Journal: Scientific Reports

Article Title: Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines

doi: 10.1038/s41598-021-98869-x

Figure Lengend Snippet: Optimization of the reverse transcription conditions. The graph shows Cq values from performing qPCR measurements of RNA dilution series comparing the Maxima First Strand cDNA Synthesis Kit for RT-qPCR (red lines) and the High-Capacity cDNA Reverse Transcription Kit (blue lines). Three technical replicates for both kits at each concentration point are marked as hollow circles. Least squares linear regression was performed to the average of the technical replicates in the range of RNA amount from 100 to 800 ng per reaction. Individual graphs were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Article Snippet: Individual graphs were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Techniques: Quantitative RT-PCR, Concentration Assay

Journal: Scientific Reports

Article Title: Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines

doi: 10.1038/s41598-021-98869-x

Figure Lengend Snippet: Cq values of twelve candidate reference genes in human cancer (red) and normal (blue) cell lines. Each dot represents the average Cq value of three biological replicates for each cell line. Candidate reference genes are arranged according to the comprehensive ranking in a decreasing order of expression stability. The boxes represent the data between the 25th and 75th percentile, while whiskers show the data range from the 10th to the 90th percentile. The minimum and maximum values are depicted as ‘x’. The average values are represented as squares and the median values are illustrated as lines. This graph was created with OriginPro 2018 (OriginLab Corp.).

Article Snippet: Individual graphs were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines

doi: 10.1038/s41598-021-98869-x

Figure Lengend Snippet: Relative expression of the candidate reference genes upon serum starvation. Relative expression values of serum starved cell lines can be compared to the average relative expression of the non-treated biological replicates selected as control and set to 1, which is represented by a dotted line. Error bars show standard deviation of three biological replicates (n = 3) for each cell line. The number of asterisks indicate increasing possibility that gene expression remains constant upon serum starvation. *p > 0.8, **p > 0.95 as calculated by the CFX Maestro software. This graph was created with OriginPro 2018 (OriginLab Corp.).

Article Snippet: Individual graphs were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Techniques: Expressing, Standard Deviation, Software

Journal: Scientific Reports

Article Title: Discovery of two new isoforms of the human DUT gene

doi: 10.1038/s41598-023-32970-1

Figure Lengend Snippet: Optimization of the reverse transcription reaction. Cq values resulting from qPCR measurements of RNA dilution series are shown comparing the Maxima First Strand cDNA Synthesis Kit for RT-qPCR (black lines) and the High-Capacity cDNA Reverse Transcription Kit (grey lines). At each concentration point three technical replicates for both kits are depicted as hollow circles. Least squares linear regression was performed to the average of the technical replicates in the range of RNA amount from 100 to 800 ng per reaction. Individual graphs for ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 and for ( E ) DUT-all were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Article Snippet: Individual graphs for ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 and for ( E ) DUT-all were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Techniques: Quantitative RT-PCR, Concentration Assay

Journal: Scientific Reports

Article Title: Discovery of two new isoforms of the human DUT gene

doi: 10.1038/s41598-023-32970-1

Figure Lengend Snippet: Relative normalized gene expression data for the dUTPase targets and correlation analysis of the Cq values. ( A ) In each panel, the expression value of the cell line with the lowest expression was set to 1. The scale of the y axis is logarithmic with base 10 and is shown uniformly from 1 to 100 in each panel. The error bar shows the standard deviation of three biological replicates (n = 3) for each cell line. The individual colours correspond to the colours used in Table . Individual graphs were created with CFX Maestro 2.0 (Bio-Rad). ( B ) Correlation analysis of the Cq values of the DUT-N with the DUT-all target and ( C ) the DUT-M with the DUT-3 target. The range displayed on the axes is constant in both graphs for comparability. Regression coefficient values were determined with least squares linear regression to all data points. Individual graphs were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Article Snippet: Individual graphs for ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 and for ( E ) DUT-all were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Techniques: Expressing, Standard Deviation

Journal: Scientific Reports

Article Title: Discovery of two new isoforms of the human DUT gene

doi: 10.1038/s41598-023-32970-1

Figure Lengend Snippet: Relation of the relative normalized expression level of the different isoforms ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 to the overall dUTPase expression measured with the DUT-all target. All cancer cell lines were included in a group which were used for pairwise comparisons to each normal cell line. Cancer cell lines are coloured red. The individual colours for the normal cell lines correspond to the colours used in Table . The y axis shows ratio indicators that are the ratio of the relative normalized expression value of each isoform to the overall expression value on a logarithmic scale. The mean of each group is indicated with black lines. The p values indicate the results of pairwise comparisons. The differences were found to be significant at p < 0.0018 and are indicated with asterisks (*). Individual graphs were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Article Snippet: Individual graphs for ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 and for ( E ) DUT-all were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Discovery of two new isoforms of the human DUT gene

doi: 10.1038/s41598-023-32970-1

Figure Lengend Snippet: Relative normalized expression of the dUTPase isoforms ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 and ( E ) the DUT-all target in HeLa (red), A-549 (orange) and MDA-MB-231 (yellow) cell lines upon serum starvation and ( F ) Western blot analysis of the dUTPase proteins in U-937 cell line. ( A-E ) NT, non-treated (plain columns); SS, serum starved (striped columns). The individual colours correspond to the colours used in Table . The scale of the y axis is logarithmic with base 10 and is shown uniformly from 1 to 10 in each panel. In each panel the biological group with the lowest expression was set to 1. Error bars show standard deviation of three biological replicates (n = 3) for each cell line. The number of asterisks indicates increasing possibility that gene expression changes upon serum starvation. * p < 0.1, ** p < 0.01, *** p < 0.001 as calculated by the CFX Maestro software. ( F ) Three technical replicate samples for the detection of dUTPase proteins using western blot. On the left side the target dUTPase proteins and the actin protein as reference are depicted with arrows. On the right side the corresponding theoretical molecular weight values are indicated. The individual full-size images are available as Supplementary Figure . Individual graphs for ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 and for ( E ) DUT-all were created with CFX Maestro 2.0 (Bio-Rad). ( F ) The image was created with Image Lab 4.1 software (Bio-Rad). The figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Article Snippet: Individual graphs for ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 and for ( E ) DUT-all were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Techniques: Expressing, Western Blot, Standard Deviation, Software, Molecular Weight

Journal: Scientific Reports

Article Title: Discovery of two new isoforms of the human DUT gene

doi: 10.1038/s41598-023-32970-1

Figure Lengend Snippet: Schematic figure illustrating the main aspects of this study. Dark blue colour indicates the DUT-M isoform, red colour indicates the DUT-N isoform, and the novel isoforms DUT-3 and DUT-4 are coloured light blue and orange, respectively. In the upper right corner representative amplification curves are shown. The font size of the name of the isoforms corresponds to their relative expression levels. The hypothetical cellular localisation of the dUTPase isoforms is depicted by dashed lines. The figure was created using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Article Snippet: Individual graphs for ( A ) DUT-M, ( B ) DUT-N, ( C ) DUT-3, ( D ) DUT-4 and for ( E ) DUT-all were created with OriginPro 2018 (OriginLab Corp.) and the figure was assembled using CorelDRAW Graphics Suite 2020 (Corel Corporation).

Techniques: Amplification, Expressing