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Sample GSM268277 Query DataSets for GSM268277
Status Public on Jun 10, 2008
Title Patient 077 Core Set (custom panel)
Sample type RNA
 
Source name primary prostate cancer
Organism Homo sapiens
Characteristics Case-Control Group: NED
Training or Validation: val
Age (yrs) at RRP: 62
PSA (ng/ml) at RRP: 7.5
Revised Gleason Score: 6
Stage: T2N0
Ploidy: NA
First Rising PSA (ng/ml): NA
Time (yrs) from RRP to first rising PSA: NA
Second Rising PSA (ng/ml): NA
Time (yrs) from RRP to second rising PSA: NA
PSA Slope (ng/ml/yr): NA
Time (yrs) from PSA recurrence to systemic disease: NA
Years of Followup after RRP: 17.0841889117043
patient's status: Alive
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-077
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 3831.178
GI_10938013-S 14863.04167
GI_33457353-S 2045.081333
GI_4507456-S 4221.653667
GI_5174574-S 12447.22567
sarroybu-S 1954.244667
1557685_at-S 701.7496667
1560225_at-S 843.965
1561073_at-S 4069.596
213310_at-S 2544.193
214174_s_at-S 589.931
214384_s_at-S 1155.433
216584_at-S 2829.8095
225311_at-S 4772.585667
228178_s_at-S 708.566
228687_at-S 491.713
228798_x_at-S 746.8425
229455_at-S 2591.599667
231181_at-S 666.8035
231651_at-S 723.6823333

Total number of rows: 526

Table truncated, full table size 12 Kbytes.




Supplementary file Size Download File type/resource
GSM268277_1557302054_R001_C010_Grn.idat.gz 82.9 Kb (ftp)(http) IDAT
GSM268277_1557302054_R001_C010_Grn.jpg.gz 90.2 Kb (ftp)(http) JPG
GSM268277_1557302054_R001_C010_Grn.xml.gz 680 b (ftp)(http) XML
GSM268277_1557302054_R001_C010_Red.idat.gz 82.9 Kb (ftp)(http) IDAT
GSM268277_1557302054_R001_C010_Red.jpg.gz 98.2 Kb (ftp)(http) JPG
GSM268277_1557302054_R001_C010_Red.xml.gz 678 b (ftp)(http) XML
Processed data included within Sample table

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