the first and third quartiles, and the whiskers extend to the most extreme data points.</p

Heat Map Displaying Relative Expression Levels of Small-ORF Transcripts Present within 61 Mouse Tissues from the Genomics Institute of the Novartis Research Foundation GeneAtlas

<p>Small-ORF transcripts are clustered on the vertical axis, and tissue samples are along the horizontal axis. All gene expression is displayed relative to the median level of each transcript across all 61 tissues. The coloured columns on the left-hand side of the heat map (left) correspond to the blown up sections (right). FANTOM3 clone identifiers are included in the blown up clusters. A blow-up of the tissue clustering, including the tissue names, is available as <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020052#pgen-0020052-sg001" target="_blank">Figure S1</a>.</p

Evolutionary Conservation of FANTOM CRITICA Predictions

<div><p>Only the 16,900 maximal-length isoforms of the FANTOM CRITICA predictions were considered.</p> <p>(A) Histogram of predictions where the reading frame is perfectly conserved in rat (black) or disrupted (white).</p> <p>(B) Histogram of predictions where the reading frame is perfectly conserved in human (black) or disrupted (white).</p> <p>(C and D) Sequence conservation of predictions versus (C) rat and (D) human. Sequence conservation was quantified by the percentage of nucleotides in each predicted protein-coding region that align to identical nucleotides in the other organism. These are box-and-whisker plots: the centre lines indicate the medians, the top and bottom of the boxes indicate the first and third quartiles, and the whiskers extend to the most extreme data points. The long horizontal lines indicate the percentage of sequenced nucleotides in the mouse genome that align to identical nucleotides in the other organism.</p></div

Size Distributions of Mammalian Proteins

<div><p>(A) For 29,991 full-length mouse proteins from the FANTOM annotations.</p> <p>(B) For 40,865 mouse proteins from the IPI database.</p> <p>(C) For 11,679 human proteins from Swiss-Prot.</p> <p>(D) For 31,035 mouse proteins predicted in the FANTOM cDNAs using CRITICA.</p></div