Estimation of miRNAs
Ontology highlight
ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE11176 | GEO | 2009/07/30
SECONDARY ACCESSION(S): PRJNA106871
REPOSITORIES: GEO
Similar Datasets
Project description:Our analyses of microRNA expression profiles involve the hybridization of fluorescently labeled miRNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We hybridized different amounts of microRNAs from the mirVana miRNA Reference Panel v9.1 to microarrays. Keywords: Expression Three different concentrations of miRNAs from the commercial standrads were labelled and hybridized to three microarrays.
2009-07-30 | E-GEOD-11176 | biostudies-arrayexpress
Project description:Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe the differences in genome wide miRNA expressions between wild type 293 T mammalian cells and Ago2 transformed stable cell lines. Keywords: Expression
2008-10-01 | GSE11168 | GEO
Project description:Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe a simple and effective method to regenerate such custom microarrays. Our protocol entails the use of a very low concentration of sodium hydroxide in a low salt buffer to strip RNA molecules from the arrays. The solution is also capable of removing DNA molecules hybridized to the slides, while preserving the slide coating and printed DNA probes. Slides can be stripped and reused at least twice without significantly sacrificing data quality. Keywords: expression study, new vs. stripped array comparison
2008-10-01 | GSE10305 | GEO
Project description:Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe the differences in genome wide miRNA expressions between wild type 293 T mammalian cells and Ago2 transformed stable cell lines. Keywords: Expression Comparing one control and three Ago2-overexpressing stable cell lines (A, B, C). One replicate per array.
2010-05-19 | E-GEOD-11168 | biostudies-arrayexpress
Project description:Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe a simple and effective method to regenerate such custom microarrays. Our protocol entails the use of a very low concentration of sodium hydroxide in a low salt buffer to strip RNA molecules from the arrays. The solution is also capable of removing DNA molecules hybridized to the slides, while preserving the slide coating and printed DNA probes. Slides can be stripped and reused at least twice without significantly sacrificing data quality. Keywords: expression study, new vs. stripped array comparison There are two stripping conditions in this study (1mM NaOH and 2mM NaOH in SSC buffer). For 1mM NaOH treatment, new, once-, twice-, and triple-stripped arrays are studies. For 2mM NaOH treatment, new and once-stripped arrays are measured.
2010-05-19 | E-GEOD-10305 | biostudies-arrayexpress
Project description:We present a detailed single cell analysis of the macrophage response to LPS from Salmonella enterica. By combining single cell transcriptional analysis, fluorescently labeled, LPS-coated beads, and cytometry we are able to distinguish the responses of macrophages that have internalized LPS-coated beads and those that have not.
2015-09-07 | GSE65529 | GEO
Project description:Each strain was grown overnight then diluted in fresh YPD to 10% v/v and grown for 3 hours at 30'C. Total RNA was isolated using an RNeasy mini kit, reverse transcribed, labeled with either Cy3 or Cy5, and hybridized to epoxy-coated slides with 6388, 70mer oligos (Qiagen-Operon). After an overnight hybridization, microarrays were scanned using a ScanArray Express laser scanner.
2008-12-30 | GSE14102 | GEO
Project description:MicroRNAs (miRNAs) have been shown to play an important role in many different cellular, developmental, and physiological processes. Accordingly, numerous methods have been established to identify and quantify miRNAs. The shortness of miRNA sequence results in a high dynamic range of melting temperatures and, moreover, impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here, we present a microarray based approach for global and absolute quantification of miRNAs. The method relies on an equimolar pool of about 1000 synthetic miRNAs of known concentration which is used as an universal reference and labeled and hybridized in a dual colour approach on the same array as the sample of interest. Each single miRNA is quantified with respect to the universal reference outbalancing bias related to sequence, labeling, hybridization or signal detection method. We demonstrate the accuracy of the method by various spike in experiments. Further, we quantified miRNA copy numbers in liver samples and CD34(+)CD133(-) hematopoietic stem cells. Total liver RNA was mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3â ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool (n = 6). The synthetic miRNA pool consisted of 2.5 fmol of each of 891 non redundant miRNAs sequences and miRControl 3 sequences. The array data was normalized by calculating the median of the miRControl 3 present in the liver and UR sample. The miRNA amount was calculated with respect to the corresponding miRNA in the UR.
2010-06-20 | E-GEOD-15835 | biostudies-arrayexpress
Project description:Compare miRNA expression profiles in mouse CD4 T cells overexpression of Bcl-6 vs empty vector Mouse naïve CD4+ T cells were transduced with a Bcl-6-expressing retrovirus or the control vector and cultured in Th0 condition for 2 days. Cells expressing medium to high levels of GFP were sorted and total RNAs were isolated using mirVana miRNA Isolation Kit (Applied Biosystems). MiRNA expression was profiled using Agilent 8x15K mouse miRNA microarray miRNA-v1_95_May07 (miRBase Release 9.2) by Ramaciotti Centre for Gene Function Analysis (Sydney). Each sample was run in duplicate.
2010-05-15 | E-GEOD-17000 | biostudies-arrayexpress