Project description:Comparison of expression profiles in early Drosophila embryos and unfertilised eggs (collection intervals: 30-60 min, 90-120 min and 150-180 min after egg laying). A complete summary file containing normalized data with FLYBASE CG gene identifiers, gene symbols and classifications can be found in E-MEXP-2580.additional.zip under the "Browse all available files" link
Project description:Genomewide mapping of D. melanogaster Biniou protein binding during embryonic development. Three consecutive timepoints (6-8, 8-10, 10-12 hrs after egg-laying) were assayed in two independent repeats each. Two different antibodies were used to precipitate the Biniou protein. Additionally the respective preimmune-serum was used as a control for every precipitation. The enriched DNA was hybridized to high density Affymetrix GeneChip Drosophila Tiling 1.0R array.
Project description:Genomewide mapping of D. melanogaster Tinman protein binding during embryonic development. Three consecutive timepoints (2-4, 4-6, 6-8 hrs after egg-laying) were assayed in two independent repeats each. Two different antibodies were used to precipitate the Tinman protein. Additionally the respective preimmune-serum was used as a control for every precipitation. The enriched DNA was hybridized to high density Affymetrix GeneChip Drosophila Tiling 1.0R array.
Project description:Transcription profile of cls/sox10 mutants at 4dpf compared to their wild type siblings at 4 days post fertilization. Transcription profile of hps/erbb3b mutants compared to a wild type control at 4 days post fertilization.
Project description:Mouse ErythroLeukaemic (MEL) cell lines were maintained in DMEM<br>supplemented with 10% fetal calf serum and penicillin/streptomycin. MEL<br>cells in the log phase of growth (0.5 to 1 millions cells / mL) were<br>induced to differentiate with 2% dimethylsulfoxide (DMSO) for four days.<br>Total RNA was isolated in triplicate from non-induced and DMSO-induced MEL<br>cells using RNeasy Mini Kit (Qiagen). Purity and quality of isolated RNA<br>were assessed by RNA 6000 Nano assay on a 2100 Bioanalyzer (Agilent<br>Technologies, Santa 6 Clara, CA). All samples showed a RIN>8 and were all<br>used for subsequent labeling. RNA (300 ng) was used for production of<br>end-labelled biotinylated ssDNA. Labelled ssDNA was hybridized to the<br>GeneChip Mouse Gene 1.0 ST array oligonucleotide microarray (Affymetrix,<br>Santa Clara, CA) according to manufacturers recommendations. To examine<br>the quality of the various arrays, measured intensity values were analyzed<br>using Gene Expression Console (Affymetrix, Santa Clara, CA). The analyses<br>indicated a high quality of all samples and overall comparability. The<br>microarray data was normalized by quantile normalization, and followed by<br>a summarization using Tukeys median polish algorithm (Irizarry et al.,<br>2003) in Expression Console from Affymetrix (Santa Clara, CA). Data was<br>further processed using packages within the Bioconductor project in the R<br>statistical programming environment (Gentleman et al., 2004). In order to<br>normalize between experimental batches and receive a dataset with variance<br>independent of absolute expression levels data were renormalized applying<br>vsn2 function (Huber et al., 2002). The log2 intensities for each probe<br>were used for further analysis. Differentially expressed genes were<br>determined applying the limma Bioconductor package and using the functions<br>lmFit and eBayes with default settings. Resulting p-values were adjusted<br>for multiple testing according to Benjamini-Hochberg (Hochberg and<br>Benjamini, 1990). All calculations were performed in the R statistical<br>programming environment (Huber et al., 2002) version 2.8.0. Hierarchical<br>clustering (Eisen et al., 1998) was performed using MeV4.0.01 (Saeed et<br>al., 2003) applying euclidean distance and average linkage.
Project description:Rsp5 is an essential and multi-functional E3 ubiquitin ligase in Saccharomyces cerevisiae. We previously isolated the Ala401Glu rsp5 mutant, which is hypersensitive to various stresses. To understand the function of Rsp5 in stress responses, suppressor genes whose overexpression allows rsp5A401E cells to grow at high temperature were screened. The KIN28 and POG1 genes, encoding a subunit of the transcription factor TFIIH and a putative transcriptional activator, respectively, were identified as multicopy suppressors of not only high temperature but also LiCl stresses. The overexpression of Kin28 and Pog1 in rsp5A401E cells caused an increase in the transcriptional level of some stress proteins when exposed to temperature up-shift. DNA microarray analysis under LiCl stress revealed that the transcriptional level of some proteasome components was increased in rsp5A401E cells overexpressing Kin28 or Pog1. These results suggest that the overexpression of Kin28 and Pog1 enhances the protein refolding and degradation pathways in rsp5A401E cells. Experiment Overall Design: Total RNA from S. cerevisiae was isolated by the method of Köhrer and Domdey (1991). Poly A mRNA was enriched from total RNA by Oligotex dT30 mRNA purification kit (Takara Bio). The Affimetrix yeast genome S98 arrays (YGS98 GeneChip, Affymetrix, Santa Clara, CA) were used as DNA microarray in this study. The biotinyated cRNA (15 μg) probe was hybridized to DNA microarray at 45°C for 18 h according to Affymetrix userâs manual. Experiment Overall Design: The washing and staining of arrays were performed using the GeneChip Fluidics Station 400. Experiment Overall Design: The scanning of arrays was carried out using the GeneArray scanner (Agilent technologies, Palto Alto, CA).
Project description:To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r| > 0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture. Experiment Overall Design: Gene expression profiles were correlated with beef traits measured at the same cattle.
Project description:Smoking is the leading cause of lung cancer death, although only a small percentage of smokers develop the disease. Cigarette smoke exposure is known to cause a field of injury in cells throughout the respiratory tract, and while these airway epithelial cells are morphologically normal, they can undergo genetic alterations in response to cigarette smoke exposure. We used microarrays to analyze the gene expression of epithelial cells in the extrathoracic epithelium, specifically nasal and buccal epithelium, to see if these cells underwent similar genetic alterations in response to tobacco exposure as seen in bronchial epithelial cells as has been previously reported. Experiment Overall Design: Buccal and nasal epithelial cell samples were collected from healthy current and never smokers. RNA was isolated from these samples and hybridized to Affymetrix microarrays. Gene expression from never smokers was compared to never smoker gene expression from bronchial epithelium as well as expression data from other tissues to determine commonalities in expression patterns in normal extra- and intra-thoracic samples. In addition, gene expression from smokers and nonsmokers was compared in bronchial, nasal, and buccal epithelium to determine similarities in gene expression in these tissues in response to cigarette smoker exposure.
Project description:To identify the eye-enriched genes by comparing the mRNA expression profiles from wild type fly heads (CantonS) and eye-less fly heads (sine occulis).