Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA130539 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer’s expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the MAQC reference RNA samples, stored at -80°C, were stable over a time frame of at least four years. The new gene expression data were generated with 12 microarrays (2 types of microarrays × 2 samples × 3 replicates). Three replicates for each of the two MAQC samples (A = Stratagene’s Universal Human Reference RNA; B = Ambion’s Human Brain Reference RNA) were profiled in 2009 by using both the expired U133A microarrays (expired in 2004) and the unexpired U133Plus2 microarrays. In addition, gene expression data generated with unexpired U133Plus2 microarrays (AFX), other microarray platforms, and TaqMan® assays by the MAQC project in 2005 were used as references to assess the stability of the MAQC samples stored at -80°C for four years by comparing new microarray data with those obtained four years ago. The MAQC reference data also allowed for further evaluation of the usefulness of the data generated with expired U133A microarrays.
2010-09-02 | E-GEOD-23906 | biostudies-arrayexpress
Project description:The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer’s expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the MAQC reference RNA samples, stored at -80°C, were stable over a time frame of at least four years.
2010-09-02 | GSE23906 | GEO
Project description:In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same PBL-extracted RNA
2014-08-18 | GSE60265 | 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:Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array profiling of 20 primary, multi-region high-grade glioma samples.
2015-12-31 | GSE62802 | GEO
Project description:18 zero-hour and 18 selected post-transplant (Tx) biopsy samples from 18 kidney allografts (8 acute kidney injury (AKI), 10 PBx - protocol biopsies - controls) were analyzed by using the Affymetrix GeneChip® miRNA 3.0 Array.
2015-01-15 | GSE53771 | GEO
Project description:Animal models represent a very useful tool for the study of depressive-like behaviour and for the evaluation of the therapeutic efficacy of antidepressants. Nevertheless, gene expression patterns of these different animal models and whether genes classically associated to human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in an animal model of depression: corticosterone-treated rats. Gene expression analyses were carried out using the Affymetrix® GeneChip® technology. Keywords: Treatment vs control comparative genomics study
2007-12-12 | GSE9797 | GEO
Project description:18 zero-hour and 18 selected post-transplant (Tx) biopsy samples from 18 kidney allografts (8 acute kidney injury (AKI), 10 PBx - protocol biopsies - controls) were analyzed by using the Affymetrix GeneChip® Human Gene 2.0 ST Array.
2015-01-15 | GSE53769 | GEO
Project description:Control samples used to performed gene expression comparison with breast cancer tissues. mRNA samples from normal breast tissue were amplified, labeled, and hybridized to the Affymetrix GeneChip Human Exon 1.0 ST array. After normalization and analysis of the microarray data using Partek® software (http://www.partek.com).
2021-11-03 | GSE180835 | GEO
Project description:Animal models represent a very useful tool for the study of depressive-like behaviour and for the evaluation of the therapeutic efficacy of antidepressants. Nevertheless, gene expression patterns of these different animal models and whether genes classically associated to human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in an animal model of depression: olfactory-bulbectomized rats. Gene expression analyses were carried out using the Affymetrix® GeneChip® technology. Keywords: Bulbectomized vs sham-operated comparative genomics study
2007-12-12 | GSE9789 | GEO