|
| Status |
Public on Dec 31, 2014 |
| Title |
serum-Wilms-preCT-3 (comparison 1) |
| Sample type |
RNA |
| |
|
| Source name |
serum-Wilms-preCT
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Wilms tumor patient
treatment: untreated
sample type: serum
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA including miRNAs was isolated using the protocol from Leidinger et al. with minor modifications. In detail 100µl serum sample, 250µl nuclease-free water (Life Technologies) and 750µl Trizol LS (Life Technologies) were mixed and incubated at RT for 5min. After addition of 1µl glycogen (20mg/ml) and 5µl 5mM cel spike-in control (Qiagen) and 200µl chloroform the solution was vortexed and incubated at RT for 3min followed by centrifugation at 4°C and 14 000rpm for 15min. The upper aqueous phase was transferred into a new tube and RNA was precipitated using 1.5Vol of 100% ethanol. The solution was added to a RNA binding column from the MinElute Cleanup Kit (Qiagen) and RNA was washed and purified using the buffer from the miRNeasy kit (Qiagen). Total RNA including miRNA was eluted in 15µl nuclease-free water and stored at -80°C. RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the Small RNA kit (Agilent) on a Bioanalyzer2100.
|
| Label |
Cyanine 3
|
| Label protocol |
using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456), Cyanine 3-pcp
|
| |
|
| Hybridization protocol |
The expression profile of 1205 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations
|
| Scan protocol |
Array´s were scanned with the Agilent Scanner with default settings.
|
| Description |
US11153896_253118111390_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM296/1
|
| Data processing |
Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil normalized for every comparison; 1) Wilms serum pre CT vs controls 2) wilms serum post CT vs controls and 3) Wilms serum pre CT vs Wilms serum post CT
|
| |
|
| Submission date |
Jun 20, 2013 |
| Last update date |
Dec 31, 2014 |
| Contact name |
Nicole Ludwig |
| E-mail(s) |
n.ludwig@mx.uni-saarland.de
|
| Phone |
004968411626269
|
| Organization name |
Saarland University
|
| Department |
Human Genetics
|
| Street address |
Kirrberger Strasse
|
| City |
Homburg |
| ZIP/Postal code |
66421 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16770 |
| Series (1) |
| GSE48137 |
Circulating miRNA in serum of Wilms tumor patients |
|
