Effect of mutant p53 R282W on miRNA expression
Ontology highlight
ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE73876 | GEO | 2015/10/10
SECONDARY ACCESSION(S): PRJNA298290
REPOSITORIES: GEO
Similar Datasets
Project description:We examined expression profiles of genes that could be regulated by the MAPK pathways during mouse preimplantation development. We used Affymetrix GeneChips for microarray analysis, and three independent experiments were carried out. 8-cell stage embryos were treated or untreated with MAPK inhibitors, and blastocyst stage embryos were recruited for the study. Hybridization was carried out with the GeneChip Mouse Expression Set 430 or GeneChip Mouse Genome 430 2.0 Array following Affymetrix instructions. The array was then washed and stained using the GeneChip fluidics station according to the manufacture's instructions. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Expression analysis was performed using GeneChip Operating Software 1.0 (Affymetrix) and scaled to an average probe set intensity of 500. Keywords: other
2005-04-01 | GSE2229 | GEO
Project description:To functionally characterize the role of miR-17 family in HCC, lentiviral vector-based miR inhibitor TuD was used to inhibit miR-17 family of microRNAs in Hep3B cell line Methods: Hep3B HCC cell line was acquired from American Type Culture Collection (ATCC) and miR-17 TuD or NC TuD expressing lines were generated. Microarray profiling of miR-17 TuD or NC TuD expressing samples was performed using Affymetrix HG-U133Plus2 arrays. Briefly, starting with 1 ug total RNA, amplified biotin-labeled cRNA targets were produced using the Enzo Target Labeling method. Fragmented, biotin-labeled cRNA was hybridized to the Affymetrix GeneChip® HG-U133Plus2 Genome Arrays overnight at 45C for 16 to 18 hours according to the manufacturer’s recommendations. Stain, wash (GeneChip Fluidics Station 450, EukGE-WS2v5_450 script) and scan (GCS 3000 7G with the GeneChip® AutoLoader) were performed according to the manufacturer’s recommendations. Microarray data were GC Robust Multiarray Average (GCRMA) normalized using R and the bioconductor.org package gcrma and Log2 transformed.
2017-06-01 | GSE93799 | GEO
Project description:Tomato pericarp tissues at three different stages (green, breaker and ripening) of fruit development from both the above genotypes were collected using a sterile surgical blade and flash frozen in liquid nitrogen. High quality RNA was extracted from the frozen pericarp tissue using TRI Reagent (Ambion, INC. USA) and pooled at least from three independent samples and treated with DNase-I (QIAGEN GmbH, Germany). RNA cleanup was carried out using RNeasy Plant Mini Kit (QIAGEN GmbH, Germany) and 5ug of total RNA from each sample with three biological replications were reverse-transcribed to double stranded cDNA using the GeneChipR One-Cycle cDNA Synthesis Kit. The biotin-labelled cRNA was made using the GeneChipR IVT Labelling Kit (Affymetrix, CA, USA). 15 ug of cRNA samples was fragmented and was hybridized for 16 hours at 45C to the Affymetrix tomato GeneChip Array (Santa Clara, CA, USA). After washing and staining with R-phycoerythrin streptavidin in a Fluidics Station, using the GenechipR Fluidics Station 450, the arrays were scanned by the GenechipR 3000 Scanner. The chip images were scanned and extracted using default settings and the .CEL files were produced by using the Affymetrix GeneChip Operating Software (GCOS 1.2). Samples that passed through various quality checks (data not shown) were normalized with RMA algorithm using GeneSpring GX 10 (Agilent Technologies Inc., Santa Clara, CA, USA). Probes showing twofold up- or down-regulation (in Log2 transformed values) compared to corresponding control condition were taken only into consideration for further analysis
2011-01-04 | E-MEXP-2934 | biostudies-arrayexpress
Project description:Primary renal cell carcinoma (RCC) by Affymetrix GeneChip miRNA 4.0
| EGAD00010001564 | EGA
Project description:Light-controlled in situ synthesis of DNA microarrays (Affymetrix GeneChip® Mouse Genome 430 2.0) were performed to determine the altered gene expression. Affymetrix algorithm and multiple analysis comparison software were used for assessing gene expression differences, and mRNAs that increased or decreased in the brains of NP(α-M)-treated mice relative to that in the brains of Blank-NP-treated mice were identified. For the assay, total RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara, DaLian, LiaoNing, CN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions. Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).
2018-09-14 | GSE119904 | GEO
Project description:STEE regulated a wide range of biological processes in the cerebral cortex of SAMP8 mice. RNA samples were extracted from cerebral cortices with Isogen (Nippon Gene, Toyama, Japan) and were amplified and biotinylated with Affymetrix 3’ IVT PLUS Reagent Kit (Affymetrix, Santa Clara, CA), according to the manufacturer’s instructions. The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and one hundred ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA. Biotinylated cRNA was hybridized onto Affymetrix Mouse Genome 430 PM array strips (Affymetrix) for 16 hrs at 45℃ in the hybridization station. The hybridized arrays were washed, stained, and scanned with GeneAtlas Fluidics and Imaging Station.
2020-09-14 | GSE151727 | GEO
Project description:Arabidopsis ATH1 Genome Array was used to study the expression levels of 22,500 probe-sets representing 24,000 genes. Both wild type and different transgenic lines were allowed to grow for one month under normal condition was taken for expression analysis. These plants were treated with half strength of Hoagland solution supplemented with 200mM NaCl in pots for seven days for salinity treatment. High quality RNA was extracted from the healthy leaf samples using TRI Reagent (Ambion, INC. USA) and pooled from at least four independent stressed and non-stressed samples separately, and treated with DNase-I (QIAGEN GmbH, Germany). RNA cleanup was carried out using RNeasy Plant Mini Kit (QIAGEN GmbH, Germany) and 5µg of total RNA from each sample with three biological replications were reverse-transcribed to double stranded cDNA using the GeneChipR One-Cycle cDNA Synthesis Kit. The biotin-labelled cRNA was made using the GeneChipR IVT Labelling Kit (Affymetrix, CA, USA). Twenty microgram of cRNA samples was fragmented and was hybridized for 16 hours at 45°C to the Affymetrix Arabidopsis ATH1 Genome Array (Santa Clara, CA, USA). After washing and staining with R-phycoerythrin streptavidin in a Fluidics Station, using the GenechipR Fluidics Station 450, the arrays were scanned by the GenechipR 3000 Scanner. The chip images were scanned and extracted using default settings and the .CEL files were generated using Affymetrix GeneChip Command Console (AGCC) Software.<br>Atleast two ATH1 Genome Array was used for hybridisation for each group of samples.
2014-07-30 | E-MEXP-2858 | biostudies-arrayexpress
Project description:Basophil functional state was determined using the Flow2CAST Basophil Activation Test (BAT). Human basophils were isolated from whole blood of three house dust mite (HDM) responsive donors with reactive basophils and two donors with anergic basophils. Basophil isolation was performed using the EasySep Human Basophil Enrichment kit (Stemcell). Purity of the basophils was determined by flow cytometry and ranged from 96 - 99%. For stimulation, 75,000 basophils were incubated for 4 hr with or without 50 ul of anti-FCERI antibody (Bühlmann Laboratories) in a total volume of 200 ul of Stimulation Buffer provided by the Flow2CAST kit. After incubation, the basophils were collected and re-suspended in TRIzol Reagent (Life Technologies). Total RNA was extracted using double extraction protocol using the guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen), followed by a Qiagen RNeasy Micro clean-up procedure. cDNA and ST-ssDNA were prepared, fragmented and labeled according to Nugen WT Ovation Pico RNA Amplification and WT Ovation Exon kit and Encore Biotin protocols. The labeled ssDNA was hybridized on the Affymetrix Human GeneChip 1.0 ST Arrays, which subsequently were processed and stained using GeneChip Fluidics Station 450. The stained GeneChip Arrays were scanned in the Microarray Facility at the Biopolis Shared Facility using a GeneChip Scanner 3000. Quality control for the Arrays was performed using the Affymetrix Expression Console Software.
2017-06-15 | GSE70013 | GEO
Project description:BY4730 cultures were exposed to medium containing dilutions of test agent (Cisplatin (Cis), 600mg/mL; Methylmethane sulfonate (MMS), 0.12% v/v; Bleomycin (Bleo), 0.15U/mL; NaCl, 10mg/mL; ethanol, 15% v/v) for 120 min. Control cultures were either mock-treated with the solvent, DMSO (for comparison to Cis, MMS, Bleo) or maintained in media (for comparison to ethanol and NaCl) for 120 mins. Sample preparation and processing procedures were performed according the Affymetrix Genechipâ Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA). Briefly, total RNA was isolated from thawed cell pellets using a hot phenol protocol described by Schmitt et. al. (1990). Total RNA was converted to poly(A)+ mRNA and isolated using Oligotex mRNA kit. Double stranded cDNA was generated by using T7-(dT) 24 oligo primer (Genset Corp., San Diego, CA) and Superscript Double Stranded cDNA Synthesis Kit (Gibco BRL, Carlsbad, CA). The cDNA was used for in vitro transcription (IVT) with Enzo BioArray RNA Transcript Labeling Kit to incorporate biotinylated ribonucleotides. Biotinylated cRNA (15 mg) was fragmented in 40 mM tris-acetate, pH 8.1; 30 mM MgOAc; 100 mM KOAc. Samples were then hybridized with Affymetrix probe array Yeast Genome S98 at 45°C for 16 hours with constant rotation. Hybridized probe arrays were washed and stained using an Affymetrix GeneChipâ Fluidics Station 400 and protocol EukGE-WS2. The chips were scanned using the Affymetrix GeneArray Scanner. Keywords: repeat sample
2005-04-20 | GSE2224 | GEO
Project description:We examined expression profiles of genes that could be regulated by the MAPK pathways during mouse preimplantation development. We used Affymetrix GeneChips for microarray analysis, and three independent experiments were carried out. 8-cell stage embryos were treated or untreated with MAPK inhibitors, and blastocyst stage embryos were recruited for the study. Hybridization was carried out with the GeneChip Mouse Expression Set 430 or GeneChip Mouse Genome 430 2.0 Array following Affymetrix instructions. The array was then washed and stained using the GeneChip fluidics station according to the manufacture's instructions. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Expression analysis was performed using GeneChip Operating Software 1.0 (Affymetrix) and scaled to an average probe set intensity of 500.
2007-09-25 | E-GEOD-2229 | biostudies-arrayexpress