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Sample GSM268296 Query DataSets for GSM268296
Status Public on Jun 10, 2008
Title Patient 061 Core Set (custom panel)
Sample type RNA
 
Source name primary prostate cancer
Organism Homo sapiens
Characteristics Case-Control Group: PSA
Training or Validation: trn
Age (yrs) at RRP: 65
PSA (ng/ml) at RRP: 13.2
Revised Gleason Score: 7
Stage: T3bN0
Ploidy: diploid
First Rising PSA (ng/ml): 0.2
Time (yrs) from RRP to first rising PSA: 2.78439425051335
Second Rising PSA (ng/ml): 0.3
Time (yrs) from RRP to second rising PSA: 3.56194387405886
PSA Slope (ng/ml/yr): 0.128609154929577
Time (yrs) from PSA recurrence to systemic disease: NA
Years of Followup after RRP: 11.3867214236824
patient's status: Deceased
Prostate cancer specific death: No
Extracted molecule total RNA
Extraction protocol Four freshly cut 10 micron sections of FFPE tissue were deparaffinized and the Gleason dominant cancer focus was macrodissected. RNA was extracted using the High Pure RNA Paraffin Kit from Roche (Indianapolis, IN).
Label cy3, cy5
Label protocol cy3, cy5 labeling was performed in accordance with the manufacturer's instructions
 
Hybridization protocol hybridization was performed in accordance with the manufacturer's instructions
Scan protocol Arrays were scanned using Illumina's BeadArray Reader
Description TNPr-061
Data processing Illumina's Bead Studio Software using no normalization was used to process the image files. The raw data was then normalized using cyclic loess (fastlo). The normalized value for the probes was averaged to determine the expression level for the gene. The DASL method labels each sample with a mixture of CY3 and Cy5. Only a single sample is applied to each array. The scanner measures fluorescence of both Cy3 and Cy5. This data is contained in the red and grn files for each sample. The bead studio software averages the red and green signals to provide a single value for the expression of a particular probe.
 
Submission date Feb 26, 2008
Last update date Jun 10, 2008
Contact name Robert B. Jenkins
E-mail(s) rjenkins@mayo.edu
Organization name Mayo Clinic
Department Laboratory Medicine and Pathology
Street address 200 First Street SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
 
Platform ID GPL5873
Series (1)
GSE10645 Focused gene expression microarray of tumors from 596 men with prostate cancer using RNA from archival FFPE tissue

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
EDNRA-Yu-S 3864.332
GI_10938013-S 15222.20967
GI_33457353-S 1831.81
GI_4507456-S 3332.990333
GI_5174574-S 15577.752
sarroybu-S 2060.252
1557685_at-S 704.8613333
1560225_at-S 758.015
1561073_at-S 4750.665667
213310_at-S 3316.248
214174_s_at-S 574.52
214384_s_at-S 1328.030333
216584_at-S 2459.5305
225311_at-S 6992.709
228178_s_at-S 625.484
228687_at-S 488.677
228798_x_at-S 809.573
229455_at-S 2662.305333
231181_at-S 635.2525
231651_at-S 521.8726667

Total number of rows: 526

Table truncated, full table size 12 Kbytes.




Supplementary file Size Download File type/resource
GSM268296_1557302054_R003_C008_Grn.idat.gz 82.9 Kb (ftp)(http) IDAT
GSM268296_1557302054_R003_C008_Grn.jpg.gz 92.4 Kb (ftp)(http) JPG
GSM268296_1557302054_R003_C008_Grn.xml.gz 679 b (ftp)(http) XML
GSM268296_1557302054_R003_C008_Red.idat.gz 83.0 Kb (ftp)(http) IDAT
GSM268296_1557302054_R003_C008_Red.jpg.gz 98.5 Kb (ftp)(http) JPG
GSM268296_1557302054_R003_C008_Red.xml.gz 676 b (ftp)(http) XML
Processed data included within Sample table

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