ADME_gene_expression
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010001709 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:RATIONALE: Studying the genes expressed in samples of tissue from patients with cancer may help doctors identify biomarkers related to cancer.
PURPOSE: This laboratory study is using gene expression profiling to evaluate normal tissue and tumor tissue from patients with colon cancer that has spread to the liver, lungs, or peritoneum.
| 2071958 | ecrin-mdr-crc
Project description:The purpose of this study is to obtain an "in vivo" confirmation that mesalazine induces the gene expression of μ-protocadherin and other related genes in the colon mucosa, as demonstrated in some "in vitro" experiments. .
| 2161957 | ecrin-mdr-crc
Project description:Gender dependent gene expression in the kidney of 36 day old rats using the Affymetrix GeneChip rat expression set 230 array RAE230A. mixed model ANOVA using log2 transformed signal intensity of PM. Keywords: repeat
2006-12-31 | GSE3778 | GEO
Project description:Triple negative breast tumours from archived formalin fixed paraffin embeded samples of the National Cancer Institute of Mexico were analyzed for differential gene expressión. Transcriptomic analysis of the 12 tumor samples was done with the FFPE-designed WG-DASL HT assay (Illumina) according to manufacturer’s instructions. This assay measures 29,285 annotated transcripts derived from the RefSeq database corresponding to 20,727 unique genes. Briefly, 200ng of total RNA were reverse-transcribed into biotinylated cDNA, which was then primer-extended with the Assay Specific Oligos. The cDNA was then amplified with universal primers and hybridized to Illumina Human WG DASL HT Expression BeadChip arrays. The Illumina Genome Studio V2010.2 was used to obtain the signal values (AVG-Signal), with no normalization and no background subtraction.The performance of hybridizations was evaluated by assessing the presence of outliers and the noise-to-signal ratios by calculating the ratio of centiles P95/P05 prior to normalisation for each sample. We defined outliers as samples with P95/P05 ratio <9.5. All samples were found to show a correct noise-to-signal ratio (P95/P05>9.6). For differential gene expression analysis, the public dataset GSE32124, which includes 33 fresh frozen tissue samples, generated on the Illumina HumanHT-12 v4.0 beadChip, and which contains 99.98% of the 29,285 probes of the Human WG DASL HT BeadChip was used as normal breast tissue control.
2015-05-12 | E-GEOD-62502 | biostudies-arrayexpress
Project description:Primary outcome(s): Gene expression of targeted genes
| 2625389 | ecrin-mdr-crc
Project description:Log2 gene expression count data from RNA sequencing.
| EGAD00001008793 | EGA
Project description:Studies on the early embryonic development of Xenopus laevis contributed much to the understanding of vertebrate patterning. Gastrula stages are of particular interest because establishment of the axis and germ layer formation take place during these stages. While many genes belonging to several signaling pathways including FGF, Wnt and TGF-beta, have been implicated in patterning the gastrula embryo, the hierarchical interactions between these factors are incompletely known. To study this question, we took advantage of microarray technology to create a regional gene expression profile for the Xenopus gastrula. Stage 10 Xenopus embryos were dissected into four portions. The dorsal marginal zone including the blastopore and some ectoderm and dorsal yolk plug, composed mostly of endomesoderm; the ventral marginal zone, also containing a portion of the yolk plug; the animal cap, dissected just above the floor of the blastocoel; and the vegetal region, composed of the central part of the yolk plug. To avoid possible cross contamination that might blur the microrarray data, thin junctional regions between the explants were removed. The dissected explants were homogenized in Stat 60 (TEL TEST), RNA was precipitated by isopropanol, treated with DNase I, and purified using the RNeasy kit (Qiagen). Biotinylated probe was prepared from 100 ng total RNA using the OVATION RNA amplification system (Nugen Technologies, Inc). The probes were hybridized to Affymetrix Xenopus Chips containing features that represent about 15,000 genes according to the manufacture’s instructions. Hybridized arrays were further processed by the GeneChip Fluidics system (Affymetrix), and signals were detected by the GeneChip Scanner (Affymetrix). Gene expression profiles were analyzed by the GCOS software (Affymetrix). The analysis showed that 100 transcripts were enriched in the dorsal explant (dorsal vs. ventral, signal log2 ratio>1.5), including the known dorsal markers Chordin, gsc, Admp; 90 transcripts were enriched in the ventral explant (ventral vs. dorsal, signal log2 ratio>1.5) including Sizzled, bambi, PV.1; 449 transcripts were enriched in the vegetal explant (vegetal vs. dorsal, vegetal vs. ventral, vegetal vs. animal cap, all signal log2 ratio>1.5), including Mixer, Sox17; 70 transcripts were enriched in the animal cap (animal cap vs. vegetal, signal log2 ratio>1.5; animal cap vs. dorsal, signal log2 ratio>1; animal cap vs. ventral, signal log2 ratio>1) including Epidermal type I cytokeratin and forkhead-2. RT-PCR was used to check the enrichment of some of the unknown genes; the enrichment of 8 of 9 ventral genes, and 9 of 12 dorsal genes was confirmed in these experiments. Keywords: Xenopus, gastrula, explant, gene expression, embryonic, gene regulation
2007-11-01 | GSE8990 | GEO
Project description:The molecular regulation of megakaryocytic differentiation is poorly understood. Using a myelogenous leukemia cell line, K562, which can partly recapitulate the process in response to phorbol 12-myristate 13-acetate (PMA), we performed a microarray-based gene expression profiling using Illumina HumanRef-8 Expression Beadchip to identify genes that play significant roles in megakaryopoiesis. Time course microarray data were obtained at 8 time points. Illumina HumanRef-8 Expression Beadchip has ~over 24,000 transcripts a piece. Duplicate experiments were performed for each time point. Here, we reported raw data of two independent experiments. After microarray data analysis, selecting genes with significant detection p-value produced ~14,000 probes out of total 23,920 probes. Quantile normalization was carried out for each dataset at 8 time points using the average expression value. The K-means clustering method (k=12) was used to classify those probes according to characteristic temporal pattern. We selected transcription factors shown fold changes in a time dependent manner to examine genes related for megakaryopoiesis. Finally, we can suggest that FosB which belongs to the Fos family of AP1 transcription factors is related in megakaryopoiesis.
2009-06-01 | GSE12736 | GEO
Project description:Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Columbia (WT) and Auxin response factor 2 (ARF2) T-DNA insertion mutant (arf2-6 ) were used for this study. Each experimental condition has three true replicates for a total of 12 hybridizations. Data analysis: Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The data files containing the probe level intensities (cell files) were used for background correction and normalization using the log2 scale robust multi-array analysis (RMA) procedure (Irizarry et al., 2003). The “R” environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2 converted expression intensity data within Microsoft Excel 98. Based on preliminary analysis, a hybridization signal less than 5.64385619 (= log2 50) was considered as background; all signals less than 5.64385619 were converted to 5.64385619 prior to further analysis. Keywords = Auxin Keywords = Auxin response factor Keywords: other
2005-10-19 | GSE631 | GEO
Project description:RNA was extracted from cells using Aurum Total RNA kit from Bio-Rad Laboratories, Inc., Hercules, CA following the manufacturer’s recommendations. Gene expression profiling was performed using the BeadChip HumanHT-12 v4 Expression kit from Illumina®, which contains 47,231 gene-probes (Illumina® Inc., San Diego, CA). The raw signal intensities were imported and analyzed using the GenomeStudio® data software. After background subtraction and normalization, the signal intensity values were exported to the Partek® genomics expression analysis suite using “Partek's Report Plug-in” option in the GenomeStudio® software. Differentially expressed genes in the dox- versus vehicle-treated samples were identified using the “gene expression” workflow in the Partek® software.
2012-10-29 | GSE41894 | GEO