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Sample GSM1305843 Query DataSets for GSM1305843
Status Public on Jan 14, 2014
Title advanced CaP_P232
Sample type RNA
 
Source name Human urine
Organism Homo sapiens
Characteristics disease: advanced CaP
Treatment protocol A total 14 urines from patients with CaP (7 localized and 7 advanced stage) and 5 of BPH controls were used for miRNA array analysis.
Growth protocol 19 candidate urines (prostate cancer, CaP, patients and non-cancer subjects with benign prostatic hyperplasia, BPH) were selected.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RecoverAllTM Total Nucleic Acid Isolation kit (Life Technologies, Carlsbad, CA) according to the protocol of the manufacturer. RNA quantity and integrity were examined by RNA 6000 Pico Chip Kit (Agilent Technologies, Santa Clara, CA) on Agilent 2100 Bioanalyzer.
Label Cy3
Label protocol 400 ng of total RNA was labeled with cyanine 3-pCp using the Agilent miRNA Complete Labeling kit and hybridized to the array according to the manufacturer’s protocol.
 
Hybridization protocol After purification, labeled samples were resuspended with Gene Expression Blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s Human miRNA Microarray (60K, Release 16.0) and hybridized at 55 °C for 20 h with 20 rpm rotating in Agilent Hybridization Oven. The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology).
Scan protocol The hybridization images were analyzed by Agilent DNA microarray Scanner.
Description miRNA expression in the advanced CaP 232
Data processing Feature Extraction software (version 10.10.1.1) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol. Background intensity and feature nonuniform outliers were removed by standard procedures. Data visualization and analysis were performed with GeneSpring GX (version 7.3) software (Agilent Technologies). Signal cut-off measurements were less than 0.01, and normalized to 75th percentile of signal intensity to standardize each chip for cross-array comparison. Differentially expressed miRNAs were identified using a Student’s two-sample t-test with p values cut off by 0.05 and fold change more than 2.0. One-way ANOVO was used to analyze the correlation between the expression levels of miRNAs and clinic-pathological features of the patients.
The normalized ratios were calculated by dividing the average of CaP channel intensity (localized CaPs or advanced CaPs) by the average of normalized control channel intensity (BPH).
 
Submission date Jan 13, 2014
Last update date Jan 14, 2014
Contact name Jung Min Kim
E-mail(s) jmkim2010@korea.com
Phone 82-10-3459-4776
Organization name NAR Center, Inc. & Genoplan, Inc.
Department Department of Health Genomics
Lab Genetics & Genomics
Street address Gangnam-gu Teheran-ro 216
City Seoul
ZIP/Postal code 06221
Country South Korea
 
Platform ID GPL15159
Series (1)
GSE54010 miRNA expression profiles in the 19 candidate urines (prostate cancer, CaP, patients and non-cancer subjects with benign prostatic hyperplasia, BPH)

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
A_25_P00010019 0.9092641
A_25_P00010020 27.127096
A_25_P00010021 1
A_25_P00010023 1
A_25_P00010041 1
A_25_P00010042 1
A_25_P00010043 1
A_25_P00010044 1
A_25_P00010047 0.012226122
A_25_P00010048 1
A_25_P00010053 1
A_25_P00010054 1
A_25_P00010062 3348.0352
A_25_P00010063 1
A_25_P00010070 1.1446062
A_25_P00010071 1.724589
A_25_P00010072 0.27014843
A_25_P00010073 0.01
A_25_P00010078 0.01
A_25_P00010079 0.01

Total number of rows: 3523

Table truncated, full table size 77 Kbytes.




Supplementary file Size Download File type/resource
GSM1305843_A_P232.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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