|
| Status |
Public on Oct 06, 2017 |
| Title |
Control_0hr_WT_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Ear skin, 0h, Non-treat, WT
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Ear skin
strain: C57BL/6J
genotype: WT
treatment: None
|
| Treatment protocol |
To induce psoriasiform dermatitis, both mouse ears were treated once with a topical dose of 62.5 mg of Beselna cream (outside Japan, IMQ is sold as Aldara™; 3M Pharmaceuticals, St Paul, MI, USA) containing 5% IMQ (purchased from Mochida Pharmaceutical Co., Ltd)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The tissue was homogenized by adding a 5 mm diameter Zirconium bead (Funakoshi, Japan) and shaking with a MixerMill 300 (Qiagen GmbH., Germany) at a speed of 20 Hz for 5 min. Total RNA was isolated using TRIzol reagent (InVitrogen) and purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Samples were treated with DNase with the RNase-Free DNase Set (Qiagen). RNA quality and quantity were determined. with a Bioanalyzer 2100 (Agilent Technologies)
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations to Agilent-014850 arrays were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.
|
| Scan protocol |
Scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies). The array was scanned using Agilent G2505C DNA microarray scanner.
|
| Description |
Gene expression of control from ear skin in WT mice
Ear skin, 0h, Non-treat, WT, replicate 1
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1). Expression intensities (gProcessedSignal) were replaced with 0 if glsWellAboveBG is 0 before normalization.
Quartile normalization was performed with the limma package in R
|
| |
|
| Submission date |
Oct 04, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Yayoi Natsume-Kitatani |
| Organization name |
National Institutes of Biomedical Innovation, Health and Nutrition
|
| Street address |
7-6-8 Asagi Saito
|
| City |
Ibaraki |
| State/province |
Osaka |
| ZIP/Postal code |
567-0085 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21163 |
| Series (1) |
| GSE104603 |
Expression data from Imiquimod-induced psoriasis mouse model |
|
