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Sample GSM115963 Query DataSets for GSM115963
Status Public on Jun 22, 2007
Title Iris pigment epithelium
Sample type RNA
 
Source name Primary cultured cells of iris pigment epithelium
Organism Mus musculus
Characteristics Iris pigment epithelium (Primary cultured cell)
Treatment protocol The iris tissue was triturated to make a single cell suspension, and then re-suspended in the medium.
Growth protocol Primary cultures of pigmented epithelial cells from the iris (IPE) were cultured in RPMI 1640 complete medium containing 10% fetal bovine serum (FBS). The medium of ocular PE was changed to serum free medium, with a cellular RNA extraction then performed after an overnight culture.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIZOL Reagent(Invitrogen) and used as starting material for the cDNA preparation. RNA was purified from total cellular RNA by Nucleospin RNA II (Macherey-Nagel, Inc, Germany) as outlined by the manufacturer. Integrity of total RNA was assessed qualitatively on the Agilent 2100 Bioanalizer (Agilent Technologies).
Label biotin
Label protocol 1 micro gram of total RNA was reverse transcribed using the cDNA synthesis system of MessageAmp aRNA Kit (Ambion). The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3. Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf). In vitro transcription was performed using the 3'-Amplification Reagents for IVT Labeling (Affymetrix). The cRNA was cleaned using RNeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
 
Hybridization protocol 10 migro grams of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controled adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
Scan protocol Scanning was performed in an Affymetrix GeneChip scanner 3000.
Description The primary IPE cultures were found to be greater than 99% cytokeratin positive (Clone PCK-26, Sigma) as determined by flow cytometry.
Data processing The data analysis were performed using the Affymetrix GeneChip Operating Software v1.3. using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of array was arbitrarily set to 100.
 
Submission date Jun 23, 2006
Last update date Jun 26, 2006
Contact name Yuri Futagami
Organization name Tokyo Medical and Dental University
Department Ophthalmology
Street address 1-5-45 Yushima Bunkyoku
City Tokyo
ZIP/Postal code 113-8519
Country Japan
 
Platform ID GPL1261
Series (1)
GSE5134 Role of thrombospondin-1 in T cell response to ocular pigment epithelial cells.

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 0.8 A 0.852061
AFFX-BioB-M_at 0.4 A 0.999338
AFFX-BioB-3_at 1 A 0.897835
AFFX-BioC-5_at 339.7 P 0.000044
AFFX-BioC-3_at 280.2 P 0.000044
AFFX-BioDn-5_at 507.1 P 0.000044
AFFX-BioDn-3_at 1249.7 P 0.000052
AFFX-CreX-5_at 3505 P 0.000044
AFFX-CreX-3_at 4532.8 P 0.000044
AFFX-DapX-5_at 0.7 A 0.876428
AFFX-DapX-M_at 1.5 A 0.814869
AFFX-DapX-3_at 4.4 A 0.368438
AFFX-LysX-5_at 1.5 A 0.645547
AFFX-LysX-M_at 7.9 A 0.250796
AFFX-LysX-3_at 5.4 A 0.455405
AFFX-PheX-5_at 0.3 A 0.995983
AFFX-PheX-M_at 0.9 A 0.883887
AFFX-PheX-3_at 4.3 A 0.327079
AFFX-ThrX-5_at 0.6 A 0.945787
AFFX-ThrX-M_at 7.5 A 0.250796

Total number of rows: 45101

Table truncated, full table size 1184 Kbytes.




Supplementary data files not provided

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