Journal: Nucleic Acids Research

Article Title: LncRNA Meg3 protects endothelial function by regulating the DNA damage response

doi: 10.1093/nar/gky1190

Figure Lengend Snippet: Transcriptome analysis identifies p53 signaling as the most significantly upregulated pathway upon Meg3 knockdown. HUVECs were transfected with control or Meg3 GapmeRs. 24 h after transfection, cells were treated with 10 ng/ml TNF-α for 3 h and collected for microarray gene chip analysis. Chromatin immunoprecipitation was performed using transfected cells with or without 10 ng/ml TNF-α treatment for 1 h. ( A ) Volcano plot shows differentially expressed mRNAs in ECs upon Meg3 knockdown. ( B ) KEGG signaling pathways analysis identified significantly regulated pathways among upregulated genes upon Meg3 knockdown. ( C ) Venn diagram shows p53 target genes that are regulated by Meg3. ( D ) qPCR analysis of a group of p53 target genes that were induced upon Meg3 knockdown. (E) Enrichment of p53 at the promoters of indicated genes was identified by chromatin immunoprecipitation using anti-p53 antibodies followed by qPCR analysis. Data show mean ± S.E.M., n = 3; * P < 0.05.

Article Snippet: Arraystar Human LncRNA Microarray v4.0, performed by Arraystar Inc. (Rockville, MD, USA), is designed for the global expression profiling of 40 173 human lncRNA and 20,730 protein-coding mRNA transcripts.

Techniques: Knockdown, Transfection, Control, Microarray, Chromatin Immunoprecipitation, Protein-Protein interactions

Journal: Nucleic Acids Research

Article Title: LncRNA Meg3 protects endothelial function by regulating the DNA damage response

doi: 10.1093/nar/gky1190

Figure Lengend Snippet: LncRNA pull-down assay identifies PTBP3 as a binding partner of Meg3. ( A ) LncRNA pull-down assay was used to identify the proteins associated with Meg3 transcript variant 1 (TV1) by incubating the cell lysates with biotinylated sense or antisense Meg3 RNA. The RNA–protein complexes captured by T-1 beads were subjected to silver stain after separation on SDS-PAGE gel. ( B ) The RNA–protein complexes from lncRNA pulldown using antisense Meg3 (negative control RNA), sense Meg3 (TV1), and Meg3 deletion mutants were subjected to western blot analysis of PTBP3 and GAPDH after separation on SDS-PAGE gel. GAPDH was examined as a negative control protein. ( C ) The interaction of endogenous PTBP3 with Meg3 was detected by RNA immunoprecipitation. EC lysates were immunoprecipitated with anti-PTBP3 antibody or Isotype matched control IgG. Meg3 was examined by qPCR in the immuno-precipitates using primer set 2 as shown in (D). LncRNA Neat1 was used as a positive control RNA that interacts with PTBP3. ( D ) Different sets of Meg3 primers were used to detect Meg3 by qPCR following RNA immunoprecipitation using anti-PTBP3 antibodies. Primer sets 1, 2, 5 detect Meg3 transcript variants 1 and 6 (TV1 and TV6); primer sets 3 and 4 detect Meg3 TV1; and primer sets 6 and 7 detect Meg3 TV6. ( E ) Dual-staining of Meg3 and PTBP3 in HUVECs. Linear trajectories (yellow line) crossing the cells with the intensities of Meg3 and PTBP3 signals were presented at the right side of images. White and black arrows indicate partial colocalization of Meg3 and PTBP3 in the nucleus of HUVECs. Data show mean ± S.E.M., n = 3; * P < 0.05.

Article Snippet: Arraystar Human LncRNA Microarray v4.0, performed by Arraystar Inc. (Rockville, MD, USA), is designed for the global expression profiling of 40 173 human lncRNA and 20,730 protein-coding mRNA transcripts.

Techniques: Pull Down Assay, Binding Assay, Variant Assay, Silver Staining, SDS Page, Negative Control, Western Blot, RNA Immunoprecipitation, Immunoprecipitation, Control, Positive Control, Staining

Journal: Scientific Reports

Article Title: Differentially expressed circulating LncRNAs and mRNA identified by microarray analysis in obese patients

doi: 10.1038/srep35421

Figure Lengend Snippet: Differentially expressed lncRNAs and mRNAs between obese and non-obese participants were subjected to hierarchical clustering. The color scale on the top illustrates the relative expression level of lncRNAs across all samples. Red color indicates high relative expression and green color indicates low relative expression. ( A ) lncRNA; ( B ) mRNA.

Article Snippet: We performed microarray profiling using Human LncRNA Microarray V4.0 (CapitalBio Corp, Beijing, China), including 34,235 mRNAs and 40,914 lncRNAs.

Techniques: Expressing

Journal: Scientific Reports

Article Title: Differentially expressed circulating LncRNAs and mRNA identified by microarray analysis in obese patients

doi: 10.1038/srep35421

Figure Lengend Snippet: Expression of lncRNA-p5549, lncRNA-p21015 and lncRNA-p19461 was detected by qPCR and normalized by U6 expression. (**P < 0.01)

Article Snippet: We performed microarray profiling using Human LncRNA Microarray V4.0 (CapitalBio Corp, Beijing, China), including 34,235 mRNAs and 40,914 lncRNAs.

Techniques: Expressing

Journal: Scientific Reports

Article Title: Differentially expressed circulating LncRNAs and mRNA identified by microarray analysis in obese patients

doi: 10.1038/srep35421

Figure Lengend Snippet: Correlation between lncRNAs concentrations and studied variables in the cross-sectional study Data are R ( p ).

Article Snippet: We performed microarray profiling using Human LncRNA Microarray V4.0 (CapitalBio Corp, Beijing, China), including 34,235 mRNAs and 40,914 lncRNAs.

Techniques:

Journal: Scientific Reports

Article Title: Differentially expressed circulating LncRNAs and mRNA identified by microarray analysis in obese patients

doi: 10.1038/srep35421

Figure Lengend Snippet: Clinical characteristics of subjects included in longitudinal studies.

Article Snippet: We performed microarray profiling using Human LncRNA Microarray V4.0 (CapitalBio Corp, Beijing, China), including 34,235 mRNAs and 40,914 lncRNAs.

Techniques:

Journal: Scientific Reports

Article Title: Differentially expressed circulating LncRNAs and mRNA identified by microarray analysis in obese patients

doi: 10.1038/srep35421

Figure Lengend Snippet: Baseline and diet-induced weight loss levels of lncRNA-p5549 ( A ) lncRNA-p21015 ( B ) and lncRNA-p19461 ( C ) in obese participants. **P <0.01. Date are shown as mean (SD).

Article Snippet: We performed microarray profiling using Human LncRNA Microarray V4.0 (CapitalBio Corp, Beijing, China), including 34,235 mRNAs and 40,914 lncRNAs.

Techniques:

Journal: BMC Cancer

Article Title: LncRNA ENST00000539653 acts as an oncogenic factor via MAPK signalling in papillary thyroid cancer

doi: 10.1186/s12885-019-5533-4

Figure Lengend Snippet: LncRNA microarray analysis in papillary thyroid cancer (PTC) tissues compared with matched adjacent noncancerous thyroid tissues. a Hierarchical clustering analysis of differentially expressed lncRNAs. Red and green colors indicate high and low expression, respectively. In the heat map, columns represent samples and rows represent each lncRNA. b Volcano plot of differentially expressed lncRNAs between PTC and paired noncancerous thyroid tissue. The vertical lines correspond to 2.0-fold upregulation and downregulation, and the horizontal line represents a P value of 0.05

Article Snippet: The cRNAs labeled with Cy3-dCTP were processed and hybridized onto a 4 × 180 K human LncRNA Microarray V4.0 (Agilent Technologies), which is designed for global profiling of 40,916 lncRNAs.

Techniques: Microarray, Expressing