Journal: Cytotechnology

Article Title: Optimization and evaluation of electroporation delivery of siRNA in the human leukemic CEM cell line

doi: 10.1007/s10616-010-9309-6

Figure Lengend Snippet: Whole-genome microarray data on electroporated cells

Article Snippet: RNA exonuclease 1 homolog BC130374 1.7 Up GAGE13 G antigen 13 Open in a separate window A whole-genome microarray was performed on RNA from untreated CEM cells, electroporated cells, and cells transfected with negative control siRNA or dCK siRNA transfected cells (dCK) 48 h after electroporation/transfection.

Techniques: Microarray, Control, Negative Control

Journal: Stem Cell Research & Therapy

Article Title: HMGB1-modified mesenchymal stem cells attenuate radiation-induced vascular injury possibly via their high motility and facilitation of endothelial differentiation

doi: 10.1186/s13287-019-1197-x

Figure Lengend Snippet: Microarray analysis of differentially expressed genes in MSCs during endothelial differentiation. In EC-MSC coculture system, there MSC samples for each group were collected at days 0 and 7, respectively, and sent to microarray analysis of differentially expressed genes. The inclusion criteria for differentially expressed genes were the absolute fold change of RNA levels > 1.5 and P value < 0.05. The analysis yielded 2482 (999 upregulated and 1483 downregulated) genes in MSC-H cells and 1325 (671 upregulated and 654 downregulated) genes in MSC-C cells. These genes were enriched in GO terms ( a ) and KEGG pathways analysis ( b ). The enriched terms that were present in both MSC-C and MSC-H groups were marked by asterisks. The MSC-H cells yielded a cluster of the most enriched terms with high similarity to MSC-C cells. Approximately one-half of the most enriched GO terms and pathways were consistent between them. Nevertheless, multiple pathways were noteworthy of being exclusively enriched in MSC-H cells, including MAPK and p53 signaling. c The number of differentially expressed genes (significance genes) enriched in the shared GO terms was counted and compared between groups. MSC-H cells yielded 1.7-fold (ranged from 1.5 to 1.9-fold) greater number of significance genes than MSC-C cells on average. d The number of differentially expressed genes (significance genes) enriched in the shared signaling pathways was counted and compared between groups. Similarly, MSC-H cells had an average 1.4-fold (ranged from 1.3 to 1.8-fold) increase of significance gene counts than the MSC-H cells

Article Snippet: Microarray analysis of MSC gene expression profile was performed by GeneChem (Shanghai, China).

Techniques: Microarray, Protein-Protein interactions

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