|
| Status |
Public on Oct 01, 2015 |
| Title |
FP22 nickel |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
allergic contact dermatitis_skin_nickel
|
| Organism |
Homo sapiens |
| Characteristics |
indication: allergic contact dermatitis
allergen: nickel
tissue: skin
sample type: Whole tissue extract
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems, Naerum, Denmark) following the manufacturer’s instructions. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
|
| Label |
Hy3
|
| Label protocol |
200 ng total RNA from sample was labelled with Hy3™ and Hy5™ fluorescent label using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
Reference: mixture of all samples
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems, Naerum, Denmark) following the manufacturer’s instructions. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
|
| Label |
Hy5
|
| Label protocol |
200 ng total RNA from sample was labelled with Hy3™ and Hy5™ fluorescent label using the miRCURY™ LNA Array power labelling kit (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 7'th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0.
The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).
|
| Scan protocol |
After 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. 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 |
Sample 14
1_Exiqon*.txt and 0_Exiqon*.txt contains Hy3 (ch1) and Hy5 (ch2) raw data, respectively.
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., Bioinformatics; 23: 2700-2707, 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
|
| |
|
| Submission date |
Jun 25, 2014 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Marianne Bengtson Løvendorf |
| E-mail(s) |
mabelo01@geh.regionh.dk
|
| Organization name |
Gentofte Hospital
|
| Department |
Dermato-Allergology
|
| Street address |
Niels Andersens Vej 65
|
| City |
Hellerup |
| ZIP/Postal code |
2900 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL18058 |
| Series (2) |
| GSE58814 |
Allergic contact dermatitis to nickel is characterized by a specific microRNA signature [skin] |
| GSE58817 |
Allergic contact dermatitis to nickel is characterized by a specific microRNA signature |
|
