 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 22, 2015 |
| Title |
Study Sample 17 (Cancer) |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Cancer
sample type: Whole Blood
gender: Female
|
| Treatment protocol |
500μl of whole blood from each patient were drawn into an RNAprotect Animal Blood Tube (Qiagen, Hilden, Germany). Following gentle inversion, the tubes were incubated for 2h at ambient temperature, according to the manufacturer's instructions, in order to allow for efficient cell lysis. All tubes were then stored at -80˚C prior to RNA purification.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA purification that contained miRNA was carried out using the RNeasy Protect Animal Blood kit (Qiagen), according to the manufacturer's instructions
|
| Label |
Hy3™
|
| Label protocol |
300ng of total RNA from both sample and reference were then labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark), following the procedure described by the manufacturer.
|
| |
|
| Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th and 7th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 17.0 and 19.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria). Following hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes
|
| Scan protocol |
The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).
|
| Description |
miRNA profile
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Spike-in controls were added in various concentrations in both the Hy3™ and the Hy5™ labeling reactions to evaluate the labeling reaction, hybridization, and the performance of the array experiment.
Principal Component Analysis (PCA) was applied in order to explore the naturally arising sample classes based on the expression profile. A heat map diagram was produced that showed the results of a two-way hierarchical clustering of microRNAs and samples. The clustering was done using the complete-linkage method together with the euclidean distance measure. The statistical significance of the relative expression of miRNAs between the control and the study groups was determined using the Student's t-test. Furthermore, the Benjamini-Hochberg multiple testing adjustment method was applied to the p-values for the control of possible false positive results.
These 113 features refer to human miRNAs which were present in all study samples.
|
| |
|
| Submission date |
Jan 21, 2015 |
| Last update date |
Jan 22, 2015 |
| Contact name |
NIKOLAOS SIAFAKAS |
| E-mail(s) |
tymfr@hotmail.com
|
| Organization name |
ATTIKON UNIVERSITY HOSPITAL
|
| Department |
CLINICAL MICROBIOLOGY
|
| Street address |
1, RIMINI STR.
|
| City |
HAIDARI |
| State/province |
ATHENS |
| ZIP/Postal code |
124 62 |
| Country |
Greece |
| |
|
| Platform ID |
GPL19677 |
| Series (1) |
| GSE65143 |
Let-7, mir-98 and mir-181 as biomarkers for cancer and schizophrenia |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1588024_1_Exiqon_19720300_S01.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
|
|
|
|
 |
