Journal: The FASEB Journal

Article Title: Extracellular vesicles extracted from young donor serum attenuate inflammaging via partially rejuvenating aged T-cell immunotolerance

doi: 10.1096/fj.201800059R

Figure Lengend Snippet: Characteristics of serum-extracted EVs. A) Comparison of the sizes of EVs extracted from young murine serum by the ExoQuick reagent pretreated with and without using 0.2-μm filters. B) Morphology of EVs from young murine serum used in this project for rejuvenation of inflammaging, photographed by atomic force microscopy (AFM). C, D) Different miRNA expression profiles in heatmap (C) and quantified summary (D) of EVs from young vs. old murine serum, analyzed by murine miRNA microarray with Mus musculus miRBase version-21 arrays that contained 1900 unique mature miRNA probes (miRNA microarray service via LC Sciences).

Article Snippet: C , D ) Different miRNA expression profiles in heatmap ( C ) and quantified summary ( D ) of EVs from young vs. old murine serum, analyzed by murine miRNA microarray with Mus musculus miRBase version-21 arrays that contained 1900 unique mature miRNA probes (miRNA microarray service via LC Sciences).

Techniques: Comparison, Microscopy, Expressing, Microarray

Journal: Database: The Journal of Biological Databases and Curation

Article Title: RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

doi: 10.1093/database/baw151

Figure Lengend Snippet: Architecture of the RiceATM platform. Step 1: Eight agronomic traits are represented in the RiceATM web server. The user can select an interesting trait and identify the associated miRNAs. Step 2: After selecting the agronomic trait, the user must fill in the ‘High cumulative percentage’ and “Low cumulative percentage” fields to identify the high- and low-quantity groups. The miRNA expression data on these two groups are selected for analysis. Step 3: In the microarray data pretreatment step, the user can select quantile normalization and data adjustment to normalize the microarray data. Step 4: To identify the miRNAs associated with the agronomic trait in the two groups of cultivars, RiceATM supports Student’s t -tests or ANOVAs. Step 5: Finally, the user can select the miRanda or psRNATarget algorithm to predict the target genes of the associated miRNAs.

Article Snippet: The mature miRNA sequences and six control probes (four positive and two negative) were used to produce the customized rice miRNA microarray (Combimatrix Custom Array 4 × 2 K, CA, USA).

Techniques: Expressing, Microarray

Journal: Database: The Journal of Biological Databases and Curation

Article Title: RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

doi: 10.1093/database/baw151

Figure Lengend Snippet: Example of browsing the RiceATM platform. (A) Eight agronomic traits affecting yield are represented in RiceATM, including the heading date, plant height, panicle number, panicle length, panicle weight, spikelet number, seed-set %, and 1000-seed weight. Here, we select ‘Heading Date’ as a demonstration. (B) RiceATM includes 187 rice cultivars: 155 japonica and 32 indica. The user can select total (japonica plus indica), japonica or indica cultivars to analyse by checking the ‘Variety’ box. In this example, we select the k-means clustering algorithm to select the high and low heading date groups for the total cultivars. (C) In the data pretreatment step, we use quantile normalization and then clip the minimum value at 800 to normalize the microarray data. (D) Differentially expressed miRNAs are evaluated by ANOVA and then subjected to target gene prediction by the psRNATarget algorithm. Thus, RiceATM shows the regulatory miRNA network. Large orange circles, miRNAs with high expression in the high-quantity group; large green circles, miRNAs with high expression in the low-quantity group; small blue circles, targeted mRNAs.

Article Snippet: The mature miRNA sequences and six control probes (four positive and two negative) were used to produce the customized rice miRNA microarray (Combimatrix Custom Array 4 × 2 K, CA, USA).

Techniques: Microarray, Expressing

Journal: Database: The Journal of Biological Databases and Curation

Article Title: RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

doi: 10.1093/database/baw151

Figure Lengend Snippet: Expression trend of candidate miRNAs in the early and late heading date groups of rice cultivars. Four miRNA derived from RiceATM analysis and associated with heading date were subjected to a real-time PCR assay. Early, early heading date group, n = 4; Late, late heading date group, n = 4. Actin served as the internal control. (A) miR172d-3p; (B) miR818c; (C) miR820c and (D) miR399f. * P < 0.05, compared with the early group.

Article Snippet: The mature miRNA sequences and six control probes (four positive and two negative) were used to produce the customized rice miRNA microarray (Combimatrix Custom Array 4 × 2 K, CA, USA).

Techniques: Expressing, Derivative Assay, Real-time Polymerase Chain Reaction, Control

Journal: Annals of Medicine

Article Title: MiR-223-3p regulates erythropoiesis by targeting TGFBR3/Smad signaling pathway in hemoglobin H-Constant Spring disease

doi: 10.1080/07853890.2025.2530690

Figure Lengend Snippet: Comparison of the expression profiles of miRNAs(A-C) and mRNAs (D-F) between HbH-CS patients and healthy controls. (A) Scatter plot showing the distribution of miRNA expression. (B) Volcano plot showing the differential expression of miRNAs. (C) The clustering heatmap showed differentially expressed miRNAs between patients with HbH-CS patients and healthy controls. (D) Scatter plot showing the distribution of mRNA expression. (E) Volcano plot showing the differential expression of mRNAs. (F) The clustering heatmap showed differentially expressed mRNAs between patients with HbH-CS patients and healthy controls.

Article Snippet: MiRNAs associated with hematopoietic cell lineage, apoptosis, and cell cycle were searched in the database, which were stratified by Arraystar miRNA expression profiling microarray data filtered according to p < 0.05 and log FC >1.5.

Techniques: Comparison, Expressing, Quantitative Proteomics

Journal: Annals of Medicine

Article Title: MiR-223-3p regulates erythropoiesis by targeting TGFBR3/Smad signaling pathway in hemoglobin H-Constant Spring disease

doi: 10.1080/07853890.2025.2530690

Figure Lengend Snippet: Bioinformatics analysis. (A) Venn diagram showed stratified operations of miRNAs from the original data and online database. (B) Intersection plot of mRNAs from our previous ArrayStar human mRNA array and miR-223-3p target gene predicted by online database. (C) Prediction plot of miR-223-3p target gene. Yellow circled node, miR-223-3p; blue rectangle type node, mRNA. (D, E) The qRT-PCR was performed to detect the relative expression levels of miR-223-3p (D) and TGFBR3 (E) in the samples from healthy normal subjects and HbH-CS patients. Normal group, n = 17; HbH-CS group, n = 17, mean ± SEM, ** p < 0.01, *** p < 0.001.

Article Snippet: MiRNAs associated with hematopoietic cell lineage, apoptosis, and cell cycle were searched in the database, which were stratified by Arraystar miRNA expression profiling microarray data filtered according to p < 0.05 and log FC >1.5.

Techniques: Quantitative RT-PCR, Expressing

Journal: Circulation Research

Article Title: Inhibition of miR-15 Protects Against Cardiac Ischemic Injury

doi: 10.1161/CIRCRESAHA.111.244442

Figure Lengend Snippet: A, Representative images after TTC staining indicate that although the area at risk (AAR, red and white) is comparable between the different treatment groups, the infarcted area (IA, white) is smaller in the tiny 15b-treated animals (control indicates control oligonucleotide). B, Quantification of cross sections of the infarcted hearts indicate that the AAR is ≈50% of the LV for all 3 treatment groups, whereas administration of 0.5 mg/kg of tiny 15b during reperfusion results in a significant reduction in infarct size compared with either saline or control oligo (*P<0.05 versus saline and control by ANOVA; control indicates control oligonucleotide). C, Real-time PCR analysis on tissue of the ischemic region 24 hours after reperfusion indicates inhibition of miR-15b in response to tiny 15b treatment (*P<0.05 versus saline and control oligonucleotide treated by ANOVA). D, Left ventricular end-diastolic pressure recordings 24 hours after reperfusion reveals an increase with saline treatment and a reduction with tiny 15b treatment (control indicates control oligonucleotide, *P<0.05 versus sham Kruskal-Wallis test). E, Ontology analysis of transcripts upregulated ≥1.5-fold in the ischemic region of hearts 24 hours after reperfusion treated with tiny 15b treatment compared with saline, based on microarray profiling. Negative regulators of apoptosis and cell death are significantly overrepresented. F, Echocardiography shows a reduction in ejection fraction (EF) and increases in LV volumes 2 weeks after infarct, all of which are significantly improved in response to tiny 15b treatment (*P<0.05 versus saline and control by ANOVA for EF and LVESV, versus saline only LVEDV; sham indicates no ischemia/reperfusion; control, control oligo). G, Representative images of Picrosirius red-stained cross sections demonstrate a reduction in collagen content of the left ventricle 2 weeks after reperfusion with tiny 15b treatment. Quantification of fibrosis as a percentage of total left ventricular area reveals a statistically significant reduction in the tiny 15b-treated group (*P<0.05 versus saline-treated by ANOVA). LV indicates left ventricle.

Article Snippet: Microarray for miRNAs and mRNAs Microarray analysis was performed on total RNA, using a service provider (LC Sciences, Houston, TX) as described previously.

Techniques: Staining, Control, Saline, Real-time Polymerase Chain Reaction, Inhibition, Microarray