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Sample GSM7119517 Query DataSets for GSM7119517
Status Public on Sep 22, 2023
Title prostate cancer patient pre-treatment serum, DOD9
Sample type RNA
 
Source name peripheral venous source
Organism Homo sapiens
Characteristics patient id: DOD9
disease state: prostate cancer
tissue: serum
sample type: serum
ap: 0
grade of prostate cancer at biopsy: high-grade (1)
capra risk: HIGH
capra score: 6
fraction: microRNA
Treatment protocol n/a
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the miRNeasy Serum/Plasma kit (Qiagen).
Label SYBR Green
Label protocol PCR assay were performed using a miRCURY LNA miRNA Custom PCR Panel Catalog#YCA25430 (Qiagen) following the manufacturers instructions. Reverse transcription was performed from 5ยต L total RNA using the miRCURY LNA RT Kit (Qiagen). Quantitative real-time PCR were performed (Applied Biosystems ViiA 7) with 40 cycles at 95C for 10 seconds and 56C for 60 seconds.
 
Hybridization protocol n/a
Scan protocol n/a
Data processing The raw data (raw CT) values were input into GeneGlobe with a CT cutoff value of 33. In the GeneGlobe preprocessing, all CTs greater than 33 were changed to a value of 33 and the CTs were adjusted for the interplate calibrator (UniSp3) according to the miRCURY LNA miRNA PCR Panels & Assays Data Analysis Handbook.
Normalization values for each sample were calculated using the NormFinder method in GeneGlobe. The microRNAs used for normalization of serum samples included: miR-107, miR-24-3p, let-7i-5p, miR-19b-3p, miR-16-5p, miR-320a, miR-23a-3p, miR-21-5p, let-7b-5p, and miR-25-3p. The microRNAs included for normalization of serum EV samples included: included hsa-miR-107, hsa-miR-24-3p, hsa-miR-30c-5p, hsa-miR-93-5p, hsa-let-7i-5p, hsa-miR-222-3p, hsa-miR-27a-3p, hsa-miR-23a-3p, hsa-miR-21-5p, and hsa-miR-27b-3p.
These normalized values were then used to make comparisons between groups (adverse pathology versus not adverse pathology) to determine significantly different microRNAs using p < 0.05
The significant microRNAs were then used to generate random forest models to predict adverse pathology
The Fold Change Template shows the p-values for each microRNA. The microRNAs with p<0.05 were included in the random forest model to predict adverse pathology.
 
Submission date Mar 28, 2023
Last update date Sep 22, 2023
Contact name Morgan Zenner
E-mail(s) zenner2@uic.edu
Phone 8473728777
Organization name University of Illinois at Chicago College of Medicine
Department Pathology
Lab Larisa Nonn
Street address 909 South Wolcott Ave
City Chicago
State/province IL
ZIP/Postal code 60612
Country USA
 
Platform ID GPL33285
Series (1)
GSE228371 Real-time quantitative PCR analysis of pre-treatment serum microRNAs from patients with prostate cancer

Data table header descriptions
ID_REF
VALUE Normalized values

Data table
ID_REF VALUE
hsa-let-7a-5p -2.029962234
hsa-miR-103a-3p -1.016454391
hsa-miR-106a-5p -0.384526901
hsa-miR-107 -1.145278625
hsa-miR-146a-5p -4.896556549
hsa-miR-223-3p 1.643425293
hsa-miR-24-3p -1.499299698
hsa-miR-26b-5p -3.231719666
hsa-miR-30c-5p -3.118598633
hsa-miR-451a 6.495367355
hsa-miR-874-3p -6.107961349
hsa-miR-93-5p 0.105648346
hsa-let-7i-5p -1.239221268
hsa-miR-1246 -4.004800491
hsa-miR-18b-5p -3.783931427
hsa-miR-19b-3p 1.687868423
hsa-miR-194-5p -3.755538635
hsa-miR-222-3p -3.877999954
hsa-miR-16-5p 3.705663986
hsa-miR-320a -0.870139771

Total number of rows: 40

Table truncated, full table size 1 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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