Journal: Scientific Reports

Article Title: TGFβ inhibition and mesenchymal to epithelial transition initiation by Xenopus egg extract: first steps towards early reprogramming in fish somatic cell

doi: 10.1038/s41598-023-36354-3

Figure Lengend Snippet: Gene Ontology (GO) flow diagram of the terms related to cell surface receptor signaling pathway ( A ) and KEGG pathways ( B ). The analysis was performed on the cluster of upregulated genes in treated cells (fold change > 2) using WebGestalt web tool. The set of genes spotted on the microarray was used as the reference gene list. A: The black and the dotted lines represent respectively direct and indirect and KEGG pathway ( www.kegg.jp/kegg/kegg1.html ), p values (P) below 0.05 and false discovery rate (FDR) below 0.05 are indicated. Both A and B highlight the disturbance of the TGFβ and Wnt signaling pathways in response to egg extract treatment.

Article Snippet: Agilent 8 × 60 K high-density oligonucleotide microarray (GEO platform no. GPL32340) was spotted with a set of 52,362 distinct goldfish oligonucleotides.

Techniques: Cell Surface Receptor Assay, Microarray

Journal: Scientific Reports

Article Title: TGFβ inhibition and mesenchymal to epithelial transition initiation by Xenopus egg extract: first steps towards early reprogramming in fish somatic cell

doi: 10.1038/s41598-023-36354-3

Figure Lengend Snippet: Differentially expressed genes related to TGFβ and Wnt signaling pathways. ( A ) Cytoscape representation of the genes described in Tables , . The darkest the node color, the highest the fold change (down regulation in green shades, upregulation in red shades; see Tables , for fold change values). ( B ) Expression profile from qRT-PCR analysis of several genes associated to the TGFβ signaling pathway ( smad7-1, smad7-2, dusp6-1, dusp6-2, zeb1b, mmp9 ), to Wnt/β-catenin signaling pathway ( notum1a, frzb ), to both pathways ( bambia, fn1b ), a mesenchymal marker gene ( col1a1a ), and a set of genes related to pluripotency ( nanog, pou2, sox2, c-myca1 and c-myca2 ). Data are presented as fold change (FC) between treated and non-treated (control) cells. Error bars: SEM errors of the FC mean. A total of 5 to 9 paired samples (treated versus control cells) were analyzed per gene. Statistical test was performed using the nonparametric Wilcoxon test comparing the paired normalized expression values between egg extract treated and control cells. *Significant differences (p < 0.05) between treated and control values. Grey bars: upregulated genes; white bars: down regulated genes. Extensions -1 or -2 in the gene name correspond to duplicated gene copies in goldfish. It should be noted that these qPCR data confirm the microarray results indicating a deregulation of both signaling pathways.

Article Snippet: Agilent 8 × 60 K high-density oligonucleotide microarray (GEO platform no. GPL32340) was spotted with a set of 52,362 distinct goldfish oligonucleotides.

Techniques: Expressing, Quantitative RT-PCR, Marker, Microarray

Journal: Scientific Reports

Article Title: TGFβ inhibition and mesenchymal to epithelial transition initiation by Xenopus egg extract: first steps towards early reprogramming in fish somatic cell

doi: 10.1038/s41598-023-36354-3

Figure Lengend Snippet: Gene Ontology (GO) flow diagram of the terms related to lipid metabolic process ( A ) and KEGG pathways ( B ). The analysis was performed on the cluster of genes downregulated in treated cells (fold change > 2) using WebGestalt web tool. The set of genes spotted on the microarray was used as the reference gene list. ( A ) The black and the dotted lines represent respectively direct and indirect connections between GO terms. ( B ) Dre, Danio rerio prefix of the KEGG identifier. For each GO term and KEGG pathway ( www.kegg.jp/kegg/kegg1.html ), p values (P) below 0.05 and false discovery rate (FDR) below 0.05 are indicated. Both A and B figures highlight the disturbance of lipid metabolism after egg extract treatment, and specifically cholesterol and fatty acid biosynthesis.

Article Snippet: Agilent 8 × 60 K high-density oligonucleotide microarray (GEO platform no. GPL32340) was spotted with a set of 52,362 distinct goldfish oligonucleotides.

Techniques: Microarray

Journal: Environmental Health

Article Title: The effect of oxythioquinox exposure on normal human mammary epithelial cell gene expression: A microarray analysis study

doi: 10.1186/1476-069X-3-9

Figure Lengend Snippet: Genes altered following oxythioquinox exposure. Table represents data mined from HuGeneFL microarrays (Affymetrix). All genes selected have a signal log ratio of ± 0.6 unless otherwise noted. Representative genes for each group were selected based on their function and are shown here.

Article Snippet: Gene transcription in each cell strain was analyzed using high-density oligonucleotide DNA microarrays (HuGeneFL, Affymetrix™) and changes in the expression of selected genes were verified by real-time polymerase chain reaction at extended time points (ABI).

Techniques: Transduction, Activity Assay, Permeability

Journal: Environmental Health

Article Title: The effect of oxythioquinox exposure on normal human mammary epithelial cell gene expression: A microarray analysis study

doi: 10.1186/1476-069X-3-9

Figure Lengend Snippet: Expression pattern for CYP2A13. DNA microarray analysis of NHMEC strains. Analysis was performed as described on HuGeneFL high-density oligonucleotide microarrays (Affymetrix). Results are plotted as duration of exposure vs signal log ratio (SLR). Signal log ratio is a measure of comparative expression of the treatment vs. vehicle control (0.001% DMSO). Signal log ratio of one is equal to a fold change of two. A SLR of 0.6 (Fold Change ~1.5) was the arbitrary limit of our analysis. All genes given an Absent call by analysis software are shown with a SLR of zero. Asterisks indicate a statistically significant variation in expression from the control level as measured by Tukey's Biweight analysis.

Article Snippet: Gene transcription in each cell strain was analyzed using high-density oligonucleotide DNA microarrays (HuGeneFL, Affymetrix™) and changes in the expression of selected genes were verified by real-time polymerase chain reaction at extended time points (ABI).

Techniques: Expressing, Microarray, Software

Journal: Environmental Health

Article Title: The effect of oxythioquinox exposure on normal human mammary epithelial cell gene expression: A microarray analysis study

doi: 10.1186/1476-069X-3-9

Figure Lengend Snippet: Expression pattern for dihydrodiol dehydrogenase. DNA Microarray analysis of NHMEC strains. Analysis was performed as described on HuGeneFL high-density oligonucleotide microarrays (Affymetrix). Results are plotted as duration of exposure vs signal log ratio (SLR). Signal log ratio is a measure of comparative expression of the treatment vs. vehicle control (0.001% DMSO). Signal log ratio of one is equal to a fold change of two. A SLR of 0.6 (Fold Change ~1.5) was the arbitrary limit of our analysis. All genes given an Absent call by analysis software are shown with a SLR of zero. Asterisks indicate a statistically significant variation in expression from the control level as measured by Tukey's Biweight analysis.

Article Snippet: Gene transcription in each cell strain was analyzed using high-density oligonucleotide DNA microarrays (HuGeneFL, Affymetrix™) and changes in the expression of selected genes were verified by real-time polymerase chain reaction at extended time points (ABI).

Techniques: Expressing, Microarray, Software

Journal: BMC Genomics

Article Title: Transcriptome architecture across tissues in the pig

doi: 10.1186/1471-2164-9-173

Figure Lengend Snippet: Differential GO categories across embryo layers . Percentage of the most frequent GO categories within extreme genes for each embryonic layer ( A , ectoderm; B , mesoderm; C , endoderm; D , all genes in A, B and C ). The number in each category is the false discovery rate (FDR) that the category is over represented with respect to the GO frequency across all genes in the microarray. The FDR is shown only if < 0.20.

Article Snippet: Briefly, the cDNA synthesis was undertaken with 5 μg of total RNA, labelled with biotin and hybridized to individual high-density oligonucleotide microarray chips (GeneChip ® Porcine) from Affymetrix (Santa Clara CA) containing a total of 23,937 probe sets (23,256 transcripts), representing 20,201 Sus scrofa genes, 11,265 of these genes were annotated by Tsai et al. (2006).

Techniques: Microarray

Journal: BMC Genomics

Article Title: Transcriptome architecture across tissues in the pig

doi: 10.1186/1471-2164-9-173

Figure Lengend Snippet: Proportion of functional annotation categories . Percentage of the most frequent GO categories within the most significant differentially expressed genes between sexes (Table 3) and between breeds (Table 4). The number in each category is the false discovery rate (FDR) that the category is over represented with respect to the GO frequency across all genes in the microarray. The FDR is shown only if < 0.20.

Article Snippet: Briefly, the cDNA synthesis was undertaken with 5 μg of total RNA, labelled with biotin and hybridized to individual high-density oligonucleotide microarray chips (GeneChip ® Porcine) from Affymetrix (Santa Clara CA) containing a total of 23,937 probe sets (23,256 transcripts), representing 20,201 Sus scrofa genes, 11,265 of these genes were annotated by Tsai et al. (2006).

Techniques: Functional Assay, Microarray