{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Isidore Rigoutsos"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-71950"],"description":["The product of genomic loci coding for micro RNAs (miRNAs) produce many isoforms (isomiRs). IsomiRs differing at their 5’ end have different seed regions and therefore are expected to target different genes. We used microarrays to study the effect of different isomiRs in the context of breast cancer. The product of genomic loci coding for micro RNAs (miRNAs) produce many isoforms (isomiRs). IsomiRs differing at their 5’ end have different seed regions and therefore are expected to target different genes. We used microarrays to study the effect of different isomiRs in the context of breast cancer. Breast cancer MDA-MB-231 cells were cultured and were subject to a negative control treatment or transfected with one of the three selected isomiRs: the archetype miRNA, the miR-183-5p|2|-2| or the miR-183-5p|+2|+2| isomiR. Each treatment was done in triplicate. RNA was extracted and hybridized on Affymetrix microarrays."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was extracted from the cells using the TRizol reagent (Life Technologies) according to the manufacturer's instructions.","Scaning - Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.","Sample Treatment - The mirVana miRNA mimic for miR-183-5p, the Negative Control #1, or the two miRVana customized miRNA mimics for the two isomiRs (miR-183-5p|-2|-2|, 5'-TGTATGGCACTGGTAGAATTCA-3' and miR-183-5p|+2|+2|, 5'-TGGCACTGGTAGAATTCACTGT-3') (Life Technologies) were transfected at a final concentration of 50nM using the Lipofectamine RNAiMAX transfection Reagent (Life Technologies). Transfection was performed for 48h.","Labeling - Fragmented biotin labeled cDNA (from 100 ng of RNA) was prepared using the GeneChip WT Plus Kit (Affymetrix, Santa Clara, CA) according to manufacturer's in-structions.","Growth Protocol - MDA-MB-231 cells were grown in DMEM medium (Fisher Scientific) supplemented with 10% fetal bovine serum (Life Technologies), 1% Penicillin and Strep (Fisher Scien-tific), and 1% glutamine (Fisher Scientific), at 37oC in a humidified atmosphere contain-ing 5% CO2.","Hybridization - Affymetrix gene chips, Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, CA), were hybridized with 5 μg fragmented and biotin-labeled cDNA in 200 μl of hybridization cocktail."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Isidore Rigoutsos","Aristeidis Telonis","Yi Jing"],"data_protocol":["Data Transformation - Data processing and normalization was performed by Expression Console Software v 1.4.1 using the SST-RMA algorithm. ID_REF =  VALUE = SST-RMA"],"additional_accession":[]},"is_claimable":false,"name":"Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity","description":"The product of genomic loci coding for micro RNAs (miRNAs) produce many isoforms (isomiRs). IsomiRs differing at their 5’ end have different seed regions and therefore are expected to target different genes. We used microarrays to study the effect of different isomiRs in the context of breast cancer. The product of genomic loci coding for micro RNAs (miRNAs) produce many isoforms (isomiRs). IsomiRs differing at their 5’ end have different seed regions and therefore are expected to target different genes. We used microarrays to study the effect of different isomiRs in the context of breast cancer. Breast cancer MDA-MB-231 cells were cultured and were subject to a negative control treatment or transfected with one of the three selected isomiRs: the archetype miRNA, the miR-183-5p|2|-2| or the miR-183-5p|+2|+2| isomiR. Each treatment was done in triplicate. RNA was extracted and hybridized on Affymetrix microarrays.","dates":{"release":"2015-09-23T00:00:00Z","modification":"2023-09-13T23:01:41.933Z","creation":"2022-03-04T19:21:10.957Z"},"accession":"E-GEOD-71950","cross_references":{"GEO":["GSE71950"],"EFO":["EFO_0002768"]}}