Journal: World Journal of Gastroenterology

Article Title: Transcriptome analysis creates a new era of precision medicine for managing recurrent hepatocellular carcinoma

doi: 10.3748/wjg.v29.i5.780

Figure Lengend Snippet: Comparisons of real-time quantitative reverse transcription PCR, microarrays, and RNA-sequencing and their applications in hepatocellular carcinoma recurrence

Article Snippet: The surfacing of commercial platforms, such as Human UniGene Set RZPD 1 clone set for cDNA microarrays and Affymetrix Human Genome U95Av2 array for oligonucleotide arrays, have made the technology for both types of arrays widely accessible[ ].

Techniques: Isolation, cDNA Library Assay, Amplification, Labeling, Fluorescence, Hybridization, Sequencing, High Throughput Screening Assay

Journal:

Article Title: Gene Expression in Asthmatic Airway Smooth Muscle

doi: 10.1513/pats.200705-059VS

Figure Lengend Snippet: GENE EXPRESSION STUDIES USING CULTURED AIRWAY SMOOTH MUSCLE CELLS

Article Snippet: More recently, microarrays have been applied to study asthma therapy by investigating the effects of β-agonists on gene expression in cultured airway smooth muscle cells ( 29 ). table ft1 table-wrap mode="anchored" t5 TABLE 2. caption a7 Author ( Reference No. ) Source of Cells Exposures Method of Gene Expression Profiling Findings Lee and coworkers ( 28 ) Commercially available human airway smooth muscle cells IL-13 (100 ng/ml) Affymetrix Genechip HuGeneFL arrays coding for ∼6,500 human genes 204 Genes induced two-fold, including smooth muscle MHC, phospholipase A2, diacyglycerol kinase δ, and IL-13Rα1 Syed and coworkers ( 30 ) 3 Lung transplant donors IL-13 (10–100 ng/ml) Research Genetics and Incyte Genomics cDNA microarrays coding for 8,159 genes A large number of genes induced 1.5-fold or by FDR analyses (total no. not given), including VCAM1, IL-13Rα2, Tenascin C, and histamine receptor H1 IL-13R130Q * Jarai and coworkers ( 27 ) 2 Patients undergoing lung resection IL-13 † Affymetrix HG-U95Av2 microarrays coding for ∼12,500 genes H1 receptor and tenascin were highly induced by IL-13 TGF-β † IL-1β † McGraw and coworkers ( 29 ) Wild-type and transgenic mice overexpressing β 2 -adrenergic receptor None University of Cincinnati Genomic and Microarray Laboratory array coding for 8,734 cDNAs 319 Genes induced 164 Repressed (including phospholamban) Open in a separate window Definition of abbreviations: FDR = false discovery rate; IL-13Rα1 = IL-13 receptor α1; MHC = myosin heavy chain; RT-PCR = reverse transcription–polymerase chain reaction; TGF = transforming growth factor; VCAM = vascular cell adhesion molecule.

Techniques: Expressing, Cell Culture, Transgenic Assay, Microarray

Journal:

Article Title: Estradiol and Selective Estrogen Receptor Modulators Differentially Regulate Target Genes with Estrogen Receptors ? and ? D⃞

doi: 10.1091/mbc.E03-06-0360

Figure Lengend Snippet: Subset of the regulated genes in each treatment identified by the microarrays

Article Snippet: These findings demonstrate that only 38 of the 228 (17%) genes are regulated by both ERα and ERβ with E 2 . table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Differential gene regulation by E 2 and SERMs in the U2OS-ERα and U2OS-ERβ cell lines Open in a separate window (A) Doxycycline-induced U2OS-ERα and U2OS-ERβ cells were treated with 10 nM E 2 , 1 μM raloxifene, or 1 μM tamoxifen for 18 h. Microarray data obtained from human Affymetrix U95Av2 gene chips from untreated versus ligand-treated samples were analyzed using the Affymetrix Microarray Suite Version 5.0.

Techniques: Modification, Transduction, Coagulation, Activation Assay, De-Phosphorylation Assay

Journal:

Article Title: Estradiol and Selective Estrogen Receptor Modulators Differentially Regulate Target Genes with Estrogen Receptors ? and ? D⃞

doi: 10.1091/mbc.E03-06-0360

Figure Lengend Snippet: Regulation of selected genes by E2 and SERMs in the U2OS-ERα and ERβ cell lines. Doxycycline-induced U2OS-ERα and ERβ cells were treated for 18 h with 10-11-10-8 M E2 (A), 10-8-10-6 M raloxifene (B), or 10-8-10-6 M tamoxifen (C). The extracted total RNA was analyzed by RT-PCR as described in MATERIALS AND METHODS. The genes examined were the WISP-2, α-AT, NKG2C, cDNA clone image 996282, NKG2E, and G0S2. Glyceraldehyde-3-phosphate dehydrogenase was used as an internal control. The data presented were representative of at least three experiments.

Article Snippet: These findings demonstrate that only 38 of the 228 (17%) genes are regulated by both ERα and ERβ with E 2 . table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Differential gene regulation by E 2 and SERMs in the U2OS-ERα and U2OS-ERβ cell lines Open in a separate window (A) Doxycycline-induced U2OS-ERα and U2OS-ERβ cells were treated with 10 nM E 2 , 1 μM raloxifene, or 1 μM tamoxifen for 18 h. Microarray data obtained from human Affymetrix U95Av2 gene chips from untreated versus ligand-treated samples were analyzed using the Affymetrix Microarray Suite Version 5.0.

Techniques: Reverse Transcription Polymerase Chain Reaction

Journal:

Article Title: Estradiol and Selective Estrogen Receptor Modulators Differentially Regulate Target Genes with Estrogen Receptors ? and ? D⃞

doi: 10.1091/mbc.E03-06-0360

Figure Lengend Snippet: Summary of genes commonly regulated by E 2 and SERMs in the U2OS-ERα and U2OS-ERβ cell lines

Article Snippet: These findings demonstrate that only 38 of the 228 (17%) genes are regulated by both ERα and ERβ with E 2 . table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Differential gene regulation by E 2 and SERMs in the U2OS-ERα and U2OS-ERβ cell lines Open in a separate window (A) Doxycycline-induced U2OS-ERα and U2OS-ERβ cells were treated with 10 nM E 2 , 1 μM raloxifene, or 1 μM tamoxifen for 18 h. Microarray data obtained from human Affymetrix U95Av2 gene chips from untreated versus ligand-treated samples were analyzed using the Affymetrix Microarray Suite Version 5.0.

Techniques:

Journal:

Article Title: Estradiol and Selective Estrogen Receptor Modulators Differentially Regulate Target Genes with Estrogen Receptors ? and ? D⃞

doi: 10.1091/mbc.E03-06-0360

Figure Lengend Snippet: Regulation of SERM-specific genes in the U2OS-ERα cell line. (A) U2OSERα cells were treated with 1 μg/ml doxycycline and 1 μM raloxifene or 1 μM tamoxifen for 3 h. The expression patterns of TGFβ3 (induced by raloxifene), G0S2 (induced by tamoxifen), and thrombin receptor (inhibited by tamoxifen) were evaluated by semiquantitative RT-PCR. (B) U2OS-ERα and ERB cells were treated for 18 h with doxycycline and SERMs, and the expression patterns of TGFβ3, G0S2, and thrombin receptor were measured by real-time qualitative RT-PCR.

Article Snippet: These findings demonstrate that only 38 of the 228 (17%) genes are regulated by both ERα and ERβ with E 2 . table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Differential gene regulation by E 2 and SERMs in the U2OS-ERα and U2OS-ERβ cell lines Open in a separate window (A) Doxycycline-induced U2OS-ERα and U2OS-ERβ cells were treated with 10 nM E 2 , 1 μM raloxifene, or 1 μM tamoxifen for 18 h. Microarray data obtained from human Affymetrix U95Av2 gene chips from untreated versus ligand-treated samples were analyzed using the Affymetrix Microarray Suite Version 5.0.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction

Journal:

Article Title: Estradiol and Selective Estrogen Receptor Modulators Differentially Regulate Target Genes with Estrogen Receptors ? and ? D⃞

doi: 10.1091/mbc.E03-06-0360

Figure Lengend Snippet: Regulation of selected genes by E2 and SERMs in the breast cancer MCF-7 cell line. ERα expressing MCF-7 cells were treated for 18 h with 10 nM E2 (A), 1 μM raloxifene (B), or 1 μM tamoxifen (C). The expression patterns of K19, WISP-2, α-AT, NKG2C, unknown cDNA 996282, NKG2E, and G0S2 were determined by semiquantitative RT-PCR.

Article Snippet: These findings demonstrate that only 38 of the 228 (17%) genes are regulated by both ERα and ERβ with E 2 . table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Differential gene regulation by E 2 and SERMs in the U2OS-ERα and U2OS-ERβ cell lines Open in a separate window (A) Doxycycline-induced U2OS-ERα and U2OS-ERβ cells were treated with 10 nM E 2 , 1 μM raloxifene, or 1 μM tamoxifen for 18 h. Microarray data obtained from human Affymetrix U95Av2 gene chips from untreated versus ligand-treated samples were analyzed using the Affymetrix Microarray Suite Version 5.0.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction