{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Jean-Charles Soria"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-2868"],"description":["Focal and temporal tumor heterogeneity can represent a major challenge for biology-guided therapies. This study proposes to investigative molecular discrepancies between primary colorectal cancer samples and matched metastases"],"repository":["biostudies-arrayexpress"],"pubmed_title":["Comparative analysis of primary tumor and matched metastases in colorectal cancer patients: evaluation of concordance between genomic and transcriptional profiles"],"sample_protocol":["Labeling - Agilent miRNA Microarray System with miRNA complete labeling and hybridization kit was used for Cy3 labeling. Briefly, isolated total RNA were dephosphorylated, labeled with pCp-Cy3 and hybridized on arrays for 20h at 55°C in a rotating oven (Robbins Scientific) at 20 rpm.","Hybridization - Agilent miRNA Microarray System with miRNA complete labeling and hybridization kit was used for Cy3 labeling. Briefly, isolated total RNA were dephosphorylated, labeled with pCp-Cy3 and hybridized on arrays for 20h at 55°C in a rotating oven (Robbins Scientific) at 20 rpm.","Nucleic Acid Extraction - Total RNAs were extracted using the TriReagent method (TriReagent, Euromedex, Strasbourg, France). The following sequence was performed as quickly as possible for each sample: pellet cells were placed in 1.6 mL of TriReagent. To separate the aqueous phase and isopropanol precipitation, cell homogenates (1.6 mL) were added to 320 µL of chloroform and incubated at room temperature for 15 min and then centrifuged at 12,000 g for 15 min at 4°C. The upper aqueous phase (about 800 µL) containing RNA was collected. RNAs were then precipitated from the aqueous phase adding isopropanol (one volume of isopropanol for one volume of aqueous solution) 10 min at room temperature followed by a centrifugation at 12,000 g for 10 min at 4°C. Pellets were washed twice with ethanol 7","Scaning - Scanning perform with a Agilent G2505C DNA Microarray scanner using default parameters : 100% PMT, 3 um resolution, at 20°C in low ozone concentration environment. Microarray images were analysed using Feature Extraction software version (10.7.3.1) from Agilent technologies. Default settings were used."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Guillaume Meurice","Jean-Charles Soria","Stéphane Vignot, Céline Lefebvre, Garrett M. Frampton, Guillaume Meurice, Roman Yelensky, Gary Palmer, Frédérique Capron, Vladimir Lazar, Laurent Hannoun, Vincent A. Miller, Fabrice André, Philip J. Stephens, Jean-Charles Soria, Jean-Philippe Spano"],"additional_accession":[]},"is_claimable":false,"name":"P24_STVI_colorectal_cancer_MIR","description":"Focal and temporal tumor heterogeneity can represent a major challenge for biology-guided therapies. This study proposes to investigative molecular discrepancies between primary colorectal cancer samples and matched metastases","dates":{"release":"2014-12-30T00:00:00Z","modification":"2022-01-28T17:31:57.634Z","creation":"2022-01-28T17:31:57.634Z"},"accession":"E-MTAB-2868","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0003815"]}}