The labeled cRNAs were hybridized onto the human LncRNA Expression Microarray V3.0 (Arraystar, Rockville, MD), which was designed for the global profiling of human lncRNAs and protein-coding transcripts. The third lncRNA microarray generated for each sample detected approximately 30586 lncRNAs and 26109 coding transcripts. Then, lncRNAs were carefully constructed using well-respected public transcriptome databases (Refseq, UCSC Known Genes, and Genecode), as well as landmark publications.
Human lncrna expression microarray v3
Manufactured by Arraystar
The Human LncRNA Expression Microarray V3.0 is a lab equipment product designed for the detection and analysis of long non-coding RNA (lncRNA) expression in human samples. The microarray provides comprehensive coverage of well-annotated human lncRNAs, enabling researchers to study their expression profiles across different experimental conditions.
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Lab products found in correlation
Genespring gx v11, by Agilent Technologies (1 mentions)
Trizol reagent, by Thermo Fisher Scientific (1 mentions)
Mrna only eukaryotic mrna isolation kit, by Illumina (1 mentions)
Agilent scanner g2505c, by Agilent Technologies (1 mentions)
Agilent feature extraction software version 11.0.1.1, by Agilent Technologies (1 mentions)
3 protocols using human lncrna expression microarray v3
1
Global Profiling of Human LncRNAs
2
Transcriptomic Analysis of lncRNAs and mRNAs
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Expression changes of lncRNAs and mRNAs were assessed by the manufacturer using the Human LncRNA Expression Microarray V3.0 (Arraystar). The expression data were normalized using the Robust Multi-Array Average method. The lncRNAs and mRNAs were considered differentially expressed if they had a >2-fold change and were statistically significant (paired t test P < 0.05) for any of the time points of IL-1β treatment. Heatmaps were constructed using the “heatmap.2” function from the “gplots” Bioconductor package (67 ). Additionally, the “ggplot2,” “sm,” and “violinplot” Bioconductor packages were used for graph visualization. Neighboring transcript pairs were identified based on genomic distance (20 to 500 kbp) between them with the help of the “GenomicRanges” Bioconductor package (68 (link)). Spearman correlation coefficient (rho) was calculated using base R, and statistical significance between 2 rho values was determined using Fisher Z-transformation. ChIP followed by sequencing analysis was performed as described in SI Appendix .
3
Profiling Aortic Plaque lncRNAs
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Total RNA was extracted from either human aortic atherosclerotic plaques (from 3 subjects) or human healthy aortic artery specimens (from 3 subjects) with TRIzol reagent (Invitrogen) according to the manufacturer's protocol. mRNA was purified from total RNA using mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre) and each purified sample transcribed into fluorescent cRNA using a random priming method. Labeled cRNAs were hybridized with Human LncRNA Expression Microarray v3.0 (8×60K, Arraystar) and scanned using Agilent Scanner G2505C. Data were normalized and analyzed with the use of Agilent Feature Extraction software (version 11.0.1.1) and GeneSpring GX v11.5.1 (Agilent). Differentially expressed genes were identified using Volcano Plot filtering. The expression microarray data have been deposited in the NCBI Gene Expression Omnibus, with the accession number GSE97210.
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