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Series GSE10028 Query DataSets for GSE10028
Status Public on Dec 01, 2008
Title Low-Fat, Low-Glycemic Load Diet, Surgical Manipulation and Prostate Gene Expression
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Prostate Microarrays for two studies on Low-Fat, Low-Glycemic Load Diet intervention in prostate cancer and the effect of Surgical Manipulation on Prostate Gene Expression.

Influence of Surgical Manipulation on Prostate Gene Expression: Implications for Molecular Correlates of Treatment Effects and Disease Prognosis
"Measurements of tissue gene expression are increasingly used for disease stratification, clinical trial eligibility, and assessment of neoadjuvant therapy response. However, the method of tissue acquisition alone could significantly influence the expression of specific transcripts or proteins. This study examines whether there are transcript alterations associated with surgical resection of the prostate gland by radical retropubic prostatectomy."

Low-Fat, Low-Glycemic Load Diet and Gene Expression in Human Prostate Epithelium: A Feasibility Study of Using cDNA Microarrays to Assess the Response to Dietary Intervention in Target Tissues
"We examined the feasibility of using gene expression changes in human prostate epithelium as a measure of response to a dietary intervention."
Keywords: Low-fat, Low-Glycemic Load, Prostate Cancer, Radical Prostatectomy, Ischemia
 
Overall design Participants were 12 men with clinically localized prostate cancer, who elected to undergo radical prostatectomy and received no neoadjuvant therapy. Study activities began within 2 weeks of diagnosis. Participants were randomly assigned to one of three groups: group I received instructions to follow a low-fat/low-glycemic load diet (<20% energy from fat and total daily glycemic load <100) and group II was instructed to follow a ‘‘standard American’’ diet (35% energy from fat
and total daily glycemic load >200) and group III received no dietary intervention. No participant received previous hormonal ablation, chemotherapy, or radiotherapy. At time of radical prostatectomy and after induction of anesthesia,we obtained four in situ prostate biopsy cores using an 18-gauge prostate needle biopsy gun (Bard Inc, Murray Hill, NJ), and immediately embedded and froze them. Radical prostatectomy was performed as follows: The prostate was mobilized from surrounding tissue, and the dorsal venous complex was divided and oversewn. After dissecting the adjacent neurovascular bundle(s), where appropriate, the urethra was incised, the prostate was dissected free of
the rectum, and the vascular pedicles were ligated. The seminal vesicles were then mobilized from the surrounding tissue, and the prostate was dissected free of the bladder neck and removed. We immediately obtained four ex vivo biopsy cores following the same protocol just described. The time interval from ligation of vascular pedicles to ex vivo biopsy was defined as the ischemia time. Biopsy cores were embedded individually in polyethylene glycol freezing media (Tissue-Tek OCT
Compound, Sakura Finetek), placed in isopentane that was precooled in liquid nitrogen, and stored at 80C. We used laser capture microdissection to collect 5,000 epithelial cells from histologically benign epithelial glands and extracted RNA using a standardized protocol. We prepared and hybridized spotted cDNA microarrays as previously described (10), using RNA from a single batch of reference standards for each hybridization. Fluorescent array images were collected for both
Cy3and Cy5 using a GenePix 4000B fluorescent scanner (Axon Instruments), and GenePix Pro 4.1 software was used to grid and extract image intensity data. Spots of poor quality, as determined by visual inspection, were removed from further analysis. To normalize log ratio data, a print tip–specific Lowess curve was fit to the log-intensity versus log-ratio plot, using 20.0% of the data to calculate the fit at each point. This curve was used to center the log-ratio for each spot. Data were filtered to exclude poorly hybridized cDNAs by removing values
with average foreground minus background intensity levels less than 300. We used the average of the two duplicate cDNA spots on each microarray chip in subsequent analyses.
 
Contributor(s) Lin DW, Coleman IM, Hawley S, Dumpit R, Gifford D, Kezele P, Hung H, Abbott DE, Neuhouser ML, Schenk JM, Knudsen BS, Kristal AR, Nelson PS
Citation(s) 17932364, 16822846
Submission date Dec 26, 2007
Last update date Jan 17, 2013
Contact name Denise Mauldin
E-mail(s) dmauldin@fhcrc.org
Phone 2066673480
Fax 2066672917
URL http://www.pedb.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Peter Nelson
Street address 1100 Fairview Ave N D4-100
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL4766 FHCRC Human Prostate PEDB cDNA Array v8
Samples (36)
GSM253451 Time: Before Intervention, Treatment: Control, Type: Needle (030133_BI)
GSM253452 Time: Before Intervention, Treatment: None, Type: Needle (030061_BI)
GSM253453 Time: Before Intervention, Treatment: Control, Type: Needle (030077_BI)
Relations
BioProject PRJNA108585

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10028_RAW.tar 45.0 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table
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