Journal: Journal of Biological Chemistry

Article Title: Expression Profiles of Arabidopsis thaliana in Mineral Deficiencies Reveal Novel Transporters Involved in Metal Homeostasis

doi: 10.1074/jbc.m309338200

Figure Lengend Snippet: FIG. 6. Functional characterization of AtOPT3. A, hybridization of an 600-bp AtOPT3 cDNA probe, corresponding to the 3-terminal exon, to RNA extracted from Arabidopsis roots of plants grown in control conditions (Ctl), copper (-Cu), manganese (-Mn), zinc (-Zn), and iron (-Fe) deficiency. The ethidium bromide-stained RNA gel is shown for quantification. B, growth of ctr1 expressing AtOPT3 on YPG-Ura plates supplemented with 10 M CuSO4 compared with the mutant transformed with the vector alone. C, growth of smf1 expressing AtOPT3 on manganese-limited medium, with and without 1 mM EGTA compared with the growth of the mutant transformed with the vector alone.

Article Snippet: Genome-wide Analysis Provides Insight into Metal Transport—We have used Affymetrix Arabidopsis DNA chips containing 8,300 genes (which cover about one-third of the ge- FIG. 7.

Techniques: Functional Assay, Hybridization, Control, Staining, Expressing, Mutagenesis, Transformation Assay, Plasmid Preparation

Journal: Cellular and Molecular Gastroenterology and Hepatology

Article Title: Interferon-λ3 Promotes Epithelial Defense and Barrier Function Against Cryptosporidium parvum Infection

doi: 10.1016/j.jcmgh.2019.02.007

Figure Lengend Snippet: IECs up-regulate numerous ISGs in response to C parvum infection. Intestinal epithelium was harvested from ileum mucosa of neonatal piglets at the time of peak infection (days 3–5 after infection) (n = 8) and from age-matched uninfected controls (n = 4) for performance of gene expression analysis using microarrays. ( A ) Representative photomicrograph of ileum mucosa from an uninfected control and C parvum –infected piglet used for microarray analysis. H&E stain. Scale bar : 20 μm. ( B ) Villus height and crypt depth (μm) and the percentage of total villus IECs that were infected with C parvum in control (n = 4) and C parvum –infected (n = 8) piglets used for microarray analysis. Each data point represents the average of 5 measurements per piglet. Scale bars : means ± SD. ** P < .01, Student t test comparison between uninfected and C parvum –infected piglets. Heat map of significantly ( C ) up-regulated and ( D ) down-regulated genes in infected ( C parvum ) and control (Uninf) exfoliated ileum villus epithelial cells. Each control and infected biological replicate is represented. Gene IDs:fold change are listed to the right of the heat map. Known ISGs are highlighted in red. ( E ) qRT-PCR analysis of porcine ileum mucosal total cellular mRNA for the presence of ISG15 mRNA. Samples were obtained from piglets used for microarray analysis at peak C parvum infection (days 3–5, n = 5) and age-matched controls (n = 5). For each sample, the Ct value for ISG15 was normalized to expression of the housekeeping gene cyclophilin (ΔCt). Fold-change differences between each sample were compared with a representative uninfected sample using the 2 -ΔΔCt method. Scale bars : means ± SD. ** P < .01, Student t test comparison between uninfected and C parvum –infected piglets. ( F ) Fluorescence in situ hybridization showing ISG15 mRNA (red fluorescence) in villus epithelial cells of ileum mucosa from piglets at peak C parvum infection and absent in villus epithelium of control piglets. Photomicrograph representative of results of 2 independent experiments. Scale bar : 50 μm.

Article Snippet: The fragmented complementary RNA was diluted in hybridization buffer (2 N -morpholino-ethanesulfonic acid, NaCl, EDTA, Tween 20, herring sperm DNA, acetylated bovine serum albumin) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix).

Techniques: Infection, Gene Expression, Control, Microarray, Staining, Comparison, Quantitative RT-PCR, Expressing, Fluorescence, In Situ Hybridization

Journal: Oncotarget

Article Title: A lesson for cancer research: placental microarray gene analysis in preeclampsia

doi:

Figure Lengend Snippet: Summary of microarray studies in preeclampsia

Article Snippet: Hoegh 2010 Denmark , 11 PE 18 ctrl , , , , Cs/vag. , Maternal side, center of cotyledons, stored differently, Pooled RNA. , Affymetrix HG-U133A Gene Chip , 12 up and 9 down in PE vs. ctrl. , Bradykinin B1 receptor, 14-3-3, INHBA, LEP , Placentation, oxidative stress, inflammation.

Techniques: Microarray, Sampling, Dissection, Expressing, Cell Function Assay

Journal: Oncogene

Article Title: Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays.

doi: 10.1038/onc.2008.251

Figure Lengend Snippet: Figure 2 RNA expression by seven genes relative to pathological differentiation. The box plots indicate the distribution of RNA levels measured by QRT–PCR in 134 tumour samples grouped by level of differentiation. The seven genes yielded significant P-values (Po0.01) based on Affymetrix data testing the different tumour differentiation classes. Colours correspond to the sample groups (green: well differentiated (n ¼ 40); orange: moderately differentiated (n ¼ 68); red: poorly differentiated (n ¼ 29)). The y axis gives the DCt values relative to the control genes (R18S and RPLP0). The bottom table shows the fold difference (FC) between the geometric mean values between the different classes and associated Wilcoxon P-value.

Article Snippet: Prediction analysis Initial selection was based on univariate and multivariate Cox analyses (survival R package v2.26) of Affymetrix gene chip variables using 81 samples, divided into three groups: training group S1 (20M and 20 NM samples), training group S2 (10M and 10 NM samples) and a validation group S3 (11M and 10 NM samples).

Techniques: RNA Expression, Quantitative RT-PCR, Control

Journal: Oncogene

Article Title: Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays.

doi: 10.1038/onc.2008.251

Figure Lengend Snippet: Figure 4 QRT–PCR validation of genes associated with metastasis. Transcripts (22) selected from the transcriptome array analysis (Affymetrix; Cox P-value o0.05) were quantitated by QRT–PCR analysis with 134 samples of M (n ¼ 46) and NM (n ¼ 88). Top: box plots (NM blue, M red) representing the distributions of the log2 value of the DCt values after power transformation. Bottom: the fold difference (FC) between the geometric mean values from M divided by NM samples and the p value calculated from the Cox univariate tests for each of the genes, using the entire population of 134 samples analysed by QRT–PCR.

Article Snippet: Prediction analysis Initial selection was based on univariate and multivariate Cox analyses (survival R package v2.26) of Affymetrix gene chip variables using 81 samples, divided into three groups: training group S1 (20M and 20 NM samples), training group S2 (10M and 10 NM samples) and a validation group S3 (11M and 10 NM samples).

Techniques: Quantitative RT-PCR, Biomarker Discovery, Transformation Assay