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: After fragmentation steps following the manufacturer’s protocol, the cRNAs were immediately hybridized into the Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 h at 65 °C in a rotating microarray hybridization oven (Agilent, Santa Clara, CA, USA) prior to washing.

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: After fragmentation steps following the manufacturer’s protocol, the cRNAs were immediately hybridized into the Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 h at 65 °C in a rotating microarray hybridization oven (Agilent, Santa Clara, CA, USA) prior to washing.

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: After fragmentation steps following the manufacturer’s protocol, the cRNAs were immediately hybridized into the Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 h at 65 °C in a rotating microarray hybridization oven (Agilent, Santa Clara, CA, USA) prior to washing.

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: After fragmentation steps following the manufacturer’s protocol, the cRNAs were immediately hybridized into the Agilent SurePrint G3 Human Gene Expression v3 8x60K for 17 h at 65 °C in a rotating microarray hybridization oven (Agilent, Santa Clara, CA, USA) prior to washing.

Techniques: Construct, Microarray

Journal: BMC Bioinformatics

Article Title: Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

doi: 10.1186/1471-2105-4-37

Figure Lengend Snippet: Microarray quality control parameters.

Article Snippet: After fragmentation in pieces of 50 to 200 bases long, 15 μg of labeled cRNA sample was hybridized onto oligonucleotide U133A microarrays, using standard protocols with the Affymetrix microarray oven and fluidics station at the Columbia University Genome Center.

Techniques: Microarray

Journal: PLoS ONE

Article Title: Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry

doi: 10.1371/journal.pone.0201462

Figure Lengend Snippet: Fold changes obtained by microarray (fill) and by qPCR (hatched) when fed the M diet (dark grey) or the V diet (light grey) for genes involved in sensory perception (R23h versus A22h), immunity (R23h versus AB1h) and for amino acid metabolism (R23h versus A22h).

Article Snippet: Hybridisation was performed in a microarray hybridisation oven (Agilent) for 17h at 65°C.

Techniques: Microarray

Journal: PLoS ONE

Article Title: Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry

doi: 10.1371/journal.pone.0201462

Figure Lengend Snippet: Correlation between gene expression patterns obtained through real-time PCR and microarray approaches.

Article Snippet: Hybridisation was performed in a microarray hybridisation oven (Agilent) for 17h at 65°C.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Microarray