Journal: BMC Genomics

Article Title: MicroRNA-146 function in the innate immune transcriptome response of zebrafish embryos to Salmonella typhimurium infection

doi: 10.1186/1471-2164-14-696

Figure Lengend Snippet: Microarray analysis of miRNA expression during bacterial infections of zebrafish embryos and adult fish. The Venn diagrams show the miRBase annotated miRNAs or miRNA star sequences (*) that were up-regulated (A) or down-regulated (B) during infection of zebrafish embryos with S. typhimurium SL1027 or infection of adult zebrafish with M. marinum Mma20. S. typhimurium infection of embryos was performed by micro-injection into the caudal vein at 28 hpf and miRNA expression was analyzed at 8 hpi in comparison with control embryos mock-injected with PBS. Adult zebrafish were infected with M. marinum by intraperitoneal infection and miRNA expression at 6 dpi was compared with PBS-injected controls.

Article Snippet: Custom-designed 8×15 k microarray slides were ordered from Agilent Technologies.

Techniques: Microarray, Expressing, Infection, Injection

Journal: Frontiers in Genetics

Article Title: Systematic Identification of circRNA–miRNA–mRNA Regulatory Network in Esophageal Squamous Cell Carcinoma

doi: 10.3389/fgene.2021.580390

Figure Lengend Snippet: Differentially expressed circRNAs in the plasma of ESCC patients.

Article Snippet: The resulting hybridization solution (50 μl) was placed in a gasket slide, which was then assembled with the Arraystar Human CircRNA Microarray Slides V2.0 (8 × 15K; Arraystar), with a total of 13,617 circRNA probes on the microarray, according to the kit’s instructions.

Techniques: Clinical Proteomics

Journal: Frontiers in Genetics

Article Title: Systematic Identification of circRNA–miRNA–mRNA Regulatory Network in Esophageal Squamous Cell Carcinoma

doi: 10.3389/fgene.2021.580390

Figure Lengend Snippet: Differentially expressed circRNAs in ESCC patients. (A) The scatter plot of differentially expressed circRNAs. Green lines represent fold change of 2.0. (B) Volcano plot of differentially expressed circRNAs. The green vertical lines correspond to a fold change of 2.0, and the green horizontal line corresponds to a P -value of 0.05. (C) Hierarchical clustering of differentially expressed circRNAs. Each column represents a sample and each row represents a circRNA. The color reflects the expression level of circRNAs and changes from red (high) to black (medium) to green (low). (D) Bar plot shows the distributions of the differentially expressed circRNAs in human chromosomes.

Article Snippet: The resulting hybridization solution (50 μl) was placed in a gasket slide, which was then assembled with the Arraystar Human CircRNA Microarray Slides V2.0 (8 × 15K; Arraystar), with a total of 13,617 circRNA probes on the microarray, according to the kit’s instructions.

Techniques: Expressing

Journal: Frontiers in Genetics

Article Title: Systematic Identification of circRNA–miRNA–mRNA Regulatory Network in Esophageal Squamous Cell Carcinoma

doi: 10.3389/fgene.2021.580390

Figure Lengend Snippet: CircRNA–miRNA–mRNA interaction network in ESCC. CircRNAs are represented by diamonds; miRNAs are shown as triangles; the DEGs are represented by ellipses. Red represents upregulated expression, and blue color represents downregulated expression. circRNA, circular RNA; miRNA, microRNA; ESCC, esophageal squamous cell carcinoma; DEGs, differentially expressed genes.

Article Snippet: The resulting hybridization solution (50 μl) was placed in a gasket slide, which was then assembled with the Arraystar Human CircRNA Microarray Slides V2.0 (8 × 15K; Arraystar), with a total of 13,617 circRNA probes on the microarray, according to the kit’s instructions.

Techniques: Expressing

Journal: Frontiers in Genetics

Article Title: Systematic Identification of circRNA–miRNA–mRNA Regulatory Network in Esophageal Squamous Cell Carcinoma

doi: 10.3389/fgene.2021.580390

Figure Lengend Snippet: Sub-network of circRNAs, miRNAs, and hub genes. circRNAs are represented by diamonds; miRNAs are shown as triangles; hub genes are represented by ellipses. Red represents upregulated expression, and blue color represents downregulated expression. circRNA, circular RNA; miRNA, microRNA.

Article Snippet: The resulting hybridization solution (50 μl) was placed in a gasket slide, which was then assembled with the Arraystar Human CircRNA Microarray Slides V2.0 (8 × 15K; Arraystar), with a total of 13,617 circRNA probes on the microarray, according to the kit’s instructions.

Techniques: Expressing

Journal: Nucleic Acids Research

Article Title: Multifactorial control of the expression of a CRISPR-Cas system by an extracytoplasmic function σ/anti-σ pair and a global regulatory complex

doi: 10.1093/nar/gky475

Figure Lengend Snippet: Myxococcus xanthus CRISPR-Cas systems and the DdvS regulon. ( A ) The three M. xanthus CRISPR-Cas systems and their location in the 9.14 Mb circular chromosome. Colored rectangles indicate the cas gene clusters of each system, whose type is labeled below. The four CRISPR arrays and the number of spacers in each are indicated. Vertical blue and red bars indicate genes ddvS and ddvA , respectively, and the unfilled bars are for genes encoding hypothetical proteins. The arrow points in the direction of transcription. ( B ) Venn diagram representation of microarray transcriptomic data for genes upregulated in the ddvA − strain (MR1543) relative to the WT strain (DK1622; blue), and downregulated in the ddvA − Δ carD strain (MR1544) or in the ddvA − Δ carG strain (MR1545) relative to MR1543 (green and pink, respectively). Genes and microarray data with differential expression are listed in Table and .

Article Snippet: An 8 × 15k microarray platform format (8 microarrays per slide each with 15 000 probes) was designed using eArray ( https://earray.chem.agilent.com/earray/ ; Agilent Technologies, Santa Clara, USA), and in each microarray spot 7316 out of the 7441 annotated genes in the M. xanthus genome (excluding 79 RNA genes, 43 pseudogenes and genes with duplicate annotations) were represented by 60-bp amplicon probes (in duplicate and distributed randomly per microarray, with empty array features filled with randomly chosen amplicon probes).

Techniques: CRISPR, Labeling, Microarray, Expressing

Journal: bioRxiv

Article Title: Kar4 is Required for the Normal Pattern of Meiotic Gene Expression

doi: 10.1101/2023.01.29.526097

Figure Lengend Snippet: (A) Heatmap of microarray data across the first 16 hours post induction of meiosis in wild type and kar4 Δ/Δ. Expression was normalized to wild type pre-induction of sporulation (t=0). Genes were clustered in Cluster3.0 and the heatmaps were constructed with Java TreeView. Red boxes highlight three clusters of altered late gene expression. (B) Table of the top gene ontology terms of the three clusters (A, B, and C) of impacted genes in kar4 Δ/Δ. (C) Heatmap of RNA-seq data showing the expression level of key meiotic regulators in wild type and kar4 Δ/Δ.

Article Snippet: Labeled cRNA was fragmented and allowed to hybridize to agilent microarray slides (8×15k, AMADID:017566) for 17 hours at 65°C and 20 RPM.

Techniques: Microarray, Expressing, Construct, RNA Sequencing Assay

Journal: bioRxiv

Article Title: Kar4 is Required for the Normal Pattern of Meiotic Gene Expression

doi: 10.1101/2023.01.29.526097

Figure Lengend Snippet: (A) Gene Ontology results of the YEASTTRACT list of Ime1p dependent genes (Left) and of the gold-standard list of Ime1p dependent genes found in this study (Right). (B) Heatmap of microarray data showing the expression profile of Ime1p dependent genes in wild type and kar4 Δ/Δ. The black box highlights the reduced and delayed expression of a set of these genes in kar4 Δ/Δ. (C) List of Kar4p dependent genes that are also Ime1p dependent (Left) and the top gene ontology terms of those genes (Right).

Article Snippet: Labeled cRNA was fragmented and allowed to hybridize to agilent microarray slides (8×15k, AMADID:017566) for 17 hours at 65°C and 20 RPM.

Techniques: Microarray, Expressing

Journal: bioRxiv

Article Title: Kar4 is Required for the Normal Pattern of Meiotic Gene Expression

doi: 10.1101/2023.01.29.526097

Figure Lengend Snippet: (A) Heatmap of microarray data of Ime1p dependent genes after IME1 overexpression in wild type and kar4 Δ/Δ. Black box highlights the ability of IME1 overexpression to rescue the defect in expression of these genes seen in kar4 Δ/Δ without IME1 overexpression. (B) Heatmap of microarray data in wild type and kar4 Δ/Δ with IME1 overexpressed (Left) and IME1 and RIM4 overexpressed (Right). Red boxes highlight the three gene clusters that show a defect in expression in kar4 Δ/Δ after IME1 overexpression but are rescued to some extent by additionally overexpressing RIM4 . (C) NDT80 RNA-seq normalized counts from wild type and kar4 Δ/Δ with IME1 overexpressed and from kar4 Δ/Δ with IME1 and RIM4 overexpressed. Counts were normalized using the standard normalization method in DESeq2. Error bars represent standard deviation between two biological replicates.

Article Snippet: Labeled cRNA was fragmented and allowed to hybridize to agilent microarray slides (8×15k, AMADID:017566) for 17 hours at 65°C and 20 RPM.

Techniques: Microarray, Over Expression, Expressing, RNA Sequencing Assay, Standard Deviation

Journal: The Journal of International Medical Research

Article Title: Potential mechanism of circRNA_000585 in cholangiocarcinoma

doi: 10.1177/03000605211024501

Figure Lengend Snippet: Primer details for quantitative real-time reverse transcription–polymerase chain reaction of circRNA_000585.

Article Snippet: The labelled cRNA mixture was diluted by adding 25 μl of 2× hybridization buffer, and 50 μl of the hybridization solution was transferred into the gasket slide, which was then assembled onto the circRNA expression microarray slide (Arraystar Human circRNA Array V2 [8 × 15 K]).

Techniques: Reverse Transcription Polymerase Chain Reaction, Sequencing, Amplification

Journal: The Journal of International Medical Research

Article Title: Potential mechanism of circRNA_000585 in cholangiocarcinoma

doi: 10.1177/03000605211024501

Figure Lengend Snippet: Heatmap of circular (circ)RNA expression levels in cholangiocarcinoma (CCA) tumour specimens (P1–3) and matched para-cancer specimens (C1–3) from three patients with CCA. Each block represents different circRNA expression levels (red represents high expression; green represents low expression).

Article Snippet: The labelled cRNA mixture was diluted by adding 25 μl of 2× hybridization buffer, and 50 μl of the hybridization solution was transferred into the gasket slide, which was then assembled onto the circRNA expression microarray slide (Arraystar Human circRNA Array V2 [8 × 15 K]).

Techniques: RNA Expression, Blocking Assay, Expressing

Journal: The Journal of International Medical Research

Article Title: Potential mechanism of circRNA_000585 in cholangiocarcinoma

doi: 10.1177/03000605211024501

Figure Lengend Snippet: Fold change in circular (circ)RNA expression levels in cholangiocarcinoma (CCA) tumour specimens and matched para-cancer specimens from three patients with CCA. (A) scatter plot (dots above the upper line represent fold-change >1.5, dots below the lower line represent fold-change >–1.5); and (B) volcano plot of circRNA expression (red dots represent fold-change >1.5 or >–1.5).

Article Snippet: The labelled cRNA mixture was diluted by adding 25 μl of 2× hybridization buffer, and 50 μl of the hybridization solution was transferred into the gasket slide, which was then assembled onto the circRNA expression microarray slide (Arraystar Human circRNA Array V2 [8 × 15 K]).

Techniques: RNA Expression, Expressing

Journal: The Journal of International Medical Research

Article Title: Potential mechanism of circRNA_000585 in cholangiocarcinoma

doi: 10.1177/03000605211024501

Figure Lengend Snippet: Vertical scatter plot showing elevated circRNA_000585 expression in cholangiocarcinoma (CCA) tumour tissue versus matched para-cancer tissue from 15 patients with CCA (central horizontal line represents mean, upper and lower horizonal lines represent SD; P = 0.003 between groups).

Article Snippet: The labelled cRNA mixture was diluted by adding 25 μl of 2× hybridization buffer, and 50 μl of the hybridization solution was transferred into the gasket slide, which was then assembled onto the circRNA expression microarray slide (Arraystar Human circRNA Array V2 [8 × 15 K]).

Techniques: Expressing

Journal: The Journal of International Medical Research

Article Title: Potential mechanism of circRNA_000585 in cholangiocarcinoma

doi: 10.1177/03000605211024501

Figure Lengend Snippet: Association between circRNA_000585 expression and clinicopathological characteristics in 15 patients with cholangiocarcinoma.

Article Snippet: The labelled cRNA mixture was diluted by adding 25 μl of 2× hybridization buffer, and 50 μl of the hybridization solution was transferred into the gasket slide, which was then assembled onto the circRNA expression microarray slide (Arraystar Human circRNA Array V2 [8 × 15 K]).

Techniques: Expressing

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium

doi: 10.3389/fbioe.2020.00047

Figure Lengend Snippet: Weighed Venn diagrams of the number of transcripts and proteins whose concentration was significantly altered in B. megaterium growing in M9 minimal medium with 0.6, 1.2 and 1.8 M NaCl, respectively. A gene or a transcript was considered significantly regulated when its concentration was either 1.75-fold higher or lower compared to 0 M NaCl. Gene expression was determined by microarray analysis and intracellular proteins were identified and quantified by proteome analysis using LC-IMS E .

Article Snippet: Then, samples were loaded on an Agilent microarray slide (8 × 15 K custom made) comprising 2–3 60 bp DNA probes for each gene of B. megaterium and hybridization took place for 17 h at 65°C and 10 min –1 in a hybridization oven (Agilent Technologies, Waldbronn, Germany).

Techniques: Concentration Assay, Expressing, Microarray

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium

doi: 10.3389/fbioe.2020.00047

Figure Lengend Snippet: Pox route and overflow metabolism in B. megaterium DSM319 growing in M9 minimal medium supplemented with different NaCl concentrations. Purple arrows correspond to reactions of the Pox route while red arrows indicate organic acid secretions. Gene expression was determined by microarray analysis using purified RNA samples obtained from four biological replicates. Intracellular proteins were identified and quantified by proteome analysis using LC-IMS E for cells originating from three biological replicates. Values are indicated as fold change compared to expression in cells grown at 37°C in M9 minimal medium without additional NaCl supplementation. Metabolites were quantified by mass spectroscopy. Ach: acetyl-CoA hydrolase; AckA: acetate kinase; AcsA: acetyl-CoA synthetase; Ldh: lactate dehydrogenase; Pdh: pyruvate dehydrogenase; Pox: pyruvate oxidase; Pta: phosphate acetyltransferase.

Article Snippet: Then, samples were loaded on an Agilent microarray slide (8 × 15 K custom made) comprising 2–3 60 bp DNA probes for each gene of B. megaterium and hybridization took place for 17 h at 65°C and 10 min –1 in a hybridization oven (Agilent Technologies, Waldbronn, Germany).

Techniques: Expressing, Microarray, Purification, Mass Spectrometry

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium

doi: 10.3389/fbioe.2020.00047

Figure Lengend Snippet: Integrated view of the response of the central carbon metabolism of B. megaterium DSM319 to ionic osmotic stress. Transcriptome and proteome data are indicated as the determined fold change compared to cultivation in minimal medium without NaCl supplementation. Gene expression was determined by microarray analysis using purified RNA samples obtained from four biological replicates. Intracellular proteins were identified and quantified by proteome analysis using LC-IMS E for cells originating from three replicates. Bar plots represent intracellular metabolite concentrations in μmol g CDW –1 . Intracellular metabolite concentrations were determined by LC-MS/MS using a differential method, i.e., subtracting extracellular metabolite concentration from the global metabolite concentration.

Article Snippet: Then, samples were loaded on an Agilent microarray slide (8 × 15 K custom made) comprising 2–3 60 bp DNA probes for each gene of B. megaterium and hybridization took place for 17 h at 65°C and 10 min –1 in a hybridization oven (Agilent Technologies, Waldbronn, Germany).

Techniques: Expressing, Microarray, Purification, Liquid Chromatography with Mass Spectroscopy, Concentration Assay

Journal: Biological Research

Article Title: Microarray profiling and functional analysis of differentially expressed plasma exosomal circular RNAs in Graves’ disease

doi: 10.1186/s40659-020-00299-y

Figure Lengend Snippet: The list of differential expressed circRNAs in plasma exosome samples from patients with GD and healthy control subjects

Article Snippet: The circRNA expression microarray slide (AS-S-CR-H-V2.0, Arraystar Human circRNA Arrays V2, 8 × 15 K; Arraystar Inc.) was used.

Techniques: Clinical Proteomics, Control

Journal: Biological Research

Article Title: Microarray profiling and functional analysis of differentially expressed plasma exosomal circular RNAs in Graves’ disease

doi: 10.1186/s40659-020-00299-y

Figure Lengend Snippet: The circRNA-miRNA-mRNA regulatory network of hsa_circRNA_000102. CircRNA, miRNA, and mRNA are indicated as spheres in brown, red, blue color, respectively. CircRNA circular RNA, miRNA microRNA, mRNA messenger RNA

Article Snippet: The circRNA expression microarray slide (AS-S-CR-H-V2.0, Arraystar Human circRNA Arrays V2, 8 × 15 K; Arraystar Inc.) was used.

Techniques:

Journal: Biological Research

Article Title: Microarray profiling and functional analysis of differentially expressed plasma exosomal circular RNAs in Graves’ disease

doi: 10.1186/s40659-020-00299-y

Figure Lengend Snippet: The top 10 significantly enriched terms of biological process by GO analysis of hsa_circRNA_000102 associated genes. GO analysis was divided into three parts: biological process, cell component and molecular function

Article Snippet: The circRNA expression microarray slide (AS-S-CR-H-V2.0, Arraystar Human circRNA Arrays V2, 8 × 15 K; Arraystar Inc.) was used.

Techniques:

Journal: Biological Research

Article Title: Microarray profiling and functional analysis of differentially expressed plasma exosomal circular RNAs in Graves’ disease

doi: 10.1186/s40659-020-00299-y

Figure Lengend Snippet: The top 10 significant enriched pathways by KEGG pathway analysis of hsa_circRNA_000102 associated genes

Article Snippet: The circRNA expression microarray slide (AS-S-CR-H-V2.0, Arraystar Human circRNA Arrays V2, 8 × 15 K; Arraystar Inc.) was used.

Techniques: