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: Bioengineered

Article Title: Curcumol enhances cisplatin sensitivity of gastric cancer: involvement of microRNA-7 and the nuclear factor-kappa B/snail family transcriptional repressor 1 axis

doi: 10.1080/21655979.2022.2070975

Figure Lengend Snippet: Curcumol upregulates miR-7 expression in GC cells. a, miRNAs with differential expression in cells after curcumol treatment identified by microarray analysis; b, miR-7 expression in cells after 80 μM curcumol treatment examined by RT-qPCR (* p < 0.05; two-way ANOVA); c, miR-7 expression in tumor and the paired normal tissues evaluated by RT-qPCR (n = 33; * p < 0.05; the unpaired t test); d, correlation between miR-7 expression and the patient’s survival (* p < 0.05; Kaplan-Meier analysis); e, miR-7 expression in MKN45 and HGC27 cells after different doses of curcumol treatment examined by RT-qPCR (* p < 0.05, ** p < 0.01; two-way ANOVA).

Article Snippet: This reaction was performed at 37°C for 30 min. After that, the labeled RNA was hybridized with Human miRNA Expression Microarray V4.0 (Arraystar, Rockville, MD, USA) for 24 h. The gene expression data were obtained using a GeneChip TM Scanner 3000 7 G system (#00-0210, 2008, Thermo Fisher Scientific) and analyzed by the R Language Program (Version 3.6.3, R).

Techniques: Expressing, Quantitative Proteomics, Microarray, Quantitative RT-PCR

Journal: bioRxiv

Article Title: PAK6 rescues pathogenic LRRK2-mediated ciliogenesis and centrosomal cohesion defects in a mutation-specific manner

doi: 10.1101/2024.04.11.589075

Figure Lengend Snippet: (a) Distribution of PAK6 candidate interactors according to their Z-score retrieved from a Human Proteome Microarray probed with recombinant full-length human PAK6. (b) A GO:BP analysis using gProfiler g:GOSt ( https://biit.cs.ut.ee/gprofiler/gost ) was performed for PAK6 candidate interactors with Z score >2.5 (left) and for PAK6 interactors annotated in PPI web-based tools PINOT, HIPPIE and MIST (PHM) (right). GO:BP terms with 2000 (array) and 1000 (PHM) term size were grouped into semantic categories. (c) Venn diagrams showing overlaps between the primary cilium proteome (GO:0005929, 640 genes) and the experimental (array) PAK6 interactome (left) or the literature-based (PHM) PAK6 interactome (right). (d) Protein network of overlapping PAK6 interactors with the primary cilium proteome (c) (including PAK6) obtained with STRING ( https://string-db.org/cgi/input?sessionId=b1S4T5BW27rz&input_page_show_search=on ); number of nodes: 11, number of edges: 11, average node degree: 2, average local clustering coefficient: 0.591, expected number of edges: 3, PPI enrichment P -value: 0.000502. Blue nodes are ciliary proteins present in the experimental PAK6 interactome (array) and grey nodes are those found in the literature-based PAK6 interactome.

Article Snippet: HuProt TM Human Proteome Microarray v4.0 was purchased from Cambridge Protein Arrays (Babraham Research Campus, Cambridge, UK) and employed to screen PAK6 interactor candidates following manufacturer’s instructions.

Techniques: Microarray, Recombinant

Journal: Communications Medicine

Article Title: Preclinical characterization of an active immunotherapy targeting calcitonin gene-related peptide

doi: 10.1038/s43856-025-00870-2

Figure Lengend Snippet: Proteome and peptide screens were used to evaluate potential off-target binding of affinity-purified p4796kb antibodies. a Manhattan plot displays results from the HuProt Human Proteome Microarray screen of antibody binding. Colors represent each block from the array, containing approximately 1000 proteins each. Spots represent individual protein intensity score from array. Hits are annotated with protein names. b Manhattan plot from peptide counter screen of 21 putative hits from proteome screen. Overlapping 15mer peptides were synthesized and printed on arrays. Spots represent individual peptide intensity scores from array. Peptide sequences of hits are displayed. Sera from guinea pigs immunized with p4796kb were tested for binding to putative hits from screens ( c ) and calcitonin family ( d ) measured by ELISA. Pre-immune sera were used as controls. Data are presented as means +/− SEM; n = 3. *** p < 0.0001.

Article Snippet: Guinea pig sera collected at week 15 post p4796kb immunization were assessed for their potential off target binding using HuProtTM Human Proteome Microarrays v4.0 (Cambridge Protein Arrays Ltd., Cambridge, UK) with over 20,000 individual proteins, representing more than 16,000 human genes, including the peptides of the calcitonin/CGRP peptide family.

Techniques: Binding Assay, Affinity Purification, Microarray, Blocking Assay, Synthesized, Enzyme-linked Immunosorbent Assay