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Status |
Public on Jun 01, 2020 |
Title |
27559 |
Sample type |
RNA |
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Source name |
clear cell renal cell carcinoma primary tumor
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Organism |
Homo sapiens |
Characteristics |
tissue: clear cell renal cell carcinoma primary tumor institution: LHMC group: validation and survival analyses age_years: 56 gender_1_male: 1 obese_1 is bmi>=30: 1 death_a=alive, c=died of ccrcc, o=death from other cause: C time_months to last fu or death: 51 Stage: 1b tumor size_cm: 4.5 _1=progress to metastatic disease in 5yrs: 1 grade: 4
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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
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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
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Hybridization protocol |
n/a
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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).
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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 |
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