|
| Status |
Public on Dec 31, 2016 |
| Title |
adult_expression |
| Sample type |
RNA |
| |
|
| Source name |
Transcriptomic profiling in the dorsal skin tissue of the C57BL/6J 3 months old mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: dorsal skin
developmental stage: adult
age: 3 months
|
| Treatment protocol |
Dorsal skin tissue samples from C57BL/6J mouse strain at different stages of development were prepared in the Tri-City's Academic Animal Experiment Centre of the Medical University of Gdańsk. All tissues were collected in RNAlater stabilization reagent (QIAGEN. cat. no. 76104), transported on dry ice and stored at -80o C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs was purified using the RNeasy Mini Kit (QIAGEN. cat. no. 74104) coupled with on-column DNA digestion following the manufacturer’s protocols.
|
| Label |
Cy3
|
| Label protocol |
First strand cDNA synthesis was performed with Maxima Reverse Transcriptase (ThermoScientificBio. cat. no. EP0742) using 3 µg of total RNA, 400 U of the Maxima Reverse Transcriptase (200 U/ul), 5 x reaction buffer (250 mM Tris-HCl, 375 mM KCl, 15 mM MgCl, 50 mM DTT) and oligo dT15.(200 pmoles) in a total volume of 40 µl. Second strand cDNA was synthesized using cDNA Synthesis System (Roche, cat. no. 11 117 831 001) according to the second strand synthesis manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Probe labeling and hybridization was performed with Roche NimbleGen kit using the standard protocol for eukaryotic RNA samples and NimbleGen mouse gene expression 12x135K array (Roche, cat. no. 05543797001). The cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit (Roche, cat. no. 06370411001), and hybridized to slides using a NimbleGen hybridization system (Roche, cat. no. 05583683001).
|
| Scan protocol |
The slides were scanned using MS200 Scanner (Roche, NimbleGen) at 2 µm resolution by using high-sensitivity and autogain settings.
|
| Description |
transcriptomic profiling performed for the pool of three total RNA samples extracted from three pairs of skins collected from 3-months old mice of the C57BL/6J strain
|
| Data processing |
The data from scanned images were processed and normalized using a robust multi-chip average (RMA) algorithm using DEVA 1.0.2 software with default settings (Roche)
|
| |
|
| Submission date |
Apr 14, 2015 |
| Last update date |
Dec 31, 2016 |
| Contact name |
Pawel Sachadyn |
| E-mail(s) |
psach@pg.gda.pl
|
| Phone |
+48 583471605
|
| Organization name |
Gdansk University of Technology
|
| Department |
Molecular Biotechnology and Microbiology
|
| Street address |
Narutowicza 11/12
|
| City |
Gdansk |
| ZIP/Postal code |
80-233 |
| Country |
Poland |
| |
|
| Platform ID |
GPL10192 |
| Series (2) |
| GSE67876 |
The transcriptome of murine foetal skin and scarless wound healing |
| GSE67878 |
The methylome and transcriptome of murine foetal skin and scarless wound healing |
|
