Journal: Journal of Clinical Biochemistry and Nutrition

Article Title: Atopic dermatitis causes lipid accumulation in the liver of NC/Nga mouse

doi: 10.3164/jcbn.11-29

Figure Lengend Snippet: The change in liver mRNA expression of lipid and sugar metabolism-related genes that were increased or decreased by allergy measured using DNA microarray and qRT-PCR assay

Article Snippet: DNA microarray analysis (GeneSQUARE, Multiplex Assay DNA Microarray Lifestyle Diseases Gene Expression For Mouse) using the total RNA collected in each group was performed by Kurabo Ind. (Osaka, Japan).

Techniques: Expressing, Microarray, Control

Journal: Nature communications

Article Title: Superoxide dismutase 1 acts as a nuclear transcription factor to regulate oxidative stress resistance

doi: 10.1038/ncomms4446

Figure Lengend Snippet: (a) Sod1 is required for the induction of oxidative response (OR) genes. WT or sod1 Δ cells were treated without or with 0.4 mM H 2 O 2 for 20 min and analyzed for global gene expression profile. 123 Sod1-dependent genes were identified and most of the known genes belong to five related functional categories. (b) Shown is the relative induction level of OR genes by H 2 O 2 in each category in WT and sod1 Δ cells. Data represents average fold change of induction in each category. (c) Shown is the heat map of genes in the oxidative stress response category. (d) Validation of representative genes ( GRE2 , Genes de Respuesta a Estres 2; TSA2 : Thiol-Specific Antioxidant 2; YML131; STF2 : STabilizing Factor 2) in the oxidative stress response category by RT-qPCR. Error bars indicate ± SD from triplicates of two independent experiments. * p < 0.05. (e) Nuclear Sod1 is critical for the induction of OR genes. Yeast cells expressing different forms of Sod1 were treated with 0.4 mM H 2 O 2 for 20 min. Representative genes were validated by RT-qPCR. Error bars indicate ± SD from triplicates of two independent experiments. * p < 0.05. (f) The induction of OR genes by ROS was attenuated in Sod1 S60,99A cells. Yeast cells expressing Sod1 or Sod1 S60,99A were treated with 0.4 mM H 2 O 2 for 20 min. Expression of GRE2 and RNR3 were determined by RT-qPCR. Error bars indicate ± SD from triplicates of two independent experiments. * p < 0.05. (g) ROS treatment increases the association of Sod1 with promoter of oxidative responsive genes. WT (SZy1051) and sod1 Δ (SZy1050) cells were treated with 0.4 mM H 2 O 2 for 20 min. The binding of Sod1 to representative promoters were analyzed by chromatin immunoprecipitation (ChIP). (h) Quantification of the Fig. 5g experiment. Error bars indicate ± SD from triplicates of two independent experiments. * p < 0.05, Student’s t -test.

Article Snippet: DNA microarray analysis of yeast global gene expression was carried out by Rutgers RUCDR Analytical and Informatics Services using the following procedure.

Techniques: Gene Expression, Functional Assay, Biomarker Discovery, Quantitative RT-PCR, Expressing, Binding Assay, Chromatin Immunoprecipitation

Journal: The Journal of Pathology: Clinical Research

Article Title: A 12‐gene signature to distinguish colon cancer patients with better clinical outcome following treatment with 5‐fluorouracil or FOLFIRI

doi: 10.1002/cjp2.17

Figure Lengend Snippet: A: Supervised hierarchical clustering displaying the genes significantly modulated between the resistant and sensitive cell lines (52 under‐ and 51 over‐expressed in resistant cell lines) using a cutoff of twofold change on expression and FDR < 0.01. B: Fold difference in gene expression between sensitive and resistant cell lines detected by qRT‐PCR analyses. Seven genes were selected from the list of altered genes for this analysis. The results from sensitive or resistant cell lines were pooled to obtain an estimated fold change. C: Correlation between the qRT‐PCR and the microarray expression data. The fold difference detected by qRT‐PCR between sensitive and resistant cell lines correlated significantly confirming the microarray results (Pearson's correlation or ρ = 0.739, p ‐value = 0.013).

Article Snippet: Hence, we used a publically available gene expression DNA microarray dataset generated by Almac Diagnostics on 359 FFPE tissue specimens from stage II colon cancer that did not receive adjuvant chemotherapy.

Techniques: Expressing, Gene Expression, Quantitative RT-PCR, Microarray

Journal: In Vitro Cellular & Developmental Biology. Animal

Article Title: Trisomy 12 compromises the mesendodermal differentiation propensity of human pluripotent stem cells

doi: 10.1007/s11626-023-00824-9

Figure Lengend Snippet: Comparison of global gene expression in trisomy 12 hPSC lines. ( A ) Cluster dendrogram of microarray data from trisomy 12 hPSC lines and their original lines. N = 3 from each lines. ( B–D ) Scatter plot of signal intensity for all microarray probes. Each dot in the plot shows the mean signal intensity of each probe averaged from 3 samples of H9 ( X-axis ) and H9(+ 12) ( Y-axis ) hESC lines ( B ), 201B7 ( X-axis ) and 201B7(+ 12) ( Y-axis ) hiPSC lines ( C ), and 19–9-7 T ( X-axis ) and 19–9-7 T(+ 12) ( Y-axis ) hiPSC lines ( D ). ( E , F ) Pie charts of significantly upregulated ( E ) or downregulated ( F ) probes of the trisomy 12 hPSC lines in common from microarray analysis (FDR < 0.1). ( G , H ) Pie charts of significantly upregulated G or downregulated H probes of the trisomy 12 hPSC lines in common from microarray analysis (FDR < 0.1). The area in blue indicates the ratio of the probes targeting chromosome 12. The area in red indicates the probes targeting the other chromosomes. ( I , J ) The list of “PANTHER” pathways and their p values extracted from the commonly upregulated genes I and downregulated gene J.

Article Snippet: Gene expression microarray experiments were performed by DNA Chip Research Inc (Tokyo, Japan).

Techniques: Comparison, Gene Expression, Microarray