Journal: Cell Death Discovery

Article Title: High-glucose-induced miR-214-3p inhibits BMSCs osteogenic differentiation in type 1 diabetes mellitus

doi: 10.1038/s41420-019-0223-1

Figure Lengend Snippet: a The measurement of blood glucose concentrations in STZ-induced diabetic mice and control WT mice ( n = 5). b Representative dual-energy X-ray images of mouse femur from STZ-induced diabetic mice or control mice. c Bone mineral density (BMD) of STZ-induced diabetic mice or control mice ( n = 5). d Heatmap of differentially expressed miRNAs of bone specimens from STZ-induced diabetic mice or normal mice. e , f qRT-PCR analysis of miRNA expression in bone specimens from STZ-induced diabetic mice or control mice ( n = 3). All data are expressed as mean ± SEM, * p < 0.05, ** p < 0.01

Article Snippet: Then miRNA microarray was performed at CapitalBio Technology Ltd.

Techniques: Control, Quantitative RT-PCR, Expressing

Journal: The Journal of Obstetrics and Gynaecology Research

Article Title: Exosomal microRNA ‐139‐5p from mesenchymal stem cells accelerates trophoblast cell invasion and migration by motivation of the ERK / MMP ‐2 pathway via downregulation of protein tyrosine phosphatase

doi: 10.1111/jog.14495

Figure Lengend Snippet: Exosomes exerted its role in PE through the delivery of miR‐139‐5p. (a) Microarray analysis of the top 10 miRNAs differentially expressed in trophoblasts treated with exosomes. (b) The exosomes significantly enriched miR‐139‐5p (unpaired t ‐test, ** P < 0.01). (c) The expression of miR‐139‐5p in exosomes of hucMSC transfected with miR‐139‐5p inhibitor measured by RT‐qPCR (one‐way ANOVA, ** P < 0.01). (d) Cell proliferation in trophoblasts treated with exo‐NC and exo‐inhibitor detected by CCK‐8 assay (two‐way ANOVA, ** P < 0.01). exo‐NC. exo‐inhibitor. (e) Cell migration in trophoblasts treated with exo‐NC and exo‐inhibitor detected by wound healing assay (two‐way ANOVA, ** P < 0.01). exo‐NC. exo‐inhibitor. (f) Cell invasion in trophoblasts treated with exo‐NC and exo‐inhibitor detected by Transwell assay (unpaired t ‐test, ** P < 0.01). (g) Cell apoptosis rate of trophoblasts treated with exo‐NC and exo‐inhibitor detected by TUNEL staining (unpaired t ‐test, ** P < 0.01).

Article Snippet: Then, the cDNA was marked and hybridized with the miRNA Expression Microarray (Arraystar).

Techniques: Microarray, Expressing, Transfection, Quantitative RT-PCR, CCK-8 Assay, Migration, Wound Healing Assay, Transwell Assay, TUNEL Assay, Staining

Journal: Scientific Reports

Article Title: MicroRNA-140-5p regulates osteosarcoma chemoresistance by targeting HMGN5 and autophagy

doi: 10.1038/s41598-017-00405-3

Figure Lengend Snippet: miR-140-5p lowly expressed in chemoresistance chort. ( A ) Heatmap representation of differentially expressed microRNAs in the chemoresistant osteosarcoma cases and chemosensitive osteosarcoma cases. Rows, miRNA; columns, independent biological replicates. Downregulated microRNAs are shown in red, while upregulated microRNAs are shown in green. ( B ) Differentially expressed microRNAs between chemoresistant osteosarcoma cases and chemosensitive osteosarcoma. Expression of miR-140-5p ( C ) in 40 paired osteosarcoma and adjacent normal bone tissues (ANCT). ( D ) Kaplan-Meier analysis for overall survival in 40 osteosarcoma patients in low- and moderate- groups based on miR-140-5p expression levels.

Article Snippet: miRNA microarrays analysis was outsourced to RiBio Cor (Ribobio, Guangzhou, China).

Techniques: Expressing

Journal: Genome Biology

Article Title: Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton ( Gossypium hirsutum L.)

doi: 10.1186/gb-2009-10-11-r122

Figure Lengend Snippet: MicroRNAs detected by sequencing and their target gene families predicted in cotton

Article Snippet: miRNA microarrays were performed using the arrays manufactured by CombiMatrix (Mukilteo, WA, USA) [ ].

Techniques: Sequencing, Binding Assay

Journal: Genome Biology

Article Title: Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton ( Gossypium hirsutum L.)

doi: 10.1186/gb-2009-10-11-r122

Figure Lengend Snippet: Conservation of miRNAs in cotton and other plants

Article Snippet: miRNA microarrays were performed using the arrays manufactured by CombiMatrix (Mukilteo, WA, USA) [ ].

Techniques:

Journal: Genome Biology

Article Title: Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton ( Gossypium hirsutum L.)

doi: 10.1186/gb-2009-10-11-r122

Figure Lengend Snippet: Stem loop structures of core pre-miRNAs. (a) Stem-loop structures of miR156 in A. thaliana ( AtMIR156 ), G. hirsutum ( GhMIR156 ), and G. raimondii ( GrMIR156 ) showing overall conserved structures among them and slightly different sequence composition and structure between GhMIR156 and GrMIR15 6. (b) The conserved miR482 is located in the 3' end of the stem in Populus trichocarpa ( PtMIR482 ) and G. hirsutum ( GhMIR482 ). (c) Stem-loop structures of four novel miRNAs (Gh-MIR2948, Gh-MIR2947, GhMIR2949a, and GhMIR2950) in G. hirsutum . One of the three predicted pre- GhMIR2949a EST stem-loops is shown. Gh-miR482-5p is located in the 5' end of the stem in the new miRNA Gh-MIR2948 . Gh-miR2948 was predicted to possess different targets from Gh-miR482 (b). Mature miRNAs and miRNA* are shown in red and green, respectively. The numbers in (b, c) indicate total miRNA and miRNA* sequence reads, respectively, in four tissues examined.

Article Snippet: miRNA microarrays were performed using the arrays manufactured by CombiMatrix (Mukilteo, WA, USA) [ ].

Techniques: Sequencing

Journal: Genome Biology

Article Title: Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton ( Gossypium hirsutum L.)

doi: 10.1186/gb-2009-10-11-r122

Figure Lengend Snippet: Differential accumulation of miRNAs in microarray and sequence assays. (a) Hierarchical cluster analysis of miRNA expression variation in leaves (L), fibers (F; +7 DPA) and fiber-bearing ovules (O+; +3 DPA) of TM-1 and ovules without fibers (O-; +3 DPA) of the N1N1 mutant (N1). At, Arabidopsis thaliana ; Gm, Glycine max ; Mt, Medicago truncatula ; Os, Oryza sativa ; Pp, Physcomitrella patens ; Pt, Populus trichocarpa ; Sb, Sorghum bicolor ; So, Saccharum officinarum ; Zm, Zea mays . Vertical lines indicate similar expression patterns of miRNAs in 'blocks'. (b) Positive correlation of miRNAs between sequencing frequencies and microarray hybridization intensities detected in cotton leaves (R 2 = 0.28; P = 0.02; degrees of freedom (df) = 16). (c) Positive correlation of miRNAs between sequencing frequencies and microarray hybridization intensities detected in cotton ovules (+ 3 DPA; R 2 = 0.20; P = 0.06; df = 16).

Article Snippet: miRNA microarrays were performed using the arrays manufactured by CombiMatrix (Mukilteo, WA, USA) [ ].

Techniques: Microarray, Sequencing, Expressing, Mutagenesis, Hybridization

Journal: Genome Biology

Article Title: Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton ( Gossypium hirsutum L.)

doi: 10.1186/gb-2009-10-11-r122

Figure Lengend Snippet: Small RNA blot analysis of miRNA accumulation in cotton leaves, fiber-bearing ovules, and fibers (n = 2). U6 or tRNAs were used as hybridization and RNA loading controls. Gh-miRNAs are shown on the right. TM-1, G. hirsutum cv. TM-1; D1, G. thurberi ; A2, G. arboreum ; N1, N1N1 lintless mutant of TM-1; -1 and -3, 1 and 3 days prior to anthesis, respectively; 0, on the day of anthesis; +1, +3, and +5, 1, 3, and 5 days post-anthesis (DPA), respectively; +7 and +10, fibers harvested at 7 and 10 DPA, respectively; L, leaves; P, petals. Note that doublets in miR167 were probably produced from precursors of multiple miRNA loci in cotton. The levels of Gh-miR2950 were very low and not quantified. A fragment present in fiber in the Gh-miR2950 blot was larger than 21 nucleotides and probably an artifact.

Article Snippet: miRNA microarrays were performed using the arrays manufactured by CombiMatrix (Mukilteo, WA, USA) [ ].

Techniques: Northern blot, Hybridization, Mutagenesis, Produced

Journal: Genome Biology

Article Title: Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton ( Gossypium hirsutum L.)

doi: 10.1186/gb-2009-10-11-r122

Figure Lengend Snippet: Mapping of mRNA cleavage sites by cotton miRNAs using RNA ligase-mediated rapid amplification of 5' complementary DNA ends (RLM 5' RACE). The arrows indicate the 5' ends of miRNA-guided cleavage products, and the numbers indicate the ratios of cleaved products of the total fragments that were sequenced. Only a single cleavage product was observed within the miRNA-complementary region for each examined EST target, except for a miR166 target, in which two products resulting from adjacent sites were detected. The EST targets (from 5' to 3') with accession numbers are shown in the top strand ('+', sense strand orientation; '-', antisense strand), and Gh-miRNAs are shown in the bottom strand with the orientation from 3' (left) to 5' (right). The total lengths of the target ESTs are shown above the EST accession numbers. Wobble U-G pairs are indicated by black dots. Note that Gh-miR166 had two adjacent cleavage sites in the predicted target. ARF, auxin responsive factor.

Article Snippet: miRNA microarrays were performed using the arrays manufactured by CombiMatrix (Mukilteo, WA, USA) [ ].

Techniques: Amplification

Journal: Genome Biology

Article Title: Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton ( Gossypium hirsutum L.)

doi: 10.1186/gb-2009-10-11-r122

Figure Lengend Snippet: Quantitative RT-PCR analysis of predicted targets of miRNAs, including three novel miRNAs, in cotton. O (-3), O (0), O (+3), F (+7), and Leaf indicate RNA samples from the ovules at -3 DPA, 0 DPA, and +3 DPA, fiber at +7 DPA, and leaves, respectively. The label above each plot indicates the EST accession number followed by the predicted gene function and the corresponding miRNA. Relative expression levels (REL) were calculated using HISTONE H3 as a control.

Article Snippet: miRNA microarrays were performed using the arrays manufactured by CombiMatrix (Mukilteo, WA, USA) [ ].

Techniques: Quantitative RT-PCR, Expressing, Control

Journal: Cancer Cell International

Article Title: Identification of upstream miRNAs of SNAI2 and their influence on the metastasis of gastrointestinal stromal tumors

doi: 10.1186/s12935-019-1006-8

Figure Lengend Snippet: Unsupervised hierarchical clustering analysis of miRNA expression profiles from GISTs specimen:85 miRNAs were downregulated in high SNAI2 level GISTs compared with low SNAI2 level GISTs

Article Snippet: Labeling and hybridization were performed in accordance with the protocols in the PhalanxBio miRNA microarray system.

Techniques: Expressing

Journal: Cancer Cell International

Article Title: Identification of upstream miRNAs of SNAI2 and their influence on the metastasis of gastrointestinal stromal tumors

doi: 10.1186/s12935-019-1006-8

Figure Lengend Snippet: Prediction and screening of the upstream metastasis-associated miRNAs of SNAI2 in GISTs. a Flowchart of confirmation of the upstream metastasis-associated miRNAs of SNAI2 in GISTs. b , c The mRNA and protein levels of SNAI2 in 10 GISTs tissue, 3 high SNAI2 level GISTs and 3 low SNAI2 level GISTs were selected for the miRNA microarray. d Eight possible metastasis-associated miRNAs levels in GISTs. The miRNAs levels of five miRNAs including miRNA-1-3P, miRNA-200b-3p, miRNA-32-3P, miRNA-30c-1-3P and miRNA-363-3P were significantly lower in high SNAI2 level GISTs group compared with low SNAI2 level GISTs group

Article Snippet: Labeling and hybridization were performed in accordance with the protocols in the PhalanxBio miRNA microarray system.

Techniques: Microarray

Journal: Cancer Cell International

Article Title: Identification of upstream miRNAs of SNAI2 and their influence on the metastasis of gastrointestinal stromal tumors

doi: 10.1186/s12935-019-1006-8

Figure Lengend Snippet: SNAI2 levels after transfection of miRNA mimics and inhibitors. a , b MiR-200b-3p, miR-30c-1-3P and miR-363-3P could downregulate the SNAI2 in both protein and mRNA level

Article Snippet: Labeling and hybridization were performed in accordance with the protocols in the PhalanxBio miRNA microarray system.

Techniques: Transfection

Journal: Cancer Cell International

Article Title: Identification of upstream miRNAs of SNAI2 and their influence on the metastasis of gastrointestinal stromal tumors

doi: 10.1186/s12935-019-1006-8

Figure Lengend Snippet: The invasiveness of GIST cells after treated with miRNA-mimics and miRNA-inhibitors. The invasiveness of GISTs cells were downregulated by miRNAs mimics and upregulated by inhibitors of 3 miRNAs, miR-200b-3p, miR-30c-1-3P and miR-363-3P

Article Snippet: Labeling and hybridization were performed in accordance with the protocols in the PhalanxBio miRNA microarray system.

Techniques:

Journal: Cancer Cell International

Article Title: Identification of upstream miRNAs of SNAI2 and their influence on the metastasis of gastrointestinal stromal tumors

doi: 10.1186/s12935-019-1006-8

Figure Lengend Snippet: Luciferase reporter assays. Transfection of miRNA mimics of miR-200b-3p, miR-30c-1-3P, miR-363-3P resulted in a decrease in luciferase signal to from 73 to 83% of that in the negative control

Article Snippet: Labeling and hybridization were performed in accordance with the protocols in the PhalanxBio miRNA microarray system.

Techniques: Luciferase, Transfection, Negative Control

Journal: Cancer Cell International

Article Title: Identification of upstream miRNAs of SNAI2 and their influence on the metastasis of gastrointestinal stromal tumors

doi: 10.1186/s12935-019-1006-8

Figure Lengend Snippet:

Article Snippet: Labeling and hybridization were performed in accordance with the protocols in the PhalanxBio miRNA microarray system.

Techniques:

Journal: Cancer Cell International

Article Title: Identification of upstream miRNAs of SNAI2 and their influence on the metastasis of gastrointestinal stromal tumors

doi: 10.1186/s12935-019-1006-8

Figure Lengend Snippet:

Article Snippet: Labeling and hybridization were performed in accordance with the protocols in the PhalanxBio miRNA microarray system.

Techniques:

Journal: Diabetes

Article Title: Alterations in MicroRNA Expression Contribute to Fatty Acid–Induced Pancreatic β-Cell Dysfunction

doi: 10.2337/db07-1252

Figure Lengend Snippet: miR34a and miR146 expression is increased in pancreatic islets of db / db mice. Pancreatic islets were isolated from four wild-type mice and five diabetic db / db mice. Blood glucose level was 6.8 ± 0.4 mmol/l in control animals and 21.8 ± 1.4 mmol/l in db/db mice ( P < 0.001). RNA extracts from each islet preparation were analyzed by quantitative RT-PCR for the expression of the indicated miRNAs. Data are expressed as percent U6 content measured in the same sample.

Article Snippet: For microarray profiling, total RNAs were sent to the miRNA Microarray Service of LC Sciences (Houston, TX).

Techniques: Expressing, Isolation, Control, Quantitative RT-PCR

Journal: RNA

Article Title: Shifts in temperature within the physiologic range modify strand-specific expression of select human microRNAs

doi: 10.1261/rna.049122.114

Figure Lengend Snippet: Microarray and nCounter analysis of the effects of incubation temperature on miRNA expression pattern in human SAECs. ( A ) HEATMAP of selected miRNAs detected by microarray in hSAECs following 24 h incubation at 32°C, 37°C, or 39.5°C in the absence or presence of 1 ng/mL rhTNFα. ( B , C ) Microarray data for seven miRNAs exhibiting temperature-dependent expression and nCounter data for miR1260a expression expressed as fold-change versus 37°C cells in the absence ( B ) or presence ( C ) of TNFα. Mean ± SEM. (*) P < 0.01 versus 37°C. N = 3 for microarray and 4 for nCounter.

Article Snippet: MiRNA microarray analysis was performed by Genome Explorations.

Techniques: Microarray, Incubation, Expressing

Journal: RNA

Article Title: Shifts in temperature within the physiologic range modify strand-specific expression of select human microRNAs

doi: 10.1261/rna.049122.114

Figure Lengend Snippet: Quantitative RT-PCR confirmation of temperature effects on miRNA expression pattern in human SAECs. Human SAECs from two lots were incubated for 24 h at 32°C, 37°C, or 39.5°C without or with 1 ng/mL rhTNFα. Total RNA was collected and levels ( A ) hsa-miR-92a-1-5p, ( B ) hsa-miR-27b-5p, ( C ) hsa-miR-1260a, ( D ) hsa-miR-27a-5p, ( E ) hsa-miR-181a-3p, and ( F ) hsa-miR-18b were analyzed by qRT-PCR as described in Materials and Methods and expressed as a fold-change versus 37°C cells without TNFα. The right -hand axis displays the total expression level in copies per cell, which was calculated as described in Materials and Methods. Mean ± SEM. (*) P < 0.05 versus 37°C; (†) P < 0.05 versus 39.5°C; (§) P < 0.05 versus 37°C with TNFα; (¶) P < 0.05 versus 39.5°C with TNFα, n = 4. The temperature-responsive miRNAs were cloned into T-Vector and sequenced ( inset ).

Article Snippet: MiRNA microarray analysis was performed by Genome Explorations.

Techniques: Quantitative RT-PCR, Expressing, Incubation, Clone Assay, Plasmid Preparation

Journal: RNA

Article Title: Shifts in temperature within the physiologic range modify strand-specific expression of select human microRNAs

doi: 10.1261/rna.049122.114

Figure Lengend Snippet: Quantitative RT-PCR analysis of temperature effects on pri-miRNA, pre-miRNA, and opposite strand expression pattern in human SAECs. Human SAECs from two lots were incubated for 24 h at 32°C, 37°C, or 39.5°C without rhTNFα. Total RNA was collected and levels of the temperature-responsive strand, the sister strand, the pri-miRNA, and the pre-miRNA for ( A ) hsa-miR-92a-1, ( B ) hsa-miR-27b, ( C ) hsa-miR-27a, and ( D ) hsa-miR-181a were analyzed by qRT-PCR as described in Materials and Methods and are expressed relative to expression of each in 37°C hSEAECs. Mean ± SEM, n = 4. The P -values from one-way ANOVA are indicated.

Article Snippet: MiRNA microarray analysis was performed by Genome Explorations.

Techniques: Quantitative RT-PCR, Expressing, Incubation

Journal: RNA

Article Title: Shifts in temperature within the physiologic range modify strand-specific expression of select human microRNAs

doi: 10.1261/rna.049122.114

Figure Lengend Snippet: Clinically relevant temperature change-induced expression of miRNAs alters the PKCα protein levels. ( A ) Human SAECs were incubated at 32°C, 37°C, or 39.5°C for 24 h and cell lysates were immunoblotted for PKCα. Representative of four similar blots and quantified band densities for PKCα normalized to β-tubulin and expressed as percent of levels in 37°C cells. ( B ) HEK 293T cells were transfected either with a combination of miRNA inhibitors against hsa-miR-27b-5p, hsa-miR-1260a, and hsa-miR-92a-1-5p or an equal concentration of a non-targeting scrambled-sequence inhibitor control. Transfected and untransfected cells were incubated at 32°C, 37°C, or 39.5°C for 24 h and immunoblotted for PKCα. A representative immunoblot and quantified band densities from four similar blots normalized to ß-tubulin and expressed as percent of levels in untreated 37°C cells are shown. Mean ± SEM. (*) P < 0.05, (†) P < 0.04 versus untreated 37°C and 39.5°C cells and miRNA inhibitor-treated 32°C cells, (¶) P < 0.02 versus untreated 39.5°C cells; n = 4.

Article Snippet: MiRNA microarray analysis was performed by Genome Explorations.

Techniques: Expressing, Incubation, Transfection, Concentration Assay, Sequencing, Control, Western Blot

Journal: RNA

Article Title: Shifts in temperature within the physiologic range modify strand-specific expression of select human microRNAs

doi: 10.1261/rna.049122.114

Figure Lengend Snippet: Functional analysis of the PKCα 3′ UTR binding sites for the temperature-sensitive miRNAs. ( A ) The putative binding sequences for hsa-miR-27b-5p, hsa-miR-1260a, and hsa-miR-92a-1-5p in PKCα 3′ UTR are shown. ( B ) Sequence of pmirGLO-PKCα-WT or pmirGLO-PKCα-Mut generated by cloning repeats of the putative miR binding sites or mutated sequences, respectively, into pmirGLO. The mutated nucleotides in each miR target sequence is indicated by black text for pmirGLO-PKCα-Mut. ( C ) HEK 293T cells were transfected with a combination of synthetic miRNA mimics for hsa-miR-27b-5p, hsa-miR-1260a, and hsa-miR-92a-1-5p or an equal concentration of non-targeting scrambled control mimic and pmirGLO-PKCα-WT (wild-type) or pmirGLO-PKCα-Mut (mutant), incubated at 37°C for 24 h, and dual luciferase assays were performed. Mean ± SEM. (*) P < 0.05, n = 4.

Article Snippet: MiRNA microarray analysis was performed by Genome Explorations.

Techniques: Functional Assay, Binding Assay, Sequencing, Generated, Cloning, Transfection, Concentration Assay, Control, Mutagenesis, Incubation, Luciferase

Journal: RNA

Article Title: Shifts in temperature within the physiologic range modify strand-specific expression of select human microRNAs

doi: 10.1261/rna.049122.114

Figure Lengend Snippet: Effect of incubation temperature on cell-cycle progression. ( A ) Human SAECs were serum-starved for 24 h at 37°C, then incubated at 32°C, 37°C, or 39.5°C for an additional 24 h in serum-containing growth medium, stained with propidium iodide, and the proportion of cells in G1, S, and G2 phases was determined using flow cytometry. ( B ) HEK 293T cells were transfected with a combination of synthetic miRNA inhibitors for hsa-miR-27b-5p, hsa-miR-1260a, and hsa-miR-92a-1-5p or an equal concentration of non-targeting scrambled control inhibitor. After 24 h recovery, the cells were serum-starved for 24 h at 37°C, then incubated in serum-containing growth medium at 32°C or 37°C for 24 h, and cell-cycle analysis performed and the G1:S ratio calculated. Mean ± SEM, n = 5, (*) P < 0.05 in A . P -values are indicated in B .

Article Snippet: MiRNA microarray analysis was performed by Genome Explorations.

Techniques: Incubation, Staining, Flow Cytometry, Transfection, Concentration Assay, Control, Cell Cycle Assay