surescan high-resolution dna microarray scanner  (Agilent technologies)

Journal: bioRxiv

Article Title: Synovial fluid transcriptome dynamics in osteoarthritis progression: Implications in pathogenesis

doi: 10.1101/2024.06.24.600143

Figure Lengend Snippet: Flow chart of microarray data analysis. The agilent single color microarray platform was used having more than 58,000 transcripts and further data processing was done using agilent GeneSpring software followed by pathway analysis using GSEA database. Numbers in parentheses illustrates number of pathways enriched in each category using GSEA database. DEGs-Differentially expressed genes, ANOVA-Analysis of variance, BP-Biological pathway, CC-Cellular component, MF-Molecular function.

Article Snippet: Following hybridization, the array slides were washed and scanned with an Agilent SureScan High-Resolution DNA Microarray Scanner.

Techniques: Microarray, Software

Journal: Translational Andrology and Urology

Article Title: A comprehensive evaluation of differentially expressed mRNAs and lncRNAs in cystitis glandularis with gene ontology, KEGG pathway, and ceRNA network analysis

doi: 10.21037/tau.2020.03.01

Figure Lengend Snippet: Top 20 aberrantly expressed lncRNAs in microarray analysis

Article Snippet: The hybridized arrays were washed, fixed and scanned using an Agilent Technologies G2505C SureScan High-Resolution DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

Techniques: Microarray

Journal: Translational Andrology and Urology

Article Title: A comprehensive evaluation of differentially expressed mRNAs and lncRNAs in cystitis glandularis with gene ontology, KEGG pathway, and ceRNA network analysis

doi: 10.21037/tau.2020.03.01

Figure Lengend Snippet: Top 20 aberrantly expressed mRNAs in microarray analysis

Article Snippet: The hybridized arrays were washed, fixed and scanned using an Agilent Technologies G2505C SureScan High-Resolution DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

Techniques: Microarray

Journal: Translational Andrology and Urology

Article Title: A comprehensive evaluation of differentially expressed mRNAs and lncRNAs in cystitis glandularis with gene ontology, KEGG pathway, and ceRNA network analysis

doi: 10.21037/tau.2020.03.01

Figure Lengend Snippet: The expression microarray profiles of differentially lncRNAs (DE-lncRNAs) and coding RNAs (DE-mRNAs) in samples from three pairs of CG tissues and normal tissue. (A) DE-lncRNAs and DE-mRNAs are identified on a Volcano plot. Expression was plotted as P values of significance difference of expression (Y-axis) versus fold-difference in expression (X-axis). Horizontal green line marks a P value of 0.05. Vertical green lines mark a 2-fold increased or decreased expression in comparison to normal bladder mucosa; (B) heat map showing the expression profiles of lncRNAs and mRNAs. There were 436 differentially expressed lncRNAs and 809 differentially expressed mRNAs identified. The maps are based on the expression values of all expressed lncRNAs and mRNAs detected by microarray analysis and correspond to normalized expression values of significantly changed lncRNAs and mRNAs with 2-FCs in expression relative to normal tissue (P<0.05). Results from each tissue sample are presented in columns (normal 1–3 and CG 1–3). Red and green lines indicate high and low expression, respectively, of different RNAs. The intensity of expression is shown in the Color Key and Histogram. CG, cystitis glandularis; FC, fold change; DE, differential expression; lncRNA, long non-coding RNA; mRNA, messenger RNA.

Article Snippet: The hybridized arrays were washed, fixed and scanned using an Agilent Technologies G2505C SureScan High-Resolution DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

Techniques: Expressing, Microarray, Comparison

Journal: Translational Andrology and Urology

Article Title: A comprehensive evaluation of differentially expressed mRNAs and lncRNAs in cystitis glandularis with gene ontology, KEGG pathway, and ceRNA network analysis

doi: 10.21037/tau.2020.03.01

Figure Lengend Snippet: CNC network analysis. (A) qRT-PCR was used to validate the up-regulated DE of four mRNAs found on microarray analysis; (B) the CNC network included sequences with a Pearson’s correlation coefficient ≥0.7. Green nodes represent dysregulated lncRNAs; yellow nodes represent four mRNAs: SMAD3, ORC1, CCNA2 and CCNB2; solid lines between lncRNAs and mRNAs indicate a positive correlation; dotted lines between lncRNAs and mRNAs indicate a negative correlation. The network consists of four mRNAs and 37 related genes; (C) qRT-PCR was used to validate the up-regulated DE of four lnRNAs found in the microarray analysis. The Y-axis indicates the FC (log2 transformed) computed from the qPCR and microarray data. Gene expression is normalized to β-actin and presented as mean ± SD. All the mRNAs and lncRNAs were up-regulated in the CG tissues (*, P<0.05). CNC, coding-non-coding co-expression; FC, fold change; qRT-PCR, quantitative real-time PCR; DE, differential expression; lncRNA, long non-coding RNA; mRNA, messenger RNA; CG, cystitis glandularis; N, normal.

Article Snippet: The hybridized arrays were washed, fixed and scanned using an Agilent Technologies G2505C SureScan High-Resolution DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

Techniques: Quantitative RT-PCR, Microarray, Transformation Assay, Expressing, Real-time Polymerase Chain Reaction