Journal: Sarcoma

Article Title: miR-125b and miR-100 Are Predictive Biomarkers of Response to Induction Chemotherapy in Osteosarcoma

doi: 10.1155/2016/1390571

Figure Lengend Snippet: Expression of six miRNAs was significantly different between poor and good responders, as measured by microarray analysis of open biopsy samples (a). qRT-PCR (b–g) of these six miRNAs confirmed that miRNA-125b (b) and miR-100 (c) were expressed at significantly higher levels in chemoresistant patients.

Article Snippet: Formalin-fixed paraffin-embedded samples were sectioned at 10 μ m, and total RNA was extracted from several of such slices using the miRNeasy FFPE Kit (Qiagen). miRNA expression profiles of frozen samples were obtained by hybridizing total RNA to the Agilent human miRNA Microarray V3 (021827, 8 × 15 K, v12.0, Agilent Technologies, Santa Clara, CA), following the manufacturer's instructions.

Techniques: Expressing, Microarray, Quantitative RT-PCR

Journal: Microbial Cell Factories

Article Title: Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain

doi: 10.1186/s12934-016-0434-6

Figure Lengend Snippet: Ratios of final liquid concentrations of fermentative aromas produced by Affinity™ ECA5 and Lalvin EC1118 ® . These ratios were calculated from 16 fermentation experiments with different temperature, nitrogen and lipid contents. If the ratio value is higher than one, the compound is considered as overproduced by the evolved strain. PR propanol, ISO isobutanol, IA isoamyl alcohol, HE hexanol, ME methionol, PHE 2-phenylethanol, EA ethyl acetate, ISA isobutyl acetate, AA amyl acetate, IAA isoamyl acetate, PEA 2-phenylethylacetate, PA propanoic acid, BA butanoic acid, IBA isobutanoic acid, IVA isovaleric acid, MBA 2-methylbutanoic acid, VA valeric acid, HA hexanoic acid, OA octanoic acid, DA decanoic acid, EB ethyl butanoate, DS diethyl succinate, EL ethyl lactate, EV ethyl valerate, EH ethyl hexanoate, EO ethyl octanoate, ED ethyl decanoate, EDD ethyl dodecanoate

Article Snippet: We used the Agilent 8 × 15 k gene expression microarrays (Design ID 038619 with 40 EC1118-specific genes, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions.

Techniques: Produced

Journal: Microbial Cell Factories

Article Title: Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain

doi: 10.1186/s12934-016-0434-6

Figure Lengend Snippet: Timing of exhaustion of each nitrogen source (Point.AA0) expressed in terms of consumed sugar (g/L) for each fermentation condition. Lalvin EC1118 ® -SM70-2 mg/l of phytosterols ( closed orange circle ); Lalvin EC1118 ® -SM70-8 mg/l of phytosterols ( closed beige circle ); Lalvin EC1118 ® -SM330-2 mg/l of phytosterols ( closed blue circle ); Lalvin EC1118 ® -SM330-8 mg/l of phytosterols ( closed purple circle ); Affinity™ ECA5-SM70-2 mg/l of phytosterols ( closed orange triangle ); Affinity™ ECA5-SM70-8 mg/l of phytosterols ( closed beige triangle ); Affinity™ ECA5-SM330-2 mg/l of phytosterols ( closed blue triangle ); Affinity™ ECA5-SM330-8 mg/l of phytotserols ( closed purple triangle ). Gly glycine, Tyr tyrosine, Trp Tryptophan, Ala alanine, Arg arginine, Val valine, NH4 ammonium, Phe phenylalanine, Gln glutamine, Ser serine, Ile isoleucine, Met methionine, His histidine, Leu leucine, Glu glutamate, Thr threonine, Asp aspartate

Article Snippet: We used the Agilent 8 × 15 k gene expression microarrays (Design ID 038619 with 40 EC1118-specific genes, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions.

Techniques:

Journal: Microbial Cell Factories

Article Title: Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain

doi: 10.1186/s12934-016-0434-6

Figure Lengend Snippet: Total production of fermentative aromas for each fermentation condition

Article Snippet: We used the Agilent 8 × 15 k gene expression microarrays (Design ID 038619 with 40 EC1118-specific genes, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions.

Techniques: Concentration Assay

Journal: Microbial Cell Factories

Article Title: Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain

doi: 10.1186/s12934-016-0434-6

Figure Lengend Snippet: Changes in the specific rates of total production of isoamyl acetate in SM70 ( a ) or SM330 ( b ). Lalvin EC1118 ® −2 mg/L of phytosterol ( blue ); Lalvin EC1118 ® −8 mg/L of phytosterol ( light blue ); Affinity™ ECA5–2 mg/L of phytosterol ( red ); Affinity™ ECA5–8 mg/L of phytosterol ( pink )

Article Snippet: We used the Agilent 8 × 15 k gene expression microarrays (Design ID 038619 with 40 EC1118-specific genes, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions.

Techniques:

Journal: Microbial Cell Factories

Article Title: Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain

doi: 10.1186/s12934-016-0434-6

Figure Lengend Snippet: Production yields of acetate ester from its higher alcohol precursor

Article Snippet: We used the Agilent 8 × 15 k gene expression microarrays (Design ID 038619 with 40 EC1118-specific genes, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions.

Techniques:

Journal: Microbial Cell Factories

Article Title: Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain

doi: 10.1186/s12934-016-0434-6

Figure Lengend Snippet: Focus on the bioconversion of isoamyl alcohol to isoamyl acetate. a Changes in total isoamyl acetate production as a function of total isoamyl alcohol production in SM330 with 8 mg/L of phytosterols for Lalvin EC1118 ® ( blue ) and Affinity™ ECA5 ( red ). The arrows indicate the timing of sampling for transcriptomic analyses. b Changes in total isoamyl acetate production as a function of total isoamyl alcohol production subsequently to phytosterol additions for Lalvin EC1118 ® ( blue ) and Affinity™ ECA5 ( purple and red ). For Lalvin EC1118 ® , despite phytosterol additions, bioconversion yield between the two compounds remains identical: 0.0241 (R 2 = 0.947). For Affinity™ ECA5, four linear phases are identified; their yields of conversion are 0.0689 (R 2 = 0.990); 0.0367 (R 2 = 0.966); 0.0696 (R 2 = 0.991); and 0.0351 (R 2 = 0.955)

Article Snippet: We used the Agilent 8 × 15 k gene expression microarrays (Design ID 038619 with 40 EC1118-specific genes, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions.

Techniques: Sampling

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: CircRNA_103827 and circRNA_104816 expressions in granulosa cells according to patients’ clinical characteristics.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Biomarker Discovery

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: CircRNA_103827 and circRNA_104816 expression levels in granulosa cells according to ART outcomes.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Expressing

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: The top 10 significantly differentially expressed circRNAs between young and older women ranked by fold change.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques:

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: Comparison of candidate circRNAs (circRNA_103829, circRNA_10827, circRNA_104816, circRNA_101889, circRNA_103828, circRNA_100833, circRNA_104852, circRNA_103611) expression levels in granulosa cells from additional young (n = 20) and older (n = 20) women by qRT-PCR. YA, women with young age (≤ 30 years); AA, women with advanced age (≥ 38 years). P values were calculated by Mann-Whitney U test. Relative expressions were analyzed by 2 -ΔΔCt method which was normalized to GAPDH. For each box plotting, the central mark represents the median, the edges of the box represent the 25 th and 75 th percentiles, and the whiskers are the most extreme data points not considered outliers.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Comparison, Expressing, Quantitative RT-PCR, MANN-WHITNEY

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: ( A-E ) circRNA_103827 expression levels in granulosa cells according to (A) serum AMH levels, (B) AFC, (C) retrieved oocytes, (D) top quality embryos and (E) top quality embryo percentage. ( F-J ) circRNA_104816 expression levels in granulosa cells according to (F) serum AMH levels, (G) AFC, (H) retrieved oocytes, (I) top quality embryos and (J) top quality embryo percentage.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Expressing

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: ROC analysis to evaluate predictive performance of circRNA_103827, circRNA_104816 expressions in granulosa cells and top quality embryo proportion for ( A-C ) clinical pregnancy outcomes, as well as for ( D-F ) live births. AUC, area under the ROC curve.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques:

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: (A) CircRNA_103827/circRNA_104816 targeted “Top 5” miRNA-gene network was portrayed based on sequence-pairing prediction. A pink round node represents a gene, a blue square represents miRNA, and a yellow diamond represents a circRNA. Overlapping genes of both circRNAs in this interactive network were ANKRD20A9P , XIST and KCNQ1OT1 . (B) GO and (C) KEGG pathway analysis of circRNA_103827 and circRNA_104816 predicted target genes. The top 10 significantly enriched activities and their scores (negative logarithm of P value) were listed in the X-axis and the Y-axis, respectively.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Sequencing

Journal: Frontiers in Immunology

Article Title: Experimental Demyelination and Axonal Loss Are Reduced in MicroRNA-146a Deficient Mice

doi: 10.3389/fimmu.2018.00490

Figure Lengend Snippet: Differential expression of microRNAs (miRNAs) in the corpus callosum of mice during experimental demyelination and remyelination. Using microarray and validation by quantitative PCR (qPCR), three miRNAs, miR-146a (A) , miR-193a (B) and miR-181b (C) were differentially regulated in response to CPZ exposure in the corpus callosum. * p < 0.05, ** p < 0.01, *** p < 0.001, n = 5–8 in each group, one-way ANOVA, mean ± SEM. Abbreviation: C: un-manipulated controls covering ages of mice used in the de- and remyelinating experiments, 4wD: 4 weeks demyelination. 2dR: 2 days (acute) remyelination, 2wR: 2 weeks (full) remyelination.

Article Snippet: For microRNA profiling, the Agilent Mouse miRNA Microarray Kit (G4472A, 8 × 15k) was applied according to the manufacturer’s instruction (version 1.0) with 100–100 ng quality-checked total RNA.

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

Journal: Frontiers in Immunology

Article Title: Experimental Demyelination and Axonal Loss Are Reduced in MicroRNA-146a Deficient Mice

doi: 10.3389/fimmu.2018.00490

Figure Lengend Snippet: Expression of experimentally validated miR-146a target genes and proteins in response to CPZ exposure in wild-type and miR-146-deficient mice. (A) Expression of miR-146a target genes (miRTarBase) among 1,239 differentially expressed genes in the corpus callosum in response to CPZ exposure determined by a 4 × 44K Agilent Whole Mouse Genome Microarray (NCBI Gene Expression Omnibus with accession GSE100663). (B) The protein expression of validated miR-146a target genes SMAD4 and SNAP25 were downregulated in the corpus callosum of miR-146a KO mice compared to WT mice by liquid chromatography mass spectrometry in response to CPZ. (C) SNAP25 and (D) SMAD4 in corpus callosum lysates of miR-146a KO and WT mice in response to CPZ examined by ELISA. * p < 0.05, ** p < 0.01, *** p < 0.001, n = 8–4 in each group, mean ± SEM. Abbreviations: C: un-manipulated controls, 4wD: 4 weeks demyelination. 2dR: 2 days (acute) remyelination, 2wR: 2 weeks (full) remyelination.

Article Snippet: For microRNA profiling, the Agilent Mouse miRNA Microarray Kit (G4472A, 8 × 15k) was applied according to the manufacturer’s instruction (version 1.0) with 100–100 ng quality-checked total RNA.

Techniques: Expressing, Microarray, Liquid Chromatography, Mass Spectrometry, Enzyme-linked Immunosorbent Assay