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Sample GSM3833928 Query DataSets for GSM3833928
Status Public on Jun 01, 2020
Title 6431
Sample type RNA
 
Source name clear cell renal cell carcinoma primary tumor
Organism Homo sapiens
Characteristics tissue: clear cell renal cell carcinoma primary tumor
institution: LHMC
group: validation and survival analyses
age_years: 72
gender_1_male: 1
obese_1 is bmi>=30: 1
death_a=alive, c=died of ccrcc, o=death from other cause: A
time_months to last fu or death: 160
Stage: 1a
tumor size_cm: 4
_1=progress to metastatic disease in 5yrs: 0
grade: 2
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Ambion RecoverAll Total Nucleic Acid Isolation Kit for FFPE following the manufacturer's recommendations
Label SYBR Green
Label protocol cDNA and RT-PCR were performed using miRCURY LNA custom miRnome PCR panel, currently provided by Qiagen formerly from Exiqon, following the manufacturer's recommendations. Catalog number 339317
 
Hybridization protocol n/a
Scan protocol n/a
Description FFPE
Data processing Non-normalized data are the Cq values computed by the Bio-Rad CFX themal cycler software, no adjustment to baseline backgrounds were made
Each microRNA of interest was normalized to the average of the insignificant control miRNA: miRs-28-5p, -125-5p, and -191-5p, selected from the screening array dataset using NormFinder©. Prior to normalization each target value was scaled to the internal plate calibrator (IPC) by dividing the samples IPC by the grand average of all the IPCs and then multiplying the resulting value by the target Cq. The global mean was calculated only using microRNA with a Cq<35 detected in all 20 samples. 2^-deltaCq, where deltaCq = (Cq_Target − Cq_global_mean). All Cq values >37 were set to 40.
Fold change (delta delta Ct) values were not computed for this dataset
The file normalized_data.txt reports normalized signal (against each samples global mean).
 
Submission date May 30, 2019
Last update date Jun 01, 2020
Contact name Travis Sullivan
E-mail(s) sulliv82@lahey.org
Organization name Lahey Hospital & Medical Center
Street address 41 Mall Rd.
City Burlington
State/province MA
ZIP/Postal code 01805
Country USA
 
Platform ID GPL17107
Series (2)
GSE131960 microRNA Profile in Stage I Clear Cell Renal Cell Carcinoma Predicts Progression to Metastatic Disease [validation]
GSE131961 microRNA Profile in Stage I Clear Cell Renal Cell Carcinoma Predicts Progression to Metastatic Disease

Supplementary data files not provided
Processed data are available on Series record

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