Journal: Journal of Neuroinflammation

Article Title: Transcriptomics and proteomics analyses of the PACAP38 influenced ischemic brain in permanent middle cerebral artery occlusion model mice

doi: 10.1186/1742-2094-9-256

Figure Lengend Snippet: The experimental outline and workflow. Effect of intracerebroventricular administration of pituitary adenylate cyclase-activating polypeptide (PACAP)-38 into the ischemic mouse brain (permanent middle cerebral artery occlusion, PMCAO model) is evaluated at the molecular level in the ipsilateral (right) hemisphere. Sham control treated with saline is used for the comparison. TTC staining shows he ischemic region in the brain. The ipsilateral hemisphere is sampled and finely powdered in liquid nitrogen, followed by investigation into molecular level changes at the level of gene and protein expressions by DNA microarray and proteomics approaches, respectively.

Article Snippet: A mouse 4 × 44K whole genome oligo DNA microarray chip (G4122F, Agilent Technologies, Palo Alto, CA, USA) was used for global gene expression analysis using the ipsilateral (ischemic) hemisphere.

Techniques: Staining, Microarray

Journal: Toxicology and applied pharmacology

Article Title: Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

doi: 10.1016/j.taap.2012.11.028

Figure Lengend Snippet: Hepatic differential gene expression in the rat and mouse. Gene annotation for the rat dataset was first updated using Affymetrix release 32 annotation (http://www.affymetrix.com/support/help/releasedocs/netaffx_release_32.affx). Updated rat Affymetrix GeneChip 230 2.0 and mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by our in-house semiparametric normalization (Eckel et al., 2005), and empirical Bayes analysis methods (Eckel et al., 2004). Temporal distribution of differentially expressed genes (|fold change|≥1.5 and P1(t)≥0.99) in (A) rat and (B) mouse per time point (repressed — light gray; induced — dark gray). The total number of responsive genes at each time point is indicated in parentheses. Venn diagrams compare differentially regulated genes at each time point for (C) rat and (D) mouse.

Article Snippet: Both the updated rat Affymetrix GeneChip 230 2.0 and the mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by a semiparametric method ( Eckel et al., 2005 ), and statistically analyzed using an empirical Bayes method ( Eckel et al., 2004 ). (B) Venn diagrams of 1415 comparable differentially regulated orthologs (563 rat and 922 mouse) representing species-specific and commonly regulated TCDD-responsive orthologs using stringent (|fold change|≥1.5, P1( t )≥0.99) and relaxed criteria (|fold change|≥1.4, P1( t )≥0.90). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Correlation analysis of commonly regulated TCDD-responsive genes (|fold change|≥1.5, P1( t )≥0.99).

Techniques: Expressing

Journal: Toxicology and applied pharmacology

Article Title: Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

doi: 10.1016/j.taap.2012.11.028

Figure Lengend Snippet: Comparison of hepatic rat and mouse TCDD-elicited differential ortholog expression. (A) Comparison of unique genes, orthologs and TCDD-responsive orthologs in rat and mouse. Gene annotation for the rat Affymetrix dataset was first updated using Affymetrix release 32 annotation (http://www.affymetrix.com/support/help/releasedocs/netaffx_release_32.affx). Both the updated rat Affymetrix GeneChip 230 2.0 and the mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by a semiparametric method (Eckel et al., 2005), and statistically analyzed using an empirical Bayes method (Eckel et al., 2004). (B) Venn diagrams of 1415 comparable differentially regulated orthologs (563 rat and 922 mouse) representing species-specific and commonly regulated TCDD-responsive orthologs using stringent (|fold change|≥1.5, P1(t)≥0.99) and relaxed criteria (|fold change|≥1.4, P1(t)≥0.90).

Article Snippet: Both the updated rat Affymetrix GeneChip 230 2.0 and the mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by a semiparametric method ( Eckel et al., 2005 ), and statistically analyzed using an empirical Bayes method ( Eckel et al., 2004 ). (B) Venn diagrams of 1415 comparable differentially regulated orthologs (563 rat and 922 mouse) representing species-specific and commonly regulated TCDD-responsive orthologs using stringent (|fold change|≥1.5, P1( t )≥0.99) and relaxed criteria (|fold change|≥1.4, P1( t )≥0.90). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Correlation analysis of commonly regulated TCDD-responsive genes (|fold change|≥1.5, P1( t )≥0.99).

Techniques: Expressing

Journal: Toxicology and applied pharmacology

Article Title: Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

doi: 10.1016/j.taap.2012.11.028

Figure Lengend Snippet: Correlation analysis of commonly regulated TCDD-responsive genes (|fold change|≥1.5, P1(t)≥0.99). Gene annotation for the rat Affymetrix dataset was first updated using Affymetrix release 32 annotation (http://www.affymetrix.com/support/help/releasedocs/netaffx_release_32.affx). The updated rat Affymetrix GeneChip 230 2.0 and the mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by a semiparametric method (Eckel et al., 2005), and statistically analyzed using an empirical Bayes method (Eckel et al., 2004). Only 37% genes were positively correlated in terms of fold change and significance between rat and mouse genes (quadrant I).

Article Snippet: Both the updated rat Affymetrix GeneChip 230 2.0 and the mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by a semiparametric method ( Eckel et al., 2005 ), and statistically analyzed using an empirical Bayes method ( Eckel et al., 2004 ). (B) Venn diagrams of 1415 comparable differentially regulated orthologs (563 rat and 922 mouse) representing species-specific and commonly regulated TCDD-responsive orthologs using stringent (|fold change|≥1.5, P1( t )≥0.99) and relaxed criteria (|fold change|≥1.4, P1( t )≥0.90). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Correlation analysis of commonly regulated TCDD-responsive genes (|fold change|≥1.5, P1( t )≥0.99).

Techniques:

Journal: Toxicology and applied pharmacology

Article Title: Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

doi: 10.1016/j.taap.2012.11.028

Figure Lengend Snippet: Hepatic differential gene expression in the rat and mouse. Gene annotation for the rat dataset was first updated using Affymetrix release 32 annotation (http://www.affymetrix.com/support/help/releasedocs/netaffx_release_32.affx). Updated rat Affymetrix GeneChip 230 2.0 and mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by our in-house semiparametric normalization (Eckel et al., 2005), and empirical Bayes analysis methods (Eckel et al., 2004). Temporal distribution of differentially expressed genes (|fold change|≥1.5 and P1(t)≥0.99) in (A) rat and (B) mouse per time point (repressed — light gray; induced — dark gray). The total number of responsive genes at each time point is indicated in parentheses. Venn diagrams compare differentially regulated genes at each time point for (C) rat and (D) mouse.

Article Snippet: HomoloGene identified 11,708 orthologs represented across the rat Affymetrix 230 2.0 GeneChip (12,310 total orthologs), and the mouse 4×44K v.1 Agilent oligonucleotide array (17,578 total orthologs).

Techniques: Expressing

Journal: Toxicology and applied pharmacology

Article Title: Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

doi: 10.1016/j.taap.2012.11.028

Figure Lengend Snippet: Comparison of hepatic rat and mouse TCDD-elicited differential ortholog expression. (A) Comparison of unique genes, orthologs and TCDD-responsive orthologs in rat and mouse. Gene annotation for the rat Affymetrix dataset was first updated using Affymetrix release 32 annotation (http://www.affymetrix.com/support/help/releasedocs/netaffx_release_32.affx). Both the updated rat Affymetrix GeneChip 230 2.0 and the mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by a semiparametric method (Eckel et al., 2005), and statistically analyzed using an empirical Bayes method (Eckel et al., 2004). (B) Venn diagrams of 1415 comparable differentially regulated orthologs (563 rat and 922 mouse) representing species-specific and commonly regulated TCDD-responsive orthologs using stringent (|fold change|≥1.5, P1(t)≥0.99) and relaxed criteria (|fold change|≥1.4, P1(t)≥0.90).

Article Snippet: HomoloGene identified 11,708 orthologs represented across the rat Affymetrix 230 2.0 GeneChip (12,310 total orthologs), and the mouse 4×44K v.1 Agilent oligonucleotide array (17,578 total orthologs).

Techniques: Expressing

Journal: Toxicology and applied pharmacology

Article Title: Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

doi: 10.1016/j.taap.2012.11.028

Figure Lengend Snippet: Correlation analysis of commonly regulated TCDD-responsive genes (|fold change|≥1.5, P1(t)≥0.99). Gene annotation for the rat Affymetrix dataset was first updated using Affymetrix release 32 annotation (http://www.affymetrix.com/support/help/releasedocs/netaffx_release_32.affx). The updated rat Affymetrix GeneChip 230 2.0 and the mouse 4×44K Agilent oligonucleotide array (version 1) raw datasets were normalized by a semiparametric method (Eckel et al., 2005), and statistically analyzed using an empirical Bayes method (Eckel et al., 2004). Only 37% genes were positively correlated in terms of fold change and significance between rat and mouse genes (quadrant I).

Article Snippet: HomoloGene identified 11,708 orthologs represented across the rat Affymetrix 230 2.0 GeneChip (12,310 total orthologs), and the mouse 4×44K v.1 Agilent oligonucleotide array (17,578 total orthologs).

Techniques:

Journal: Frontiers in Physiology

Article Title: S100A8 and S100A9 Are Associated with Doxorubicin-Induced Cardiotoxicity in the Heart of Diabetic Mice

doi: 10.3389/fphys.2016.00334

Figure Lengend Snippet: Significantly regulated genes in response to DOX in diabetic heart (diabetes saline control vs. diabetes 5 days after DOX) .

Article Snippet: Microarray analysis was performed using the Agilent Service Platform with Agilent two-color mouse 4 × 44 k microarray slides.

Techniques: Microarray, Quantitative RT-PCR, Binding Assay, Transduction

Journal: Frontiers in Physiology

Article Title: S100A8 and S100A9 Are Associated with Doxorubicin-Induced Cardiotoxicity in the Heart of Diabetic Mice

doi: 10.3389/fphys.2016.00334

Figure Lengend Snippet: Transcript expressions of selected genes from microarray results . The transcript expressions of S100A8 (A) , S100A9 (B) , Mmp8 (C) , Wnt5a (D) , Fabp6 (E) , and E2f2 (F) were examined by real time RT-PCR. Data are presented as expression ratio normalized to β-tubulin gene. Data are expressed as mean ± SEM ( n = 6 per group). Two-way ANOVA indicated a significant interaction effect between the two experimental factors (i.e., diabetes and DOX treatment) in S100A8 ( P < 0.001, F = 41.74), S100A9 ( P < 0.001, F = 54.822), and Mmp8 ( P = 0.004, F = 7.495; A–C ). A significant main effect of the factor diabetes was found in Wnt5a ( P = 0.023, F = 5.783; D ). A significant main effect of the factor DOX treatment was found in Fabp6 ( P = 0.005, F = 6.222), and E2f2 ( P = 0.002, F = 7.74; E,F ). Individual means were compared among groups by one-way ANOVA with Turkey's HSD post-hoc test.

Article Snippet: Microarray analysis was performed using the Agilent Service Platform with Agilent two-color mouse 4 × 44 k microarray slides.

Techniques: Microarray, Quantitative RT-PCR, Expressing

Journal: Nature Communications

Article Title: R-spondin 3 promotes stem cell recovery and epithelial regeneration in the colon

doi: 10.1038/s41467-019-12349-5

Figure Lengend Snippet: Rspo3 from in Myh11 + myofibroblasts determines the stem cell signature and is required for Lgr5 + cell recovery. a qPCR for Rspo homologs from colon tissue from n = 3 mice. b qPCR for Rspo3 in Myh11CreErt2/Rspo3 fl/fl mice ( Rspo3 KO) and corresponding Myh11CreErt2/Rspo3 +/+ control mice at 2 weeks ( n = 5 mice per group) and 2 months ( n = 6 control mice, n = 5 Rspo3 KO mice) after injection of tamoxifen into Rspo3 KO and corresponding controls (2 months data: Mann–Whitney U -test (two-tailed) was performed). c qPCR for Lgr5 in Myh11CreErt2/Rspo3 fl/fl mice ( Rspo3 KO) and corresponding Myh11CreErt2/Rspo3 +/+ control mice at 2 weeks ( n = 5 mice per group) and 2 months ( n = 6 control mice, n = 5 Rspo3 KO mice) after injection of tamoxifen into Rspo3 KO and corresponding controls (Mann–Whitney U -test (two-tailed). d GSEA analysis of genes differentially expressed in colon tissue from Rspo3 KO versus control mice in comparison to the previously published small intestinal Lgr5 + stem cell signature gene set and in comparison to the mitotic recombination related signature gene set obtained from MSigDB (data from two microarrays from independent biological replicates per group). e H&E staining of the colon from a control and an Rspo3 KO mouse at 14 and 60 days after tamoxifen treatment, showing no marked anatomical differences. f Average crypt length in colon tissue from control ( n = 3 mice) and an Rspo3 KO ( n = 4 mice) mice 60 days after tamoxifen treatment. g Confocal microscopy image of colon tissue from control and Rspo3 KO mice at 14 and 60 days after tamoxifen treatment stained for Ki67 (red), E-cadherin (green), and DAPI. h Quantification of Ki67 + cells per crypt section of control and Rspo3 KO mice 60 days after tamoxifen treatment ( n = 3 mice per group). i Confocal microscopy images from the colon of an Lgr5DTReGFP/Myh11CreErt2/Rspo3 fl/fl and an Lgr5DTReGFP/Myh11CreErt2/Rspo3 +/+ mouse treated with a single dose of tamoxifen and DT 7 days before sacrifice. j Single-molecule in situ hybridization for Axin2 and Lgr5 on colon tissue from an Lgr5DTReGFP/Myh11CreErt2/Rspo3 fl/fl mouse treated with DT and tamoxifen (scale bar = 100 µm). Data represent mean ± SD, Student’s t -test (two tailed) was applied in all cases, unless otherwise specified. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001. Scale bar = 100 µm unless indicated otherwise. Source data are provided as a source data file

Article Snippet: After precipitation, purification, and quantification, 1.25 μg of each labeled cRNA was fragmented and hybridized to whole-genome mouse 4 × 44 K multipack microarrays (Agilent-014868, whole mouse genome 4 × 44 K microarray kit) according to the manufacturer’s protocol (Agilent Technologies).

Techniques: Injection, MANN-WHITNEY, Two Tailed Test, Staining, Confocal Microscopy, In Situ Hybridization