sureprint g3 human gene expression v2 8 × 60k microarray  (Agilent technologies)

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Top ten upregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

Techniques: Microarray, Software

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Top ten downregulated lncRNAs and mRNAs and their respective fold-changes and p -values based on the cDNA microarray dataset. The transcripts were statistically analyzed in the Agilent GeneSpring GX (v14.9.1) software using moderated t -test and Benjamin–Hochberg multiple testing corrections and had satisfied the p -value of <0.05 and fold-change cutoff of ±2.00. Data shown are from four independent experiments.

Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

Techniques: Microarray, Software

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: Difference in lncRNA and mRNA fold-changes between the cDNA microarray and in-house RT-qPCR experiments. Data shown are from three independent experiments (in triplicates) with calculated SD values to represent error bars and their statistical analyses were conducted using one-way ANOVA.

Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

Techniques: Microarray, Quantitative RT-PCR

Journal: Non-Coding RNA

Article Title: Possible Involvement of Long Non-Coding RNAs GNAS-AS1 and MIR205HG in the Modulation of 5-Fluorouracil Chemosensitivity in Colon Cancer Cells through Increased Extracellular Release of Exosomes

doi: 10.3390/ncrna10020025

Figure Lengend Snippet: ( A ) LncRNA-mRNA interaction network was constructed based on the ten selected candidate lncRNAs from the cDNA microarray dataset. The resulting mRNA interactions were predicted using the “rtool” database with −20 kcal as the minimum energy threshold and were filtered to show only mRNAs that were also dysregulated in the dataset. Data were visualized using Cytoscape v3.8.2. (Pink diamond = candidate lncRNA, blue circle = predicted putative mRNA targets). ( B ) A total of nine mRNAs were identified as both responsible in the “regulated exocytosis” hit as well as highly likely to be regulated by the candidate lncRNAs listed in ( A ). Data were visualized using Cytoscape v3.8.2. (pink diamond = candidate regulator lncRNA, blue circle = mRNA predicted involved in the biological process).

Article Snippet: In this study, purified total RNAs of both the SW480/DR and SW480/DS cells were analyzed using Agilent SurePrint G3 Human Gene Expression v3 8x60k format cDNA microarray and processed in the Agilent GeneSpring GX v14.9.1 software.

Techniques: Construct, Microarray

Journal: Epigenetics

Article Title: Upregulation of GPR133 expression impaired the phagocytosis of macrophages in recurrent spontaneous miscarriage

doi: 10.1080/15592294.2024.2337087

Figure Lengend Snippet: Differentially methylated CpG sites between healthy controls and RSM patients. (a) The purity of the isolated decidual macrophages was detected by FACS. The cells that were positive for CD45 and CD14 were considered decidual macrophages. CD45 + CD14 + cells were also positive for CD68, a pan-macrophage marker. (b) Principal component analysis clearly showed separation between normal macrophages (red square, n = 3) and RSM macrophages (yellow square, n = 3). (c) Heatmap generated from clustering- analysis of microarray data illustrating differentially methylated DNA sites in the RSM patient group relative to the control group. Blue and red represent hypomethylation and hypermethylation, respectively, whereas white indicates no change in methylation relative to the control. Each row represents the beta value of a differentially methylated CpG site and each column represents one sample. (d) Pathways enriched in differentially methylated genes were determined using the GO database.

Article Snippet: To assess differences in gene expression in decidual macrophages between RSM patients and control individuals, transcriptome profiles were obtained from the two groups of patients using the Agilent SurePrint G3 Human Gene Expression 8 × 60K microarray platform.

Techniques: Methylation, Isolation, Marker, Generated, Microarray

Journal: Epigenetics

Article Title: Upregulation of GPR133 expression impaired the phagocytosis of macrophages in recurrent spontaneous miscarriage

doi: 10.1080/15592294.2024.2337087

Figure Lengend Snippet: Validation of the microarray results via qRT – PCR. the data are presented as the means ± SDs and were analysed by two-sided unpaired Student’s t tests. ** p < 0.01.

Article Snippet: To assess differences in gene expression in decidual macrophages between RSM patients and control individuals, transcriptome profiles were obtained from the two groups of patients using the Agilent SurePrint G3 Human Gene Expression 8 × 60K microarray platform.

Techniques: Microarray, Quantitative RT-PCR

Journal: Cells

Article Title: Hyaluronic Acid Induction Promotes the Differentiation of Human Neural Crest-like Cells into Periodontal Ligament Stem-like Cells

doi: 10.3390/cells12232743

Figure Lengend Snippet: Upregulated expression of HA-related genes during the differentiation of iNCs into iPDLSCs. ( A – C ) Heat maps of gene expression data from the microarray analyses of iNCs and iPDLSCs for all genes ( A ), ECM-related genes ( B ), and HA-related genes ( C ). Upregulated genes are represented in red, and downregulated genes are represented in green. ( D ) GO enrichment analysis using the DAVID bioinformatics resources and based on >2-fold altered expression between iPDLSCs and iNCs. Data portray the top 15 significant terms ranked by the enrichment factor. The term ‘ECM-receptor interaction’ included 30 genes. ( E , F ) qPCR analysis of expression levels of five HA-related genes ( CD44 , ACAN , ITIH3 , HAS3 , and HAPLN1 ) in iNCs and iPDLSCs ( E ) and in SK-N-SH cells and SK-PDLSCs (F). β-Actin was used as an internal standard. Data are expressed as the mean ± standard deviation (n = 3); * p < 0.05, ** p < 0.01.

Article Snippet: RNA was labelled using a one-colour Low Input QuickAmp Labeling Kit (Agilent Technologies) and hybridised to a SurePrint G3 Human Gene Expression Microarray v3 (8 × 60 Kb; Agilent Technologies).

Techniques: Expressing, Microarray, Standard Deviation