MicroRNA expression profiling using microRNA microarrays on NCI-60 cell lines.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Rolf Søkilde
PROVIDER: E-GEOD-26375 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:MicroRNA expression profiling using microRNA microarrays was performed on the porcine developing brain. Two tissues, cortex and cerebellum, were sampled at each of three different developmental stages: gestation day 50 (F50), gestation day 100 (F100) and three months old (named adult), respectively. The aim was to find developmental stage-, as well as tissue-specific, microRNA candidates and validate them with qPCR. RNA samples containing the small RNA fraction were subjected to microarray analysis. Three replicates per developmental stage/tissue.
2010-09-14 | E-GEOD-24106 | biostudies-arrayexpress
Project description:MicroRNA expression profiling using microRNA microarrays on NCI-60 cell lines.
2010-12-31 | GSE26375 | GEO
Project description:Purpose: MicroRNAs play a prominent role in a variety of physiological and pathological biological processes, including cancer. For rectal cancers, only limited data are available on microRNA expression profiles, while the underlying genomic and transcriptomic aberrations have been firmly established. We therefore aimed to comprehensively map the microRNA expression patterns of this disease. Experimental design: Tumor biopsies and corresponding matched mucosa samples were prospectively collected from 72 patients (68 tumors and 70 normal mucosa) with locally advanced rectal cancers. Total RNA was extracted, and tumor and mucosa microRNA expression profiles were subsequently established for all patients. The expression of selected microRNAs was validated using semi-quantitative real-time PCR. Results: Forty-nine microRNAs were significantly differentially expressed (log2-fold difference >0.5 and P<0.001) between rectal cancer and normal rectal mucosa. The predicted targets for the identified microRNAs were enriched for the following KEGG pathways: Wnt, TGF-beta, mTOR, insulin, MAPK, and ErbB signaling. Between rectal tumor and normal tissue, miR-492, miR-542-5p, miR-584, miR-483-5p, miR-144, miR-2110, miR-652*, miR-375, miR-147b, miR-148a, miR-190, miR-26a/b, and miR-338-3p were found to be differentially expressed. Of clinical impact, miR-135b expression correlated significantly with overall survival that could be validated in a larger multicenter patient set (n=94). Conclusion: The comprehensive analysis of the rectal cancer microRNAome uncovered novel microRNAs and pathways associated with rectal cancer. This information contributes to a detailed view of rectal cancer. The identification and validation of miR-135b will help to identify novel molecular targets and pathways for therapeutic exploitation. Paired samples from rectal tumor and matched normal samples. Included are also 2 technical replicates.
2012-10-05 | E-GEOD-38389 | biostudies-arrayexpress
Project description:Background: TrkB-T1 is a BDNF receptor lacking a tyrosine kinase domain that is highly expressed in astrocytes and regulates BDNF-evoked calcium transients. Previous studies indicate that downregulation of TrkB-T1 in frontal cortex may be involved in neurobiological processes underlying suicide. Methods: In a microarray screening study (N=8), we interrogated all known microRNA in the frontal cortex of suicide completers with low expression of TrkB-T1 and normal controls. These findings were validated and followed up in a larger sample of cases and controls (N=55) Functional analyses included microRNA silencing, microRNA overexpression and luciferase assays to investigate specificity and to validate interactions between differentially expressed microRNA and TrkB-T1 Results: microRNAs Hsa-miR-185* and Hsa-miR-491-3p were upregulated in suicide completers with low expression of TrkB.T1 (Pnominal: 9.10-5 and 1.8.10-4 respectively; FDR-corrected p=0.031). Bioinformatic analyses revealed five putative binding sites for the DiGeorge syndrome linked microRNA Hsa-miR-185*in the 3M-bM-^@M-^YUTR of TrkB-T1, but none for Hsa-miR-491-3P. The increase of Hsa-miR-185* in frontal cortex of suicide completers was validated then confirmed in a larger, randomly selected group of suicide completers, where an inverse correlation between Hsa-miR-185* and TrkB-T1 expression was observed ( R=-0.404; p=0.002). Silencing and overexpression studies performed in human cell lines confirmed the inverse relationship between hsa-mir-185* and trkB-T1 expression. Luciferase assays demonstrated that Hsa-miR-185* binds to sequences in the 3M-bM-^@M-^YUTR of TrkB-T1. Conclusion: These results suggest that an increase of Hsa-miR-185* expression levels regulates, at least in part, the TrkB-T1 decrease observed in the frontal cortex of suicide completers and further implicate the 3MB 22q11 region in psychopathology. The microarray analysis consists in to compare the microRNA profile of four suicide completers with low TrkB-T1 expression level and four controls. Each RNA extract was labeled with Hy3 and hybridyzed with a reference sample labeled with Hy5. The reference sample was a pool of the eight RNA samples
2012-06-01 | E-GEOD-34120 | biostudies-arrayexpress
Project description:As part of the Spotlight on Molecular Profiling series, we present here new profiling studies of mRNA and microRNA expression for the 60 cell lines of the National Cancer Institute (NCI) Developmental Therapeutics program (DTP) drug screen (NCI-60) using the 41,000-probe Agilent Whole Human Genome Oligo Microarray and the 15,000-feature Agilent Human microRNA Microarray V2. The expression levels of approximately 21,000 genes and 723 human microRNAs were measured. These profiling studies include quadruplicate technical replicates for six and eight cell lines for mRNA and microRNA, respectively, and duplicates for the remaining cell lines. The resulting data sets are freely available and searchable online in our CellMiner database. The result indicates high reproducibility for both platforms and an essential biological similarity across the various cell types. The mRNA and microRNA expression levels were integrated with our previously published 1,429-compound database of anticancer activity obtained from the NCI DTP drug screen. Large blocks of both mRNAs and microRNAs were identified with predominately unidirectional correlations to approximately 1,300 drugs, including 121 drugs with known mechanisms of action. The data sets presented here will facilitate the identification of groups of mRNAs, microRNAs, and drugs that potentially affect and interact with one another.
| S-EPMC2879615 | biostudies-literature
Project description:Affymetrix GeneChip miRNA arrays were used to profile the expression of microRNAs in cells of sixty NCI-60 cancer cell-lines
| S-ECPF-MTAB-327 | biostudies-other
Project description:This SuperSeries is composed of the following subset Series: GSE30513: MicroRNA expression profiling of Ewing sarcoma cancer stem cells GSE31144: MicroRNA expression profiling of Ewing sarcoma cell lines upon TARBP2 depletion GSE31145: MicroRNA expression profiling of Ewing sarcoma spheres vs. adherent cells Refer to individual Series
2012-06-19 | E-GEOD-31146 | biostudies-arrayexpress
Project description:Advances in the understanding of cancer cell biology and response to drug treatment have benefited from new molecular technologies and methods for integrating information from multiple sources. The NCI-60, a panel of 60 diverse human cancer cell lines, has been used by the National Cancer Institute to screen >100,000 chemical compounds and natural product extracts for anticancer activity. The NCI-60 has also been profiled for mRNA and protein expression, mutational status, chromosomal aberrations, and DNA copy number, generating an unparalleled public resource for integrated chemogenomic studies. Recently, microRNAs have been shown to target particular sets of mRNAs, thereby preventing translation or accelerating mRNA turnover. To complement the existing NCI-60 datasets, we have measured expression levels of microRNAs in the NCI-60.
| S-ECPF-MEXP-1029 | biostudies-other
Project description:We report the identification of microRNA-138 (miR-138), as a molecular signature of GSCs and demonstrate a vital role for miR-138 to promote growth and survival of bona fide tumor-initiating cells with self-renewal potential. Total RNA from Glioma Stem Cells and Neural Stem Cells were subjected to microRNA microarray analysis, 3 replicates each.
2012-12-20 | E-GEOD-39486 | biostudies-arrayexpress
Project description:RNA Evaluation HL60 microRNA-seq from Mortazavi For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2020-01-06 | GSE142916 | GEO