Journal: Microbial Cell Factories

Article Title: Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium

doi: 10.1186/1475-2859-13-28

Figure Lengend Snippet: Growth, aromatic intermediates production, and substrate consumption during batch fermentation cultures of E. coli PB12.SA22 strain grown in complex broth. (A) Biomass production (●) Glucose consumption (◆). (B) Residual Phenylalanine (☐), Tyrosine (○), Tryptophan (△). (C) SA (▲), DHS (◆), GA (▼) production. In panel A, numbers in parenthesis indicate the sampling time of biomass for total RNA extraction used for microarray analysis (1), (2) and (3) indicates samples collected at 5, 9, and 44 h of cultivation, respectively.

Article Snippet: Samples were adjusted to a final concentration of total RNA = 1 μ g/ μ L. Aliquots of 20 μ L of total RNA were shipped to the Precision Biomarker company for microarray experiments ( http://www.precisionbiomarker.com ).

Techniques: Sampling, RNA Extraction, Microarray

Journal: JAMA oncology

Article Title: Patient-Level DNA Damage and Repair Pathway Profiles and Prognosis After Prostatectomy for High-Risk Prostate Cancer

doi: 10.1001/jamaoncol.2015.4955

Figure Lengend Snippet: A, Microarray gene expression data is converted into (B) pathway enrichment data. Expression is median-scaled and ranked across all samples gene-by-gene. B, Gene Set Enrichment Analysis preranked on gene ranks generates pathway enrichment NES, and hierarchical clustering generates a pathway heatmap. C, Spearman ρ correlation matrix of intercorrelation among the pathways across all samples. BCR indicates biochemical recurrence; BER, base excision repair; DDR, DNA damage and repair; DSB, double-strand break; GSEA, Gene Set Enrichment Analysis; HRR, homologous recombination repair; MMR, mismatch repair; NER, nucleotide excision repair; NES, Normalized Enrichment Score; NHEJ, nonhomologous end joining.

Article Snippet: 5 – 7 RNA extraction and microarray hybridization was performed in a CLIA (Clinical Laboratory Improvement Amendments)-certified, clinical operations laboratory (GenomeDx Biosciences, Inc).

Techniques: Microarray, Gene Expression, Expressing, Homologous Recombination

Journal: Journal of Clinical Laboratory Analysis

Article Title: Altered expression of circular RNAs in human placental chorionic plate‐derived mesenchymal stem cells pretreated with hypoxia

doi: 10.1002/jcla.22825

Figure Lengend Snippet: qRT‐PCR validation of expression levels of circRNAs identified by microarray analysis. The error bar stands for standard deviations

Article Snippet: Labeling and microarray hybridization Microarray hybridization was performed according to the manufacturer's procedure (Arraystar, Rockville, MD).

Techniques: Quantitative RT-PCR, Biomarker Discovery, Expressing, Microarray