Comment[ArrayExpressAccession] E-MTAB-1470 Investigation Title Genome-wide expression profiling of human carotid atheroma Comment[Submitted Name] Genome-wide expression profiling of human carotid atheroma Experiment Description The aim of this study was to identify new biomarkers and to investigate pathways involved in the progression of human carotid atheroma. The study was conducted from pieces of carotid endarterectomy collected in 32 hypertensive patients. The samples contained media and neo-intima without adventitia. They were paired, including for each patient one sample of the atheroma plaque (stage IV and over of the Stary classfication) containing core and shoulders of the plaque, and one sample of distant macroscopically intact tissue (stages I and II). In addition, clinical, biological and histological data were collected. Experimental Design disease state design replicate design ex-vivo_design all_pairs clinical history design Comment[AEExperimentDisplayName] Transcription profiling by array of carotid endarterectomy samples collected from hypertensive patients to identify new biomarkers and to investigate pathways involved in the progression of human carotid atheroma Comment[AEExperimentType] transcription profiling by array Experimental Factor Name MATERIAL PROPERTY INDIVIDUAL Experimental Factor Type material property individual Quality Control Type biological replicate Public Release Date 2013-04-01 Person Last Name Cerutti Bricca Ayari Legedz Person First Name Catherine Giampiero Hanene Liliana Person Mid Initials Person Email cerutti@univ-lyon1.fr giampiero.bricca@inserm.fr hananeayari@yahoo.fr Person Affiliation EA4173 Functional Genomics in Hypertension, University Lyon 1 & Villefranche/Saone Hospital, France EA4173 Functional Genomics in Hypertension, University Lyon 1 & Villefranche/Saone Hospital, France EA4173 Functional Genomics in Hypertension, University Lyon 1 & Villefranche/Saone Hospital, France EA4173 Functional Genomics in Hypertension, University Lyon 1 & Villefranche/Saone Hospital, France Person Roles submitter; investigator investigator investigator investigator Publication Status in preparation Protocol Name P-MTAB-30971 P-MTAB-30972 P-MTAB-30973 P-MTAB-30974 P-MTAB-30975 Protocol Type specified_biomaterial_action nucleic_acid_extraction labeling hybridization image_acquisition Protocol Description Paired carotid samples were obtained in 32 patients undergoing a carotid endarterectomy. Endarterectomy samples were dissected in the surgery room into two fragments: the atheroma plaque (Stary stages IV and over) and a distant less affected part called macroscopically intact tissue (Stary stage I and II, histological control). Each fragment was further divided: one part was immediately frozen in liquid nitrogen for RNA analyses while the other was fixed for histological analyses. Total RNA was isolated from each sample using Trizol reagent (Invitrogen, USA) following the manufacturerM-^Rs instructions, and treated with DNase (Qiagen). Only quality controlled total RNA were used for expression studies. Biotinylated cRNAs were prepared by IGBMC Microarray and Sequencing Platform according to the standard Affymetrix protocol from 1 ug total RNA. cRNAs were hybridized for 16 hours at 45oC on GeneChipM-. Human Gene 1.0 ST arrays using the GeneChipM-. Hybridization Oven 640 (Affymetrix). The GeneChips were washed and stained in the GeneChipM-. Fluidics Station 450 (Affymetrix) and scanned using the GeneChipM-. Scanner 3000 7G System (Affymetrix). Term Source Name ArrayExpress Term Source File http://www.ebi.ac.uk/arrayexpress/ SDRF File E-MTAB-1470.sdrf.txt