Journal: BioMed Research International

Article Title: Integration Analysis of MicroRNA and mRNA Expression Profiles in Human Peripheral Blood Lymphocytes Cultured in Modeled Microgravity

doi: 10.1155/2014/296747

Figure Lengend Snippet: Differentially expressed miRNAs in human PBLs incubated in MMG. (a) The expression level of each miRNA, indicated as fold change, is the mean of the expression values obtained from the transformed log2 ratio (MMG/1 g). (b) Dendrogram of miRNAs differentially expressed in MMG. The range of expression value is from −3.7 (green, downregulation) to 3.07 (red, upregulation). Grey boxes correspond to not available (N/A) fluorescent signal from the microarray platform.

Article Snippet: MicroRNAs profiling was carried out in PBL samples incubated in MMG versus 1 g. Analyses were performed by using the “Human miRNA Microarray kit (V2)” (Agilent Technologies) that allows the detection of 723 known human (miRBase v.10.1) and 76 human viral miRNAs.

Techniques: Incubation, Expressing, Transformation Assay, Microarray

Journal: BioMed Research International

Article Title: Integration Analysis of MicroRNA and mRNA Expression Profiles in Human Peripheral Blood Lymphocytes Cultured in Modeled Microgravity

doi: 10.1155/2014/296747

Figure Lengend Snippet: Microarray data validation by quantitative real-time PCR (qRT-PCR). Validation of microarray data by qRT-PCR in MMG-incubated versus 1 g incubated PBLs. The results are consistent with the cumulative microarray data of miRNAs (a) and mRNAs (b). Values (fold change, dark grey bars) are means ± S.E. of expression levels calculated as the log2 (MMG/1 g) on PBL samples from 4 to 6 different donors. The value “1” of control 1 g PBLs (light grey bars) is arbitrarily given when no change is observed (*** P < 0.001, ** P < 0.01, and * P < 0.05, t -test).

Article Snippet: MicroRNAs profiling was carried out in PBL samples incubated in MMG versus 1 g. Analyses were performed by using the “Human miRNA Microarray kit (V2)” (Agilent Technologies) that allows the detection of 723 known human (miRBase v.10.1) and 76 human viral miRNAs.

Techniques: Microarray, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Incubation, Expressing

Journal: Cancer & Metabolism

Article Title: FOXO3a/miR-4259-driven LDHA expression as a key mechanism of gemcitabine sensitivity in pancreatic ductal adenocarcinoma

doi: 10.1186/s40170-025-00377-3

Figure Lengend Snippet: miR-4259 targets the LDHA 3’UTR and inhibits LDHA-mediated gemcitabine resistance in PDAC. ( A ) The miR-4259 expression (left) and LDHA -3’UTR luciferase activity (right) in PANC-1 and PANC-1/GEM cells was measured by RT-qPCR and a luciferase reporter assay, respectively. The RT-qPCR data were normalized to the level of U47 RNA in each individual sample. ( B ) A schematic diagram representing the predicted miR-4259-binding sequences or the mutated versions of the miRNA (left). The luciferase reporter activity (right) of the LDHA -3’UTR wild-type (+ 1 ~ + 937) and LDHA -3’UTR mutant reporters (mutant sites: 498, 498/518 and 498/518/818) were measured by a dual-luciferase reporter assay in HEK-293T cells transfected with miR-4259 and a reporter at different ratios. ( C ) The luciferase reporter activity of the LDHA -3’UTR wild-type and LDHA -3’UTR mutant reporters (triple-mutant sites, 498/518/818) in PANC-1/GEM and SUIT-2 cells and their expression of miR-4259. ( D ) The LDHA and miR-4259 expression (left) of PANC-1/GEM cells transfected with the indicated plasmids were analyzed by Western blotting and RT-qPCR, respectively. The cell viability (right) of these transfectants in the presence of gemcitabine treatment was measured by the MTT assay. ( E ) The LDHA and miR-4259 expression (left) of PANC-1 cells were analyzed by Western blotting and RT-qPCR, respectively. The cell viability ( right ) of these transfectants in the presence of gemcitabine treatment was measured by the MTT assay. The results are presented as the means ± s.e.m. of three independent experiments. * P < 0.05, ** P < 0.01, *** P < 0.001 and n.s. not significant (two-tailed Student’s t -test)

Article Snippet: Five micrograms of total RNA obtained from PANC-1 and PANC-1/GEM cells were labeled and hybridized on miRNA microarrays (using the Human miRNA OneArray ® v2 (Phalanx Biotech Group, San Diego, CA, USA).

Techniques: Expressing, Luciferase, Activity Assay, Quantitative RT-PCR, Reporter Assay, Binding Assay, Mutagenesis, Transfection, Western Blot, MTT Assay, Two Tailed Test

Journal: BMC Genomics

Article Title: MMpred: functional miRNA – mRNA interaction analyses by miRNA expression prediction

doi: 10.1186/1471-2164-13-620

Figure Lengend Snippet: The differences between microarray platforms used in the project ( source: Affymetrix and Agilent data sheets )

Article Snippet: Such impediments are reflected in the relatively small number of paired miRNA-mRNA datasets available in public repositories - ( i.e. there are only nine Agilent Human miRNA Microarray (V2) datasets in GEO [ , ]; see Additional file ).

Techniques: Microarray, Sequencing

Journal: BMC Genomics

Article Title: Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations

doi: 10.1186/1471-2164-11-132

Figure Lengend Snippet: Gene expression analysis of the different GCT subgroups . ( A ) A multidimensional scaling (MDS) plot containing the differentially expressed genes (690 probe sets, q < 0.001). Each spot represents a single array. ( B ) A comparison of the transcriptome traits between ESCs and NGMGCTs by principal component analysis (PCA). ( C ) Relationships between ESCs, germinomas and NGMGCTs. Average linkage Euclidean distances between the tissues and ESC were calculated using genes distinguishing the filtrated 690-probe set. The confidence limits shown represent the standard error. ( D ) A heat map shows genes enriched in the ESCs and in the different prognostic groups ( q < 0.001). ( E-F ) Real-time PCR validation of the microarray data. Mean expression levels of the examined genes were compared to that of the GAPDH control. Each bar represents a different individual ( F ). The genes' array hybridization signals are also shown ( E ).

Article Snippet: The Agilent Human miRNA Microarray Kit V2 (Agilent, Foster City, CA, USA) containing probes for 723 human microRNAs from the Sanger database v10.1 was used.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Microarray, Hybridization