Rat Brain-Heart-Liver Control Mix Self-Self Hybridization
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE8950 | GEO | 2007/09/11
SECONDARY ACCESSION(S): PRJNA102381
REPOSITORIES: GEO
Similar Datasets
Project description:a- Self –Self Hybridisation were used to set confidence 99% interval using RNA from non-tethered cell lines that is both labelled in with cy3 cy5 (theoretically identical cDNA populations) to compared technical errors associated with such experiments Keywords: comparative hybridization to access expression profiles between Cy3 and Cy5 uniformally labelled template.
2008-03-04 | GSE10697 | GEO
Project description:Microarrays were hybridized with a mixture of solutions containing LL2 cDNA labeled with Cy3 or Cy5 (dye-swap) and LL14 cDNA labeled with Cy5 or Cy3 (dye-swap). Keywords: repeat sample
2004-12-29 | GSE2114 | GEO
Project description:To compare total RNA levels in miR-124 and mock-transfected cells (Figure S3), 5-10 ug of total RNA from miR-124-transfected cells or mock-transfected cells or universal reference RNA (Stratagene Cat# 740000) was reverse transcribed with Superscript III (Invitrogen Cat# 18080085) in the presence of aminoallul-dUTP 5-(3-aminoallyl)-dUTP (Ambion Cat# AM8439) and natural dNTPs (GE Healthsciences Cat# US77212) with 10 ug of N9 primer (Invitrogen). Subsequently, amino-allyl-containing cDNAs from miR-124 and mock-transfected cells were covalently linked to Cy5 NHS-monoesters, and universal reference cDNA was covalently linked to Cy3 NHS-monoesters (GE HealthSciences Cat# RPN5661). Cy5- and Cy3-labeled cDNAs were mixed and diluted into 50 ul of solution containing 3x SSC, 25 mM Hepes-NaOH (pH 7.0), 20 ug human Cot-1 DNA (Invitrogen Cat# 15279011), 20 ug of poly(A) RNA (Sigma Cat# P9403), 25 ug of yeast tRNA (Invitrogen Cat# 15401029), and 0.3% SDS. The sample was incubated at 95 C for 2 min, spun at 14,000 rpm for 10 mins in a microcentrifuge, then hybridized at 65 C
2009-11-10 | GSE18837 | GEO
Project description:To measure the relative changes of gene expression upon Gis2p depletion, 50 ml of delta Gis2 cells or the respective wild-type strain BY4741 were grown in YPD at 30 degrees celsius to an OD600 of 0.5- 0.6. Cells were harvested by centrifugation and washed twice with 5ml of bidistilled water (ddH2O). RNA was isolated by hot phenol extraction for microarray analysis. 20 ug of total RNA derived from wild-type and knock-out cells were reverse transcribed in the presence of 5-(3-aminoallyl)-dUTP and natural dNTPs with a mixture of N9 and dT20V primers, and cDNAs were covalently linked to Cy3 and Cy5 NHS-monoesters (GE HealthSciences Cat# RPN5661), respectively, and competitively hybridized onto yeast oligo arrays at 42 degrees celsius for 14 hours in formamide-based hybridization buffer. Microarrays were scanned with an Axonscanner 4200 (Molecular Devices) and analyzed with GenePix Pro 5.1 (Molecular devices) before uploading into Stanford Microarray Database.
2010-12-22 | GSE24004 | GEO
Project description:The objective of the present study was to use our own fabricated bovine embryo cDNA microarray to profile genome-wide expression patterns of genes during the implantation period. Duplicate readings were obtained by hybridization of a Cy3/Cy5 probe mixture for each sample. Data normalization was performed the local background intensity of each array spot was smoothed by the local weight regression (lowess) smoother and subtracted from spot intensity data. The subtracted intensity data were subjected to non-parametric regression and local variance normalization because non-parametric regression can reduce intensity-depended biases. Accuracy is improved, when compared to linear regression, if the points in the scatter plot of Cy3 vs. Cy5 are not distributed around a straight line. Keywords = Gene expression Keywords = embryo Keywords = fetus Keywords = fetal membrane Keywords = implantation period Keywords: time-course
2004-11-24 | GSE1414 | GEO
Project description:Fibroblast-like synoviocytes (FLS) were cultured from synovial tissues from 19 RA patients. RNA was isolated using the Fast Track 2.0 kit (Invitrogen, Carlsbad, California)from the FLS cultures. Fluorescent cDNA probes were prepared from 1 ug experimental mRNA by oligo dT-primed polymerization using Superscript II reverse transcriptase in the presence of Cy5 labeled dCTP. A common reference mRNA sample (CRE) that consists of a mixture of mRNAs isolated from 11 different cell-lines, was labeled with Cy3. The Cy5 and Cy3 labeled cDNAs were pooled and hybridized to a 24,000 cDNA microarray. Set of arrays that are part of repeated experiments Keywords: Biological Replicate
2006-01-19 | GSE4061 | GEO
Project description:Measure the relative changes of gene expression upon GIS2 overexpression; 100 ml of BY4741 cells bearing plasmid pBG1805-Gis2 (GIS2 under the control of the galactose promotor) or the empty plasmid pBG1805 (=control) were grown in synthetic medium lacking uracil (SC-Ura supplemented with 2% raffinose) at 30 degrees to an OD600 of 0.45- 0.5. Expression of GIS2 was induced with 2% galactose for 1.5 h and cells were harvested by centrifugation, washed twice with 800 ul of ice-cold sterile water. 100 ul (1/8) of cells were removed and RNA was isolated by hot phenol extraction for microarray analysis. 6.7 ug of total RNA derived from cells expressing the empty vector (pBG1805) or Gis2p (pBG1805-Gis) were reverse transcribed in the presence of 5-(3-aminoallyl)-dUTP and natural dNTPs with a mixture of N9 and dT20V primers, and cDNAs were covalently linked to Cy3 and Cy5 NHS-monoesters (GE HealthSciences Cat# RPN5661), respectively, and competitively hybridized on yeast oligo arrays at 42 degrees celsius for 14 hours in formamide-based hybridization buffer. Microarrays were scanned with an Axonscanner 4200 (Molecular Devices) and analyzed with GenePix Pro 5.1 (Molecular devices).
2010-12-22 | GSE24002 | GEO
Project description:Measure the relative changes of gene expression upon GIS2 overexpression; BY4741 cells bearing plasmid pBG1805-Slf1 or control plasmid pBG1805 were grown in SC ura- gal at 30 C for 6 or 24 hours. An overnight culture of cells was inoculated at an OD600 of 0.1 and further grown to an OD600 of 0.5- 0.7 in 60 ml SC Ura- Gal at 30 C. Cells were harvested by centrifugation, washed twice with 600 ul of ice-cold sterile water. 200 ul of cells were removed and RNA was isolated by hot phenol extraction for microarray analysis. 7.5 ug of total RNA derived from cells expressing the empty vector (pBG1805) or Slf1p (pBG1805_Slf1) were reverse transcribed in the presence of 5-(3-aminoallyl)-dUTP and natural dNTPs with a mixture of N9 and dT20V primers, and cDNAs were covalently linked to Cy3 and Cy5 NHS-monoesters (GE HealthSciences Cat# RPN5661), respectively, and competitively hybridized on yeast oligo arrays at 42 degrees celsius for 14 hours in formamide-based hybridization buffer. Microarrays were scanned with an Axonscanner 4200 (Molecular Devices) and analyzed with GenePix Pro 5.1 (Molecular devices).
2012-02-08 | GSE27311 | GEO
Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 1: reproducibility of labeling: mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples. Keywords: variety among tissues
2008-04-01 | GSE7530 | GEO
Project description:This series repressents the data set from the paper "Expression microarray analysis and oligo array CGH of aquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations". Biological material: One solid mouse tumor "Colon 26A" was routinely maintained by successive transplantation. A subset of mice with this tumor was treated at the maximum tolerable dosage of Gemcitabine and successively transplanted 5 times and similarly treated. The last passage was completly resistant and designated, "Colon 26G". Expression array: Total RNA was isolated from frozen mouse tumors using Tryzol. Single stranded cDNA was synthetized from 30 mg of total RNA by reverse transcription using aminoallyl labeled dUTP (Ambion). Labelling was performed according to the aminoallyl labeling protocol. Briefly, cDNA was incubated at room temperature for 1 h with fluorolink monofunctional cy5 or cy3 (Amersham) followed by 15 min 4 M hydroxylamine treatment. Uncoupled dyes were removed using Qiaquick PCR purification columns (Qiagen) and mixed with 12 mg poly(dA) (Amersham), 60 mg yeast tRNA (Sigma) and 24 mg Cot-1 DNA (Invitroen). The probe was dissolved in 127 ml hybridization mixture containing 46% formamide, 9.5% dextran sulfate, 2x SSC and 0.2% SDS. The probe was heated to 70°C for 10 min and annealed at 37°C for 1 h. Slides were hybridized for 14 h at 37°C over-night (HyArray 12™, Perkin Elmer). After hybridization the slides were washed in the HybArray 12™ with 50% formamide, 2x SSC, pH 7 at 35°C for 15 min, followed b PI buffer (0.1 M sodium phosphate, 0.1% Igepal Ca630, pH 8) at room temperature and 3 washes of 0.2x SSC, 0.1x SSC and 0.01x SSC at room temperature followed by centrifugation. Arrays were scanned using a laser scanner (ScanArray Express, Perkin Elmer) and analysed using ImaGene version 5.6. Cy5 cy3 ratios are calculating by taking the log2 of the signal mean of each spot minus the median background mean of all spots on the array. This is followed by a standard normalization for spot intensity and calculation of the ratios. Keywords: other
2005-12-21 | GSE2352 | GEO