Comment[ArrayExpressAccession]	E-GEOD-47553
MAGE-TAB Version	1.1						
Public Release Date	2013-09-22
Investigation Title	Effect of progerin on p53-deficient vascular smooth muscle cells						
Comment[Submitted Name]	Effect of progerin on p53-deficient vascular smooth muscle cells
Experiment Description	Analysis of p53-deficient (E6-expressing) human vascular smooth muscle cells (VSMCs) that express progerin, a mutated form of lamin A resposible for Hutchinson- Gilford progeria syndrome (HGPS). p53 pathway is associated with HGPS. Results provide insight into molecular mechanisms underlying vascular dysfunction of HGPS caused by other than p53 pathway. The gene expression of VSMCs induced to express E6 and either lamin A or progerin by retroviral vectors.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Kinoshita	Yamashita	Sato	Kinoshita			
Person First Name	Daisuke	Masakatsu	Kazuhiro	Daisuke			
Person Email	d.kinoopyg.0722@gmail.com						
Person Affiliation	Chiba University						
Person Address	Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Japan						
Person Roles	submitter						
Protocol Name	P-GSE47553-1	P-GSE47553-5	P-GSE47553-6	P-GSE47553-2	P-GSE47553-3	P-GSE47553-4	P-GSE47553-7
Protocol Description	The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 026652_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities. ID_REF =  VALUE = Normalized signal intensity	Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.	1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60M-0C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65M-0C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37M-0C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.	p53-deficinet (E6-overexpressing) VSMCs were infected with retroviral vectors encoding lamin A or progerin.	VSMCs were purchased from Lonza, and cultured in smooth muscle basic medium (SmBM, Clonetics) supplemented with insulin, FGF-B, EGF, GA-1000, and FBS. The cultures were incubated at 37M-bM-^DM-^C in a humidified incubator with 5% CO2.	Total RNA was isolated with RNA-Bee(Tel-Test, Inc). Cells were harvested 30 days after infected with lamin A or progerin.	Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	INFECTED WITH RETROVIRAL VECTOR TO EXPRESS						
Experimental Factor Type	infected with retroviral vector to express						
Comment[SecondaryAccession]	GSE47553						
Comment[GEOReleaseDate]	2013-09-22						
Comment[ArrayExpressSubmissionDate]	2013-05-31						
Comment[GEOLastUpdateDate]	2013-09-22						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-47553.sdrf.txt