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: Theranostics

Article Title: The c-Myc/miR-27b-3p/ATG10 regulatory axis regulates chemoresistance in colorectal cancer

doi: 10.7150/thno.37621

Figure Lengend Snippet: Oxaliplatin-resistant colorectal cancer cells express decreased levels of miR-27b-3p. (A) Different miRNA expressions levels in parental cells (SW480 and HCT116) and chemoresistant cells (SW480-OxR and HCT116-OxR) were determined by using the miRNA microarray. (B) Twenty-two miRNAs were dysregulated in oxaliplatin-resistant cells relative to their expression in the corresponding parental cells. (C) The relative levels of miRNAs in SW480, HCT116, SW480-OxR and HCT116-OxR cell lines were determined using qRT-PCR. (D) The correlation between the expression level of miR-27b-3p and IC 50 for oxaliplatin in 8 CRC cell lines (SW480, HCT116, SW480-OxR, HCT116-OxR, SW620, Caco2, HT-29 and LOVO) was shown. (E) MiR-27b-3p expression levels were decreased in human colorectal cancer samples compared with those in the paired noncancerous tissues (n=20). (F) Representative images of the expression of miR-27b-3p in paired tissues using ISH. Scale bars: 100 μm. (G) Kaplan-Meier plots for investigating the correlation of miR-27b-3p expression level with disease-free survival (DFS). Patients were split into the high- and low-expression groups by the mean expression level of the miR-27b-3p (n=62; log-rank test). *p < 0.05, **p < 0.01, ***p < 0.001.

Article Snippet: Total RNA extracted from SW480, HCT116, SW480-OxR and HCT116-OxR cells were used for Affymetrix miRNA microarray analysis (CapitalBio Corp, Beijing, China), and the process was described on the web site of CapitalBio ( http://www.capitalbio.com ).

Techniques: Microarray, Expressing, Quantitative RT-PCR

Journal: Toxicological Sciences

Article Title: Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression

doi: 10.1093/toxsci/kfx241

Figure Lengend Snippet: Neurogenic Transcription Factors that Are Potentially Targeted by the miR-466/669 Cluster

Article Snippet: The samples were hybridized onto LC Sciences murine miRNA microarray chips (Houston, Texas; Geo Platform {"type":"entrez-geo","attrs":{"text":"GPL21312","term_id":"21312"}} GPL21312 ).

Techniques:

Journal: Toxicological Sciences

Article Title: Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression

doi: 10.1093/toxsci/kfx241

Figure Lengend Snippet: The miR-466-669 cluster share sequence similarities. Sequences of mature miRNA from the miR-466-669 cluster were aligned using Clustal Omega. All mature sequences were initially aligned together and then were subdivided into 4 major groups which have high similarity. The highlighted nucleotides were used to derive the 4 consensus sequences (as light blue). An asterisk indicates the sequence identity among all miRNAs within the group.

Article Snippet: The samples were hybridized onto LC Sciences murine miRNA microarray chips (Houston, Texas; Geo Platform {"type":"entrez-geo","attrs":{"text":"GPL21312","term_id":"21312"}} GPL21312 ).

Techniques: Sequencing

Journal: Toxicological Sciences

Article Title: Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression

doi: 10.1093/toxsci/kfx241

Figure Lengend Snippet: Expression profiles of microRNAs (miRNAs) between control and arsenic exposure in differentiating P19 cells. P19 cells were induced to differentiate with or without 0.5 µM of arsenic for 9 days. MicroRNA expression was detected via a miRNA microarray and plotted as a heat map using CIM Miner (NIH). Darker shading indicates increased expression. Only statistically different miRNAs are listed in the map (Student’s t test; P value < .05).

Article Snippet: The samples were hybridized onto LC Sciences murine miRNA microarray chips (Houston, Texas; Geo Platform {"type":"entrez-geo","attrs":{"text":"GPL21312","term_id":"21312"}} GPL21312 ).

Techniques: Expressing, Control, Microarray

Journal: Toxicological Sciences

Article Title: Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression

doi: 10.1093/toxsci/kfx241

Figure Lengend Snippet: Validation of miRNA transcript levels by qPCR. Day 9 differentiated P19 cells were used to confirm miRNA expression by qPCR (n = 3 per treatment). Significantly changed miRNAs with known roles in development were examined, including miR-92a (A), miR-291a (B), miR-709 (C), miR-199a (D), and miR-9 (E). Expression values were normalized with U6 snRNA and fold differences calculated from control cells using the delta Ct method. Values are expressed as mean ± SD and statistical differences were determined by Student’s t test (*P < .05).

Article Snippet: The samples were hybridized onto LC Sciences murine miRNA microarray chips (Houston, Texas; Geo Platform {"type":"entrez-geo","attrs":{"text":"GPL21312","term_id":"21312"}} GPL21312 ).

Techniques: Biomarker Discovery, Expressing, Control

Journal: Toxicological Sciences

Article Title: Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression

doi: 10.1093/toxsci/kfx241

Figure Lengend Snippet: Arsenic exposure induces members of the miR-466-669 cluster along with its host gene, Sfmbt2. P19 cells were differentiated and RNA was extracted from cells exposed to 0 or 0.5 μM arsenite on days 0, 2, 5, and 9 (n = 3 per treatment per day). MicroRNA or mRNA expression was determined by qPCR. Day 9 samples were used to determine the expression of miRNA-466-669 cluster genes (A) and the host gene Sfmbt2 (B). Samples from days 0, 2, 5, to 9 were used to determine the expression of miR-467d (C), miR-669p (D), and Sfmbt2 (E). Expression values were normalized with U6 snRNA for the miRNAs, and Gapdh for Sfmbt2. Fold changes were compared with unexposed cells, and time-dependent qPCR expression fold changes were compared with day 0 unexposed cells. Data are shown as mean ± SD. Statistical differences were determined by ANOVA followed by Tukey’s test or by Student’s t test (*P < .05).

Article Snippet: The samples were hybridized onto LC Sciences murine miRNA microarray chips (Houston, Texas; Geo Platform {"type":"entrez-geo","attrs":{"text":"GPL21312","term_id":"21312"}} GPL21312 ).

Techniques: Expressing

Journal: Toxicological Sciences

Article Title: Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression

doi: 10.1093/toxsci/kfx241

Figure Lengend Snippet: Inhibiting the miR-466-669 cluster during differentiation rescues the morphological loss of neurons following arsenic exposure. P19 cells were transfected with 100 nM anti-miRNA oligonucleotides which target 4 consensus sequences of the miRNA-466-467-669 cluster. Cells were coexposed to 0 or 0.5 μM arsenic for the 5 days of embryoid body formation. Only the arsenic exposure was maintained for the entire 9 days of differentiation, after which cell morphology was observed. Transfections include oligonucleotides sequences that do not target any miRNAs, designated as negative control, (N.C.), and a mixed transfection that combined all consensus anti-miRNAs. Arrows indicate neuronal cells (A). The distance of cells differentiating away from the embryoid body was quantitated using ImageJ and is expressed in mm (n = 6 replicate embryoid bodies per group) (B). mRNA levels of the neuronal cell marker NeuroD1 on day 9 was assessed by qPCR (C). mRNA expression levels were normalized with Gapdh using the comparative delta Ct method. Fold changes were compared with N.C. anti-miRNA. Data are shown as mean ± SD. Two-way ANOVA followed by Bonferroni (P < .05) was run to determine interactions and statistical differences between arsenic concentrations (*) and between the N.C. anti-miRNA and consensus anti-miRNA transfections (#).

Article Snippet: The samples were hybridized onto LC Sciences murine miRNA microarray chips (Houston, Texas; Geo Platform {"type":"entrez-geo","attrs":{"text":"GPL21312","term_id":"21312"}} GPL21312 ).

Techniques: Transfection, Negative Control, Marker, Expressing

Journal: Toxicological Sciences

Article Title: Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression

doi: 10.1093/toxsci/kfx241

Figure Lengend Snippet: Consensus anti-miRNAs are active and functional and can rescue the expression of miR-466-467-669 target genes. P19 cells were transfected with all 4 miRNA inhibitors, with or without 0.5 μM arsenic (n = 3 replicates), allowed to form embryoid bodies for 5 days, and examined for mRNA expression of each of the 4 consensus sequences (A–D), 1 individual miRNA, miR-669a-3p (E), the host gene Sfmbt2 (F), and a known target gene for the consensus 1 cluster, Lats2 (G). mRNA expression levels were normalized with Gapdh, and miRNA expression levels were normalized with shRNA U6, using the comparative delta Ct method. Fold changes were compared with N.C. anti-miRNA. Data are shown as mean ± SD. Two-way ANOVA followed by Bonferroni (P < .05) was run to determine interactions and statistical differences between arsenic concentrations (*) and between the N.C. anti-miRNA and consensus anti-miRNA transfections (#) in (A–F). A 1-way ANOVA followed by Tukey’s test (P < .05) was run to determine significance (#) in (G).

Article Snippet: The samples were hybridized onto LC Sciences murine miRNA microarray chips (Houston, Texas; Geo Platform {"type":"entrez-geo","attrs":{"text":"GPL21312","term_id":"21312"}} GPL21312 ).

Techniques: Functional Assay, Expressing, Transfection, shRNA

Journal: Toxicological Sciences

Article Title: Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression

doi: 10.1093/toxsci/kfx241

Figure Lengend Snippet: Mixed consensus miRNA inhibitors rescue arsenic’s inhibitory effects on NeuroD1 expression. P19 cells were transfected with a combined mixture of the 4 anti-miRNAs, with or without 0.5 μM arsenic (n = 3 replicates per anti-miRNA and per exposure group), and allowed to form embryoid bodies for 5 days. Immunohistochemistry was used to examine expression of NeuroD1 protein (red) in the embryoid bodies. Cells were counterstained with DAPI (blue) to indicate the nuclei (A). High magnification images of cells are shown in the (A) inserts. For 10 representative cells (examples are shown in the blue boxes), expression of NeuroD1 in the whole cell, cytoplasm, and nuclei were quantified using ImageJ (B). NeuroD1 transcript levels were quantified by qPCR, and normalized with Gapdh using the comparative delta Ct method with fold changes compared with N.C. (B). Data are shown as mean ± SD. Two-way ANOVA followed by Bonferroni (P < .05) was run to determine interactions and statistical differences between arsenic concentrations (*) and between the N.C. anti-miRNA and consensus anti-miRNA transfections (#).

Article Snippet: The samples were hybridized onto LC Sciences murine miRNA microarray chips (Houston, Texas; Geo Platform {"type":"entrez-geo","attrs":{"text":"GPL21312","term_id":"21312"}} GPL21312 ).

Techniques: Expressing, Transfection, Immunohistochemistry

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: 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