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Sample GSM520772 Query DataSets for GSM520772
Status Public on Apr 10, 2010
Title interstitial stromal cells (PC-B10)
Sample type RNA
 
Source name interstitial stormal cells,captured by LCM
Organism Homo sapiens
Characteristics tissue: interstitial stromal cells
disease state: Prostatic adenocarcinoma
gleason score: Gleason (3+3)
age(yrs): 64
other: same tumor as A6
Biomaterial provider The serial frozen tissue sections for LCM were provided by The Ohio State University Prostate Cancer tissue Bank, part of the Human Tissue Resource Network (HTRN) in the Department of Pathology (Columbus, Ohio)
Treatment protocol Frozen sections were stained and dehydrated as recommended by manufacturer of the HistoGene LCM staining kit (Arcturus Bioscience, Molecular Devices). The slide was dehydrated through increasing concentrations of Ethanol and Xylene then placed in the Laser Capture Microscope (Arcturus Auto Pix). Areas of the slide with the most abundant glandular epithelial cells were identified and a Cap-Sure HS LCM cap (Molecular Devices) was aligned over the tissue. Microscopy was performed to verify cells were removed from sections and retained on the cap. After isolating the epithelial cells then the same marked slide was aligned for additional collection of interstitial stromal cells . Cell capture and lysis was completed within 2 hours to maintain quality RNA
Extracted molecule total RNA
Extraction protocol The cells captured by the LCM were lysed and RNA extracted as per manufacturer’s recommendations for Pico Pure RNA isolation kit (Arcturus Bioscience, Molecular Devices). After treatment with DNase, the RNA quantity and quality were checked using the Agilent RNA Pico-Chip on the Bioanalyzer 2100 (Agilent Bioscience, Mt View, CA). RNA quality was measured by 18s/28s ratio and degraded RNA samples were omitted. 1 ng of RNA was amplified using the RiboAmp HS kit (Arcturus Bioscience, Molecular Devices) in two-rounds of linear amplification of RNA.
Label biotin
Label protocol The total amplified cDNA was biotin labeled as recommended by the Affymetrix GeneChip Expression Analysis Technical Manual (2004).
 
Hybridization protocol Following fragmentation, 10 ug of biotin labeled cRNA was hybridized for 16 hr at 45C to Affymetrix Human Genome U133A 2.0 chips (HG_U133A 2.0) according to the Affymetrix GeneChip Expression Analysis Technical Manual (2004). The hybridized arrays were washed and stained in the Affymetrix Fluidics Station 400 using the Midi_euk2v3 labeling kit for detection by scanning.
Scan protocol The U133A 2.0 chips were scanned using an Affymetrix® GeneChip® scanner 3000. The signal intensities were normalized to the spike-controls located on the array chip. Platform used was GPL571.
Description Gene Expression data from LCM captured prostate cancer interstitial stormal cells (PC-B10), same tumor as A6.
Data processing The data were analyzed with GeneChip Operating System 1.1 using the MAS 5.0 algorithm, with Affymetrix default analysis settings and global scaling as normalization method, and using the default normalization target setting of 500.
 
Submission date Mar 11, 2010
Last update date Mar 11, 2010
Contact name Gail C Fraizer
E-mail(s) gfraizer@kent.edu
Phone 330-671-1398
Fax 330-672-3713
Organization name Kent State University
Department Biological Sciences
Street address 251 Cunningham Hall
City kent
State/province OH
ZIP/Postal code 44242
Country USA
 
Platform ID GPL571
Series (1)
GSE20758 Expression data from LCM captured prostate cancer cells

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 530.238 P 0.000146581
AFFX-BioB-M_at 658.084 P 8.14279e-05
AFFX-BioB-3_at 407.197 P 9.4506e-05
AFFX-BioC-5_at 1241.1 P 5.16732e-05
AFFX-BioC-3_at 1774.88 P 5.16732e-05
AFFX-BioDn-5_at 3796.03 P 5.16732e-05
AFFX-BioDn-3_at 4513.54 P 4.42873e-05
AFFX-CreX-5_at 16069.4 P 5.16732e-05
AFFX-CreX-3_at 17078.3 P 4.42873e-05
AFFX-DapX-5_at 10.3808 A 0.425962
AFFX-DapX-M_at 3.34681 A 0.963431
AFFX-DapX-3_at 12.1595 A 0.749204
AFFX-LysX-5_at 34.7065 A 0.205732
AFFX-LysX-M_at 7.64422 A 0.544587
AFFX-LysX-3_at 2.45857 A 0.645547
AFFX-PheX-5_at 4.5813 A 0.804734
AFFX-PheX-M_at 6.51641 A 0.897835
AFFX-PheX-3_at 11.9666 A 0.910522
AFFX-ThrX-5_at 15.6996 A 0.559354
AFFX-ThrX-M_at 30.8784 A 0.287743

Total number of rows: 22277

Table truncated, full table size 666 Kbytes.




Supplementary file Size Download File type/resource
GSM520772.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM520772.CHP.gz 121.3 Kb (ftp)(http) CHP
Processed data included within Sample table

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