Journal: Viruses

Article Title: Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray

doi: 10.3390/v15010248

Figure Lengend Snippet: Schematic representation of the study design, microarray protocol, and data analysis. ( a ) Sample acquisition and heat inactivation of virus, ( b ) SARS-CoV-2 whole proteome microarray design, ( c ) microarray staining and image acquisition, ( d ) data analysis pipeline.

Article Snippet: PEPperCHIP ® Peptide Microarray slides were brought to room temperature, assembled onto the PEPperCHIP ® incubation tray (PEPperPRINT GmbH, Germany), and equilibrated using the staining buffer for 15 min.

Techniques: Microarray, Virus, Staining

Journal: Viruses

Article Title: Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray

doi: 10.3390/v15010248

Figure Lengend Snippet: Heatmaps for IgA and IgG response showing major immunogenic regions identified in the SARS-CoV-2 whole proteome microarray. The printed proteome constitutes ORF1a/b polyprotein encoding 16 non-structural proteins (1–10 and 12–16), structural proteins (S, N, E, and M), and the accessory proteins (ORF3a, 6, 7a, 8, and 10).

Article Snippet: PEPperCHIP ® Peptide Microarray slides were brought to room temperature, assembled onto the PEPperCHIP ® incubation tray (PEPperPRINT GmbH, Germany), and equilibrated using the staining buffer for 15 min.

Techniques: Microarray

Journal: The Journal of Molecular Diagnostics : JMD

Article Title: Accurate Molecular Classification of Renal Tumors Using MicroRNA Expression

doi: 10.2353/jmoldx.2010.090187

Figure Lengend Snippet: Classification of kidney tumors using expression levels of six microRNAs (microarray data). A: Classification proceeds in two steps, following the cluster structure of the histological types (Figure 2). First, samples are classified into either the oncocytoma/chromophobe pair, or the conventional/papillary pair, using expression levels of hsa-miR-210 and hsa-miR-221 (B). In the second step, oncocytoma is differentiated from chromophobe using expression levels of hsa-miR-200c and hsa-miR-139-5p (C), and conventional is differentiated from papillary using expression levels of hsa-miR-31 and hsa-miR-126 (D). Independent test samples included oncocytoma samples (n = 19, red stars), chromophobe tumors (n = 14, black/yellow diamonds), conventional tumors (n = 17, blue squares), and papillary tumors (n = 6, green circles). The gray shaded regions indicate the thresholds for classification for each pair of microRNAs, indicating in each case the right branch in the binary classification tree (A). The 71 samples that were used for training the thresholds (see Methods and Figure 3) are shown in faded symbols in the background.

Article Snippet: 31 , 37 Briefly on Slide E coated microarray slides (Schott Nexterion, Mainz, Germany) >900 DNA oligonucleotide probes representing microRNAs were spotted in triplicate using the BioRobotics MicroGrid II microarrater (Genomic Solutions, Ann Arbor, MI) according to the manufacturer's directions.

Techniques: Expressing, Microarray

Journal: The Journal of Molecular Diagnostics : JMD

Article Title: Accurate Molecular Classification of Renal Tumors Using MicroRNA Expression

doi: 10.2353/jmoldx.2010.090187

Figure Lengend Snippet: Validation by qRT-PCR. The qRT-PCR validation set included 32 tumor samples: 8 oncocytoma tumors (red stars), 8 chromophobe tumors (yellow diamonds), 8 conventional tumors (blue squares), and 8 papillary tumors (green circles). For each decision point (Figure 4A), the plot on the left side (A, C, or E) shows the log2 expression ratio of the two microRNAs used at this node as measured by microarray (horizontal, calculated as the log2 ratio of the normalized fluorescence signal) and by qRT-PCR (vertical, calculated as the difference in normalized Ct values). In each plot, the vertical line demarcates the classification threshold trained on the microarray data, while the horizontal line indicates the classification threshold that was chosen for the qRT-PCR data, based on the microarray threshold (Methods). The plots on the right side (B, D, or F) show the qRT-PCR data (normalized Cts) of the two microRNAs in the samples of the relevant subtypes at each node. The gray shaded regions indicate the thresholds for classification for each pair of microRNAs, indicating in each case the right branch in the binary classification tree (Figure 4A). A: Log2 expression ratio of [hsa-miR-221/hsa-miR-210] in microarray and qRT-PCR. Correlation coefficient was 0.92. B: Normalized Cts of hsa-miR-221 and hsa-miR-210 in 32 samples. C: Log2 expression ratio of [hsa-miR-139-5p/hsa-miR-200c] in microarray and qRT-PCR. Correlation coefficient was 0.86. D: Normalized Cts of hsa-miR-139-5p and hsa-miR-200c in 16 oncocytoma and chromophobe samples. E: Log2 expression ratio of [hsa-miR-126/hsa-miR-31] in microarray and qRT-PCR. Correlation coefficient was 0.98. F: Normalized Cts of hsa-miR-126 and hsa-miR-31 in 16 conventional and papillary samples.

Article Snippet: 31 , 37 Briefly on Slide E coated microarray slides (Schott Nexterion, Mainz, Germany) >900 DNA oligonucleotide probes representing microRNAs were spotted in triplicate using the BioRobotics MicroGrid II microarrater (Genomic Solutions, Ann Arbor, MI) according to the manufacturer's directions.

Techniques: Biomarker Discovery, Quantitative RT-PCR, Expressing, Microarray, Fluorescence

Journal: The Journal of Molecular Diagnostics : JMD

Article Title: Accurate Molecular Classification of Renal Tumors Using MicroRNA Expression

doi: 10.2353/jmoldx.2010.090187

Figure Lengend Snippet: Classification of Renal Tumors Using Expression Levels of 6 MicroRNAs

Article Snippet: 31 , 37 Briefly on Slide E coated microarray slides (Schott Nexterion, Mainz, Germany) >900 DNA oligonucleotide probes representing microRNAs were spotted in triplicate using the BioRobotics MicroGrid II microarrater (Genomic Solutions, Ann Arbor, MI) according to the manufacturer's directions.

Techniques: Expressing, Biomarker Discovery, Microarray