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Sample GSM524662 Query DataSets for GSM524662
Status Public on Dec 31, 2010
Title iris-cellline-1
Sample type RNA
 
Source name vascular endothelial iris cells
Organism Homo sapiens
Characteristics tissue: iris
cell type: vascular endothelial cells
Treatment protocol Matched human ocular MVEC were isolated from anonymised paired human globes, enucleated within 24 hours of death and free of any known ocular disease. Isolation and culture of human macular inner choroidal endothelial cells utilising anti-CD31-coated Dynabeads (Dynal Ltd, Wirral, UK) was used with the substitution of macular choroidal tissue with isolated iris, retinal and choroidal tissues (PMID 16170129; http://www.ncbi.nlm.nih.gov/pubmed/16170129).
Growth protocol Cells were seeded onto fibronectin-coated 35mm culture dishes (Beckton Dickinson, Oxford, UK), and incubated at 37°C in a humidified atmosphere of 5% CO2.
Extracted molecule total RNA
Extraction protocol The total RNA was extracted from primary cultures of unpassaged endothelial cells when they had reached approximately 80% confluence, using the Qiagen RNeasy minikit as directed (Qiagen, Crawley, UK). Approximately 5μg of total RNA was obtained from each 35mm culture plate. RNA integrity and quality was assessed using an Agilent 2100 Bioanalyser and RNA 6000 Nano kit (Agilent Technologies).
Label biotin
Label protocol Biotinylated cRNA probes were prepared from the total RNA samples (1µg) using the microarray target amplification kit and the microarray target RNA synthesis kit (both Roche Applied Sciences) following the manufacturer’s instructions.
 
Hybridization protocol The cRNA samples were then fragmented and hybridised onto Affymetrix GeneChip ® Human Genome U133 Plus 2.0 arrays (Affymetrix, High Wycombe, Bucks, UK) by incubating at 45°C for 16 hours. Washing and staining of the arrays were carried out following Affymetrix GeneChip ® protocols using a Fluidics Station 450.
Scan protocol Arrays were scanned using an Affymetrix Scanner 3000. GCOS software (Affymetrix) was used to monitor scanning and to convert the raw image files into cell intensity files (‘.CEL’).
Description Eyes 1.CEL
Data processing CEL files were processed with the BioConductor gcrma function from the simpleaffy package.
 
Submission date Mar 20, 2010
Last update date Dec 31, 2010
Contact name Simon Cockell
E-mail simon.cockell@newcastle.ac.uk
Organization name Newcastle University
Street address Framlington Place
City Newcastle
ZIP/Postal code NE2 4HH
Country United Kingdom
 
Platform ID GPL570
Series (1)
GSE20986 Comparative Gene Expression Profiling of HUVEC and Ocular Vascular Endothelial Cells

Data table header descriptions
ID_REF
VALUE GC-RMA normalised values

Data table
ID_REF VALUE
1007_s_at 2.867330709
1053_at 10.50302152
117_at 2.702517066
121_at 3.052316166
1255_g_at 2.278998026
1294_at 5.360226024
1316_at 5.496447322
1320_at 4.475412175
1405_i_at 2.301359647
1431_at 2.278998026
1438_at 2.278998026
1487_at 7.220874628
1494_f_at 2.313715373
1552256_a_at 8.785597507
1552257_a_at 7.818770156
1552258_at 3.094049271
1552261_at 2.278998026
1552263_at 5.428095444
1552264_a_at 7.63852327
1552266_at 2.283432595

Total number of rows: 54675

Table truncated, full table size 1214 Kbytes.




Supplementary file Size Download File type/resource
GSM524662.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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