Journal: Epigenetics

Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

doi: 10.1080/15592294.2016.1205176

Figure Lengend Snippet: Strategy to identify epigenetically downregulated genes in pN+ OSCC. On the left: published gene signatures predictive of pN-status in OSCC were used to identified significantly downregulated genes in pN+ OSCC. On the right: MethylCap-Seq was performed on 6 pN0 OSCC and pN+ OSCC. All reads of MCs in gene promoter regions were ranked according to the likelihood of differential methylation and an approximate FDR. The 5,000 MCs with the lowest FDR were further tested by Mann-Whitney-U. The MC associated with genes without annotated gene functions were excluded. In the middle: the gene signature and methylation data were compared to select epigenetically regulated genes in pN+ OSCC (n = 23). From these 23 genes, epigenetically downregulated genes in pN+ OSCC were selected. Based on the amount of mRNA downregulation, statistical differences in methylation between pN0 and pN+ OSCC, and positive and negative predictive value, RAB25 was selected as the most significantly epigenetically downregulated gene in pN+ OSCC compared to pN0 OSCC.

Article Snippet: Antigen retrieval was performed using a citrate buffer (10 mM citric acid, 0.05% Tween 20, pH 6.0) and heated in a microwave oven for 15 min at 300 W. Endogenous peroxidase was blocked with a 0.3% H 2 O 2 solution for 30 min at room temperature, followed by incubation with a mouse monoclonal antibody to human RAB25 clone 3F12F3 (Santa Cruz), diluted 1:50 in PBS with 1% bovine serum albumin, overnight at 4°C.

Techniques: Methylation, MANN-WHITNEY

Journal: Epigenetics

Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

doi: 10.1080/15592294.2016.1205176

Figure Lengend Snippet: Epigenetically downregulated genes in pN+ OSCC. All 14 potentially epigenetically downregulated genes in pN+ OSCC compared to pN0 OSCC after cross-reference of expression microarray and MethylCap-Seq data (see Fig. 1 ). The positive and negative predictive value of the reads for pN+ status, associated hypermethylation, read distribution between pN0 and pN+ OSCC, and predictive value of the methylation data are illustrated. P -value for the differential DNA methylation was calculated using the Mann-Whitney-U test. Positive and negative predictive value for the methylation status of all MCs were calculated as follows: OOSCC with a read count of ≥ 3 reads were considered true positives and OOSCC with a count read <3 were considered true negatives. Subsequently, the positive predictive value was then calculated as: (true positive pN+ OOSCC) / (true positive pN+ OOSCC + false positive pN0 OOSCC). Finally, the negative predictive value was calculated as: (true negative pN0 OOSCC) / (true negative pN0 OOSCC + false negative pN+ OOSCC).

Article Snippet: Antigen retrieval was performed using a citrate buffer (10 mM citric acid, 0.05% Tween 20, pH 6.0) and heated in a microwave oven for 15 min at 300 W. Endogenous peroxidase was blocked with a 0.3% H 2 O 2 solution for 30 min at room temperature, followed by incubation with a mouse monoclonal antibody to human RAB25 clone 3F12F3 (Santa Cruz), diluted 1:50 in PBS with 1% bovine serum albumin, overnight at 4°C.

Techniques: Expressing, Microarray, Methylation, DNA Methylation Assay, Mann-Whitney U-Test

Journal: Epigenetics

Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

doi: 10.1080/15592294.2016.1205176

Figure Lengend Snippet: RAB25 mRNA levels in relation with the 3 RAB25 TSS 450K probes (cg09243900, cg15896939, and cg19580810) methylation levels in the TCGA OSCC cohort. (A) RAB25 methylation levels compared between OSCC with high RAB25 mRNA levels and OSCC with low RAB25 mRNA levels. The M-values of the 3 RAB25 Infinium 450K promoter probes were significantly higher in OSCC with low RAB25 mRNA z-scores compared to OSCC with high RAB25 mRNA z-scores. (B) Spearman correlations between RAB25 methylation and RAB25 mRNA levels. All 3 RAB25 promoter probes showed a significant negative correlation between RAB25 promoter probe M-values and RAB25 mRNA z-scores.

Article Snippet: Antigen retrieval was performed using a citrate buffer (10 mM citric acid, 0.05% Tween 20, pH 6.0) and heated in a microwave oven for 15 min at 300 W. Endogenous peroxidase was blocked with a 0.3% H 2 O 2 solution for 30 min at room temperature, followed by incubation with a mouse monoclonal antibody to human RAB25 clone 3F12F3 (Santa Cruz), diluted 1:50 in PBS with 1% bovine serum albumin, overnight at 4°C.

Techniques: Methylation

Journal: Epigenetics

Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

doi: 10.1080/15592294.2016.1205176

Figure Lengend Snippet: RAB25 expression levels between pN0 and pN+ OSCC in the UMCG and TCGA OSCC cohort. (A) pN+ OSCC in the TCGA cohort (n = 86) express significantly less RAB25 mRNA than pN0 OSCC (n = 61), as revealed by Mann-Whitney-U test. (B) pN + OSCC in the UMCG cohort (n = 87) have significantly less RAB25-positive tumor cells than pN0 OSCC (n = 91), as revealed by Mann-Whitney-U test.

Article Snippet: Antigen retrieval was performed using a citrate buffer (10 mM citric acid, 0.05% Tween 20, pH 6.0) and heated in a microwave oven for 15 min at 300 W. Endogenous peroxidase was blocked with a 0.3% H 2 O 2 solution for 30 min at room temperature, followed by incubation with a mouse monoclonal antibody to human RAB25 clone 3F12F3 (Santa Cruz), diluted 1:50 in PBS with 1% bovine serum albumin, overnight at 4°C.

Techniques: Expressing, MANN-WHITNEY

Journal: Epigenetics

Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

doi: 10.1080/15592294.2016.1205176

Figure Lengend Snippet: Correlations between RAB25 expression and tumor characteristics. A) Associations between RAB25 mRNA expression and the clinical characteristics of the TCGA OSCC cohort. B) Associations between RAB25 protein expression and the clinical characteristics of the UMCG OSCC cohort.

Article Snippet: Antigen retrieval was performed using a citrate buffer (10 mM citric acid, 0.05% Tween 20, pH 6.0) and heated in a microwave oven for 15 min at 300 W. Endogenous peroxidase was blocked with a 0.3% H 2 O 2 solution for 30 min at room temperature, followed by incubation with a mouse monoclonal antibody to human RAB25 clone 3F12F3 (Santa Cruz), diluted 1:50 in PBS with 1% bovine serum albumin, overnight at 4°C.

Techniques: Expressing, Biomarker Discovery

Journal: Epigenetics

Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis

doi: 10.1080/15592294.2016.1205176

Figure Lengend Snippet: Representative examples of RAB25 expression in 2 OSCC as detected by immunohistochemistry. Tissues were scored by the amount of RAB25-positive cells. (A) Example of a well-differentiated OSCC with a high amount of RAB25-expressing cells. (B) Example of a poorly differentiated OSCC with a very low amount of RAB25-positive cells.

Article Snippet: Antigen retrieval was performed using a citrate buffer (10 mM citric acid, 0.05% Tween 20, pH 6.0) and heated in a microwave oven for 15 min at 300 W. Endogenous peroxidase was blocked with a 0.3% H 2 O 2 solution for 30 min at room temperature, followed by incubation with a mouse monoclonal antibody to human RAB25 clone 3F12F3 (Santa Cruz), diluted 1:50 in PBS with 1% bovine serum albumin, overnight at 4°C.

Techniques: Expressing, Immunohistochemistry

Journal: Frontiers in Microbiology

Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota

doi: 10.3389/fmicb.2018.00215

Figure Lengend Snippet: Microarray results obtained by hybridization of seven cloned genes encoding different CAZymes from diverse microorganisms targeted by the FibroChip.

Article Snippet: Triplicate of probes of 25- and 54-mers were synthetized in situ on an Agilent 8 × 15K DNA microarray (Agilent Technologies, Santa Clara, CA, United States) allowing the simultaneous analysis of 16 biological samples using a two color labeling.

Techniques: Microarray, Hybridization, Clone Assay

Journal: Frontiers in Microbiology

Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota

doi: 10.3389/fmicb.2018.00215

Figure Lengend Snippet: Microarray results obtained after hybridization of genomic DNA from selected bacterial strains.

Article Snippet: Triplicate of probes of 25- and 54-mers were synthetized in situ on an Agilent 8 × 15K DNA microarray (Agilent Technologies, Santa Clara, CA, United States) allowing the simultaneous analysis of 16 biological samples using a two color labeling.

Techniques: Microarray, Hybridization

Journal: Frontiers in Microbiology

Article Title: FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota

doi: 10.3389/fmicb.2018.00215

Figure Lengend Snippet: Microarray gene expression analysis of the targeted genes from Fibrobacter succinogenes S85 cultivated with cellobiose (Clb) or wheat straw (WS) as a sole substrate. Relative expression of expressed genes on WS versus Clb is expressed as log2 ratio (WS/Clb) ± SEM. Genes are denominated by the accession number of the protein encoded.

Article Snippet: Triplicate of probes of 25- and 54-mers were synthetized in situ on an Agilent 8 × 15K DNA microarray (Agilent Technologies, Santa Clara, CA, United States) allowing the simultaneous analysis of 16 biological samples using a two color labeling.

Techniques: Microarray, Expressing

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations

doi: 10.3389/fbioe.2016.00017

Figure Lengend Snippet: Oxidative perturbation experiments in S. cerevisiae .

Article Snippet: From 25 to 37°C , Shake flasks , 0, 15, 30, 45, 60, and 120 min , Affymetrix YE6100 gene chips , Causton et al. ( ) .

Techniques: Sampling, Microarray

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations

doi: 10.3389/fbioe.2016.00017

Figure Lengend Snippet: Perturbation experiments to monitor the transcriptomic response of S. cerevisiae to the changing temperatures .

Article Snippet: From 25 to 37°C , Shake flasks , 0, 15, 30, 45, 60, and 120 min , Affymetrix YE6100 gene chips , Causton et al. ( ) .

Techniques: Sampling, Microarray