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ABSTRACT:
PROVIDER: EGAD00010002146 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:metabolite levels measured by general metabolomics (Boston, USA) (the data is raw abundance. Mapping was applied on log10 transformed data)
| EGAD00010002148 | EGA
Project description:The Iconix data set (endpoint B) was provided by Iconix Biosciences, Inc. (Mountain View, CA, USA). The study objective was to assess, upon short term exposure, hepatic tumor induction bynon-genotoxic chemicals, since there are currently no accurate and well-validated short-term tests to identify non-genotoxic hepatic tumorigens, thus necessitating an expensive 2-year rodent bioassay before a risk assessment can begin. The reanalysis has been carried out with log2 transformed gene expression levels of the raw signal values. The data in this Series were initially submitted in GEO Series GSE8251.
2010-09-29 | GSE24417 | GEO
Project description:Measurement of mRNA abundance from the following cells lines (red) versus universal mouse reference RNA (green). Wildtype v-Abl transformed pre-B cells were treated for 12 hours with 2.5 uM imatinib mesylate, 10ng/mL rapamycin or nothing. Compound Based Treatment: wildtype v-Abl transformed pre-B cells were treated with imatinib mesylate (IMA), rapamycin (RAP) or nothing (NONE)
2013-01-10 | GSE35040 | GEO
Project description:To identify the expression profiles of circRNAs in peripheral blood mononuclear cells (PBMCs) from Ankylosing Spondylitis (AS) patients and healthy controls, we used circRNA sequencing to detect circRNA in 3 samples of PBMCs from AS patients and 3 samples of PBMCs from healthy controls. In brief, total RNA was extracted and purified using Magen Hipure Total RNA Mini Kit (Magen, Guangzhou, China), followed by constructing RNA sequencing libraries with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., MA, USA). After the construction of RNA sequencing libraries, Qubit 3.0 fluorometer (Invitrogen, CA, USA) and the Agilent 2100 bioanalyzer (Applied Biosystems, CA, USA) were used for quality control. Then, the PE150 mode of HiSeq X10 (Illumina Inc., CA, USA) was used for sequencing. Differentially expressed circRNAs were screened with criteria of fold-change>1.5 and p<0.05.
2022-01-05 | GSE178408 | GEO
Project description:Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the fungistatic saponin tomatidine. Overnight batch cultures of strain S288C were diluted to an optical density at 600nm of 0.1. After 1 hour of growth at 30°C, the compounds were added and the cultures were incubated for an additional 5 hours prior to harvesting. Control cultures were treated with the solvent dimethylformamide (DMF). Tomatidine treated cultures were grown in the presence of tomatidine (dissolved in DMF) at concentations of 7.5 uM and 15 uM. Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen. Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA). Microarray hybridisation was performed using the Affymetrix GeneChip® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001). Data were analyzed using Affymetrix® Microarray Suite version 5.0 software Keywords: dose response
2004-11-06 | GSE1927 | GEO
Project description:Measurement of mRNA abundance from the following cells lines (red) versus universal mouse reference RNA (green). Wildtype v-Abl transformed pre-B cells were treated for 12 hours with 2.5 uM imatinib mesylate, 10ng/mL rapamycin or nothing. Compound Based Treatment: wildtype v-Abl transformed pre-B cells were treated with imatinib mesylate (IMA), rapamycin (RAP) or nothing (NONE) compound_treatment_design
2013-01-10 | E-GEOD-35040 | biostudies-arrayexpress
Project description:Genome-wide expression profiling was used to identify genes that showed altered expression in response to treatment with the fungistatic saponin tomatidine. Overnight batch cultures of strain S288C were diluted to an optical density at 600nm of 0.1. After 1 hour of growth at 30°C, the compounds were added and the cultures were incubated for an additional 5 hours prior to harvesting. Control cultures were treated with the solvent dimethylformamide (DMF). Tomatidine treated cultures were grown in the presence of tomatidine (dissolved in DMF) at concentations of 7.5 uM and 15 uM. Growth inhibition by the compounds was monitored by measuring the OD600nm. Cells were pelleted and frozen in liquid nitrogen. Acid-washed glass beads (0.5 mm diameter; Sigma) were added and the cells disrupted using two 20 s cycles at speed setting 6 in the Savant Bio 101 Fast Prep FP120. Total RNA was isolated using the Qiagen RNeasy kit (Qiagen, Inc., Valencia, CA, USA). Microarray hybridisation was performed using the Affymetrix GeneChip® Yeast genome S98 array using protocols described by Affymetrix, Inc. (Santa Clara, CA, USA) (as previously described (Zhu et al., 2001). Data were analyzed using Affymetrix® Microarray Suite version 5.0 software
2008-06-11 | E-GEOD-1927 | biostudies-arrayexpress
Project description:Custom Affymetrix SNP used to assay 24 mothers for desired variants. Data processed using the Affymetrix SNP Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA).
2017-11-30 | GSE107512 | GEO
Project description:In the current study a microarray (46k, University of Arizona, USA) analysis of 21 European maize (Zea mays L.) parental inbred lines (14 dent and 7 flint) was applied. The aim was the identification of parental genes which expression levels are correlated to heterosis and/or hybrid performance for grain yield (GY) and grain dry matter content (GDMC) in the hybrid progeny (F1). Therefore gene expression profiles of differentially expressed genes of the parental inbred lines at the seedling stage were correlated with GY- and GDMC-field data of 98 flint x dent factorial crosses gained at six different locations in Germany. The identification of heterosis-correlated genes is an approach for the characterization and also for the prediction of this phenomenon. For the analyses total RNA of seven days old seedlings was extracted and aminoallyl-labeled RNA probes were synthesized. RNA labeling (Cy3, Cy5) and hybridizations were performed according to the protocol of the maize oligonucleotide array project (http://www.maizearray.org). The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA). An experimental interwoven loop design was developed aiming to yield in a preferably low average variance among the hybridizations, especially between intergroup (dent lines vs. flint lines) hybridizations. As a result 12288 (28.3%) of the genes showed differential expression between any combination of inbred lines. These differentially expressed genes were used for subsequent field data correlation analyses.
2010-08-21 | GSE17754 | GEO
Project description:The main aim of the study was to compare genome-wide gene expression profiles obtained from the two widely used commercially available whole blood RNA collection systems - PAXgeneTM and TempusTM tubes. Comparisons of present call rates, variances, correlations and influence of globin reduction across the two collection systems was performed using in vivo glucocorticoid stimulation in 24 peripheral blood samples from three individuals. Three healthy male volunteers aged 30-35 years with body mass index of 20-25 were enrolled in the study.1.5 mg dexamethasone stimulated peripheral blood samples were drawn 3 hours later. For each sample, duplicate measures of 2.5 ml and 3ml blood was collected in PAXgeneTM tubes (PreAnalytiX GmbH, Hombrechtikon, Switzerland) and TempusTM tubes (Applied Biosystems, Foster City, CA, USA) respectively. The PAXgeneTM and TempusTM tubes were stored for 2.5 hours at room temperature and then transferred to -20°C. Due to the lower RNA yield from the PAXgeneTM tubes, RNA from two PAXgeneTM tubes was pooled together for the experiment . Total RNA was isolated from whole blood stored in PAXgeneTM and TempusTM tubes according to the respective manufacturer's instructions. The PAXgeneTM samples were processed using the PAXgeneTM Blood RNA Kit based on the Quiagen method for column purification of nucleic acids (PreAnalytiX GmbH, Hombrechtikon, Switzerland, catalogue number 762174). The TempusTM samples were isolated using the TempusTM Spin RNA Isolation Kit (Applied Biosystems, Foster City, CA, USA, catalogue number 4380204). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The concentration and purity of total RNA was independently assessed by 260/280 UV absorption ratios, respectively (Nanophotometer, Implen, Munich, Germany). RNA samples were divided into non-globin reduced and globin reduced groups. The GLOBINclearTM-Human Kit (Ambion, Inc., Texas, USA, catalogue number #AM1980) was used to remove globin mRNA. Sample amplification and labeling for both globin-reduced and non-reduced samples was performed using the IlluminaR TotalPrep RNA Amplification Kit (Ambion, Inc., Texas, USA, catalogue number AMIL1791).
2012-01-15 | GSE34039 | GEO