Venn diagrams of the numbers of overlapping and non-overlapping induced (≥ 1

<p><b>Copyright information:</b></p><p>Taken from "Genomic analysis of the secretion stress response in the enzyme-producing cell factory "</p><p>BMC Genomics 2007;8():158-158.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1894978.</p><p></p>5 fold) or repressed (≤ 1.5 fold) genes on the array after exposure to DTT or tunicamycin (Tun) and in the t-PA producing strain (t-PA)

Model of the secretory pathway under different ER stress conditions (t-PA secretion, tunicamycin and DTT) together with examples of genes that are transcriptionally induced or repressed

<p><b>Copyright information:</b></p><p>Taken from "Genomic analysis of the secretion stress response in the enzyme-producing cell factory "</p><p>BMC Genomics 2007;8():158-158.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1894978.</p><p></p> The gene designation is provided where previously known or, otherwise, the gene name is provided. Red, genes up-regulated by 3 conditions; orange, genes up-regulated by 2 conditions; yellow, genes up-regulated by 1 condition; light blue, genes down-regulated by 1 condition; blue, genes down-regulated by 2 conditions. N, nucleus; ER, endoplasmic reticulum; E, endosome; V, vacuole; G, Golgi. ERAD is ER-associated degradation

GeneChip results were confirmed for some genes using Northern blotting and RT-PCR

<p><b>Copyright information:</b></p><p>Taken from "Genomic analysis of the secretion stress response in the enzyme-producing cell factory "</p><p>BMC Genomics 2007;8():158-158.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1894978.</p><p></p> Examples are provided for both Northern blots (A) and RT-PCR (B). Note that the RT-PCR for the mRNA was designed to indicate enhanced splicing of the mRNA intron under stress conditions (DTT, tunicamycin and production of t-PA). This is shown as a relative increase in the amount of the processed (lower band) form of the mRNA compared to the unprocessed higher band (). Probing or PCR for an actin gene was used as a non-stress-responsive control transcript

Hierarchical clustering of records in a dendrogram (tree graph) based on the similarity of the signal log ratios obtained in each of the duplicate stress studies

<p><b>Copyright information:</b></p><p>Taken from "Genomic analysis of the secretion stress response in the enzyme-producing cell factory "</p><p>BMC Genomics 2007;8():158-158.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1894978.</p><p></p> Records (188) were selected based on differential expression in the tPA comparisons. This tree is representative for multiple clusterings performed using signals or signal log ratios. The genes have been rearranged into their cluster order and are represented on the vertical axis. The experiments are represented on the horizontal axis. The significance of the colour scale is indicated

(A) Representative absorbance profile for RNA separated by velocity sedimentation through a 15–60% sucrose gradient

<p><b>Copyright information:</b></p><p>Taken from "Genomic analysis of the secretion stress response in the enzyme-producing cell factory "</p><p>BMC Genomics 2007;8():158-158.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1894978.</p><p></p> Fractions are numbered from the top to the bottom of the gradient. (B) RNA was extracted from each fraction and subjected to electrophoresis through a formaldehyde gel. The ribosomal RNA distribution profile (25S, 18S and 5S rRNA; indicated by arrowheads) enables the the assignment of ODpeaks, corresponding to the 40S and 60S ribosomal subunits and to intact ribosomes (80S). (C) RT-PCR analysis with primers were performed from each fraction of collected gradients from treated and non-treated cells. The full length mRNA (arrow) as well as low-molecular-weight version of (arrowhead) can be visualized