Journal: Parasites & Vectors

Article Title: Microarray analysis of long non-coding RNA expression profiles uncovers a Toxoplasma -induced negative regulation of host immune signaling

doi: 10.1186/s13071-018-2697-8

Figure Lengend Snippet: The expression patterns of NONHSAT022487 and UNC93B1 after T. gondii infection. a Microarray and RT-qPCR analyses showing the transcriptional levels of lncRNA NONHSAT022487 and the UNC93B1 gene in various HFF cells as indicated: uninfected, uninfected HFF cells; inactivated, inactivated T. gondii -infected HFF cells; T. gondii , T. gondii -infected HFF cells. b Western blot image showing the protein level of UNC93B1 in various HFF cells after T. gondii infection. GAPDH was used for internal normalization. The ratio of UNC93B1/GAPDH indicated the relative expression changes in various treated HFF cells according to Western blot. c As described in a , except that THP-1 cells were used. d As described in b , except that THP-1 cells were used

Article Snippet: Human lncRNA array V4.0 (Arraystar, Rockville, MD, USA), which contains 40,173 human lncRNAs and 20,730 mRNAs, was employed in this study.

Techniques: Expressing, Infection, Microarray, Quantitative RT-PCR, Western Blot

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

Journal: Oncotarget

Article Title: Serum-circulating miRNAs predict neuroblastoma progression in mouse model of high-risk metastatic disease

doi: 10.18632/oncotarget.7615

Figure Lengend Snippet: A. Photographs of mice representing normal healthy non-tumor controls without treatment, favorable neuroblastoma with primary tumor without metastasis, and high-risk metastatic neuroblastoma with clinically mimicking metastasized tumors in the mediastinum and retroperitoneal, pelvic, abdominal, and chest cavities. B. Traverse analysis of whole miRnome expression between animals with favorable non-metastatic primary disease (X-NB) and high-risk metastatic disease (AD). A total of 852 miRNAs were compared between groups. The alterations are color coded (Red – upregulated; Blue – downregulated). The total number of altered molecules under each comparison is provided in the corresponding box. Numbers in parentheses refer to the molecules that are significantly (> or < 2 fold) modulated.

Article Snippet: These were hybridized on human miRNA One Array V4 (PhalanxBio, Inc., San Diego, CA, USA) following the manufacturer's protocol.

Techniques: Expressing, Comparison

Journal: Oncotarget

Article Title: Serum-circulating miRNAs predict neuroblastoma progression in mouse model of high-risk metastatic disease

doi: 10.18632/oncotarget.7615

Figure Lengend Snippet: A. Histograms of individual miRNA QPCR analysis showing circulating levels of randomly selected miRNAs (miR-20a, miR-27b, miR-1224-3p, miR-1260, and miR-93) in the serum of animals with non-metastatic primary disease or with high-risk metastatic disease. B. Correlation analysis of the serum-circulating profiles of miR-20a, miR-27b, miR-1224-3p, miR-1260, and miR-93 observed using the miRnome approach. The individual miRNA-QPCR analysis demonstrates goodness of fit and validates the miRnome expression profiles.

Article Snippet: These were hybridized on human miRNA One Array V4 (PhalanxBio, Inc., San Diego, CA, USA) following the manufacturer's protocol.

Techniques: Expressing

Journal: Oncotarget

Article Title: Serum-circulating miRNAs predict neuroblastoma progression in mouse model of high-risk metastatic disease

doi: 10.18632/oncotarget.7615

Figure Lengend Snippet: Automated IHC stained panels (TMA thumbnail and representative field at the magnification of 20X) showing the staining pattern and cellular localization of the serum-circulating miRNAs' protein targets (STAT3, CREB1, CCND1) in Liver, pancreas, lungs, kidney, spleens, and small intestine of mice with favorable neuroblastoma. Representative figures without primary antibody blank controls and H&E stained sections were also included.

Article Snippet: These were hybridized on human miRNA One Array V4 (PhalanxBio, Inc., San Diego, CA, USA) following the manufacturer's protocol.

Techniques: Staining

Journal: International Journal of Clinical and Experimental Pathology

Article Title: Differential long non-coding RNA (lncRNA) profiles associated with hippocampal sclerosis in human mesial temporal lobe epilepsy

doi:

Figure Lengend Snippet: Differential lncRNA expression profiles between HS and CH. A. Dendrogram of the hierarchical clustering analysis of differentially expressed lncRNAs between the two groups. Samples were arranged into groups based on their lncRNA expression levels and dendrograms were subsequently constructed. B. Differential mRNA expression profiles between HS and CH. Dendrogram of the hierarchical clustering analysis of differentially expressed mRNAs between the two groups. Samples were arranged into groups based on their mRNA expression levels and dendrograms were subsequently constructed.

Article Snippet: The isolated RNAs were used to synthesize double-stranded complementary DNA (cDNA), which was then labeled and hybridized to the Agilent Human lncRNA+mRNA Array V4.0 (CapitalBio Corp, Beijing, China) according to the manufacturer’s instructions.

Techniques: Expressing, Construct

Journal: International Journal of Clinical and Experimental Pathology

Article Title: Differential long non-coding RNA (lncRNA) profiles associated with hippocampal sclerosis in human mesial temporal lobe epilepsy

doi:

Figure Lengend Snippet: A. The 30 most significantly enriched GO terms. B. The 30 most significantly enriched pathway terms. Results are based on the differential expression of mRNAs in the lncRNA-mRNA co-expression network.

Article Snippet: The isolated RNAs were used to synthesize double-stranded complementary DNA (cDNA), which was then labeled and hybridized to the Agilent Human lncRNA+mRNA Array V4.0 (CapitalBio Corp, Beijing, China) according to the manufacturer’s instructions.

Techniques: Expressing

Journal: International Journal of Clinical and Experimental Pathology

Article Title: Differential long non-coding RNA (lncRNA) profiles associated with hippocampal sclerosis in human mesial temporal lobe epilepsy

doi:

Figure Lengend Snippet: Detailed information of nine lncRNA-mRNA pairs

Article Snippet: The isolated RNAs were used to synthesize double-stranded complementary DNA (cDNA), which was then labeled and hybridized to the Agilent Human lncRNA+mRNA Array V4.0 (CapitalBio Corp, Beijing, China) according to the manufacturer’s instructions.

Techniques: