arraystar human lncrna microarray v3.0  (KangChen Inc)

Journal: Cellular and Molecular Life Sciences: CMLS

Article Title: LncRNA LENGA acts as a tumor suppressor in gastric cancer through BRD7/TP53 signaling

doi: 10.1007/s00018-022-04642-2

Figure Lengend Snippet: A schematic diagram of the mechanism of lncRNA LENGA in GC

Article Snippet: Public datasets collection Human LncRNA microarray (Arraystar Human LncRNA V3.0) for GC and normal adjacent tissues were downloaded from the NCBIs Gene Expression Omnibus (GEO, GSE99417 ).

Techniques:

Journal: Scientific Reports

Article Title: Effects of interleukin 1β on long noncoding RNA and mRNA expression profiles of human synovial fluid derived mesenchymal stem cells

doi: 10.1038/s41598-022-12190-9

Figure Lengend Snippet: Volcano plots and heatmaps of changes in lncRNA and mRNA expression profiles in SFMSCs after IL-1β stimulation for 2 h. ( A , B ) Heatmap of differentially expressed lncRNAs ( A ) and mRNAs ( B ) showing a fold change > 1 in SFMSCs before and after IL-1β stimulation. ( C , D ) Volcano plots of lncRNA expression levels ( C ) and mRNA expression levels ( D ) before and after IL-1β stimulation. The red dots represent lncRNAs or mRNAs showing ≥ twofold upregulation, and the green dots represent downregulation ( P < 0.05). Dots labeled with Seqname represent lncRNAs or mRNAs showing ≥ tenfold. ( E , F ) Heatmap of differentially expressed lncRNAs ( E ) and mRNAs ( F ) showing a fold changes ≥ 10 and P < 0.05 in SFMSCs before and after IL-1β stimulation. Genesymbol was used to label the genes. Volcano plots was performed using R Software created by R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ . Heatmaps was performed using Gene Cluster 3.0 Software.

Article Snippet: Differentially expressed LncRNAs and mRNAs in SFMSCs before and after treatment with IL-1β in vitro were detected using human Arraystar Human LncRNA Microarray V3.0.

Techniques: Expressing, Labeling, Software

Journal: Scientific Reports

Article Title: Effects of interleukin 1β on long noncoding RNA and mRNA expression profiles of human synovial fluid derived mesenchymal stem cells

doi: 10.1038/s41598-022-12190-9

Figure Lengend Snippet: Identification of changes in lncRNA and mRNA expression profiles in SFMSCs after IL-1β stimulation for 2 h. ( A ) Circos plot showing differentially expressed lncRNAs and mRNAs on chromosomes. The first layer represents the chromosome map of the human genome. The top 30 K-score transcripts in the co-expression network of differentially expressed mRNAs are labeled in the second circle. Differentially expressed lncRNAs (blue) and mRNAs (red) with fold changes ≥ 1 are labeled in the third circle. The fourth and fifth circles represent the mean expression values of lncRNAs and mRNAs with fold changes ≥ 2 and P < 0.05. Red points represent upregulation, and blue points represent downregulation. The sixth and seventh circles represent mean expression values of lncRNAs and mRNAs with fold changes ≥ 10 and P < 0.05. Red points represent upregulation, and blue points represent downregulation. The innermost layer indicates the interaction network of the top 30 K-score transcripts labeled in the second circle. Red lines indicate linked transcripts in the same chromosome, and blue lines represent those on different chromosomes. Analysis was performed using R Software created by R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ . ( B ) Categories of lncRNAs according to the genomic loci of their neighboring genes. ( C ) Differentially expressed antisense lncRNAs and their associated coding genes. ( D ) Differentially expressed lincRNA and associated coding gene pairs (distance < 300 kb). ( E ) Differentially expressed enhancer-like lncRNAs and their nearby coding genes (distance < 300 kb); both the lncRNA and its paired mRNA showed fold changes ≥ 2 and P < 0.05 among all differentially expressed lncRNAs and mRNAs. Diamonds represent lncRNAs, and circles represent mRNAs; red represents upregulation, and blue represents downregulation; different sizes represent the absolute value of the fold change. Protein names were used to label the genes in ( A ); Genesymbol was used to label the genes in ( C – E ). Images ( C – E ) were created using CytoScape 3.8.0 Software. exon sense-overlapping: the LncRNA's exon is overlapping a coding transcript exon on the same genomic strand; intronic: the LncRNA is overlapping the intron of a coding transcript on the same genomic strand; natural antisense: the LncRNA is transcribed from the antisense strand and overlapping with a coding transcript; non-overlapping antisense: the LncRNA is transcribed from the antisense strand without sharing overlapping exons; bidirectional: the LncRNA is oriented head to head to a coding transcript within 1000 bp; intergenic: there are no overlapping or bidirectional coding transcripts nearby the LncRNA.

Article Snippet: Differentially expressed LncRNAs and mRNAs in SFMSCs before and after treatment with IL-1β in vitro were detected using human Arraystar Human LncRNA Microarray V3.0.

Techniques: Expressing, Labeling, Software

Journal: Scientific Reports

Article Title: Effects of interleukin 1β on long noncoding RNA and mRNA expression profiles of human synovial fluid derived mesenchymal stem cells

doi: 10.1038/s41598-022-12190-9

Figure Lengend Snippet: Co-expression networks of mRNAs and lncRNAs in SFMSCs after IL-1β treatment for 2 h constructed by weighted correlation network analysis. ( A ) Correlation network constructed using the mRNAs and lncRNAs in the most significant modules in Fig. A (MEgreen, top 1000 weight value). ( B ) Top K-score subnetwork. ( C ) mRNAs co-expressed with the top K-score lncRNA RP3-467K16.4 . Weighted correlation network analysis of Pearson’s correlations was used to estimate associations between the lncRNA and mRNAs. ( D ) KEGG pathway enrichment analysis of the mRNAs co-expressed with RP3-467K16.4 , with the top 10 enriched genes/ratios. Genes/ratios: number of differently expressed genes enriched in the pathway/number of all differently expressed genes associated with RP3-467K16.4. Circles, mRNAs; diamonds, lncRNAs. Different sizes represent the absolute value of the fold change. Red, upregulated; blue, downregulated. Seqname was used to label the genes. Images ( A – C ) were created using Cytoscape 3.8.0, Software. Image ( D ) was performed using R Software created by R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/ .

Article Snippet: Differentially expressed LncRNAs and mRNAs in SFMSCs before and after treatment with IL-1β in vitro were detected using human Arraystar Human LncRNA Microarray V3.0.

Techniques: Expressing, Construct, Software

Journal: Scientific Reports

Article Title: Effects of interleukin 1β on long noncoding RNA and mRNA expression profiles of human synovial fluid derived mesenchymal stem cells

doi: 10.1038/s41598-022-12190-9

Figure Lengend Snippet: Validation of microarray data. ( A ) Cellular localization of p65 determined by immunofluorescence. ( B ) Semiquantitative analysis of immunofluorescence intensity of p65 in nucleus. ( C ) Expression of the lncRNA LOC541472 in SFMSCs 2 h after stimulation with 10 ng/mL IL‐1β. ( D ) The efficiency of LOC541472 knockdown using Smart Silencer was confirmed by RT‐qPCR. IL‐6 gene expression was determined by RT‐qPCR ( E ), and IL-6 protein levels were determined by CBA assays ( F ). ( G ) Cellular localization and expression of IL6 and LOC541472 , as demonstrated by RNAscope assays. ( H ) Western blotting of IL6, phosphor-p65, p65, and β-actin. ( I ) Quantification of the blots shown in ( H ). ( J ) Gene expression of the lncRNA RP3-467K16.4 after stimulation with 10 ng/mL IL‐1β for 2 h. ( K ) The efficiency of RP3-467K16.4 knockdown using Smart Silencer was confirmed by RT‐qPCR. SFMSCs were transfected with Smart Silencer targeting RP3-467K16.4 for 48 h and then incubated with 10 ng/mL IL‐1β for 2 h, and expression of the IL8 gene was measured by RT‐qPCR ( L ), and IL8 protein levels were determined by CBA assays ( M ). ( N ) Western blotting of IKKβ, IKKα, phosphor-p65, p65, and β-actin. ( O ) Quantification of the blots shown in ( M ). NC negative control, SiL Smart Silencer targeting LOC541472 , SiR Smart Silencer targeting RP3-467K16.4 , pP65 phospho p65. * P < 0.05 vs. negative control or control group. # P < 0.05 vs. NC + IL‐1β group. N = 3. Scale bars = 100 μm.

Article Snippet: Differentially expressed LncRNAs and mRNAs in SFMSCs before and after treatment with IL-1β in vitro were detected using human Arraystar Human LncRNA Microarray V3.0.

Techniques: Biomarker Discovery, Microarray, Immunofluorescence, Expressing, Knockdown, Quantitative RT-PCR, Gene Expression, RNAscope, Western Blot, Transfection, Incubation, Negative Control, Control

Journal: Journal of Cellular and Molecular Medicine

Article Title: A novel antisense lncRNA NT5E promotes progression by modulating the expression of SYNCRIP and predicts a poor prognosis in pancreatic cancer

doi: 10.1111/jcmm.15718

Figure Lengend Snippet: LncNT5E is up‐regulated in pancreatic cancer (PC) tissues and cell lines. A, The heat map from our previous lncRNA microarray reflected the differentially expressed lncRNAs in PC and normal tissues. T represents PC tissue, and N represents normal pancreatic tissue. ENST00000421594 indicates lncNT5E. B, Relative expression of lncNT5E in 45 paired PC and adjacent normal tissues. LncNT5E expression from all tissues was normalized to 18S expression (ΔCT) and then compared with adjacent normal tissues and converted to the fold change (2 −ΔΔCT ). C, Relative expression of lncNT5E in different cell lines. Data are shown as fold change (2 −ΔΔCT ). * P < .05, ** P < .01, *** P < .001

Article Snippet: We used microarray detection (H1602063, Arraystar Human LncRNA 8 × 60 k v3.0 1‐color) to study lncRNAs in three pairs of PC and adjacent normal tissues.

Techniques: Microarray, Expressing