|
| Status |
Public on Mar 25, 2014 |
| Title |
E11.5 mouse intestine |
| Sample type |
RNA |
| |
|
| Source name |
mouse intestine E11.5
|
| Organism |
Mus musculus |
| Characteristics |
tissue: intestine
stain: ICR
|
| Treatment protocol |
Male and female mice were mated and the day of identification of a vaginal plug was E0.5. After 11days, mouse embryos were collected as E11.5.
|
| Growth protocol |
ICR mouse were harbored following the guidelines of the National Institute of Advanced Industrial Science and Technology Animal Experiment Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The primordium stomach was dissected from mouse embryo at E11.5. Total RNA was isolated from stomach using the ‘RNeasy micro kit’ (Quiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
RNA was labeled using the ‘Agilent Low Input Quick Amp Kit’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the NanoDrop-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 18 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 30 second at room temperature with acetonitrile, then dried immediately.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10. 5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non positive and significant, and Feature Non above background outliers were excluded.
|
| |
|
| Submission date |
Feb 25, 2014 |
| Last update date |
Mar 25, 2014 |
| Contact name |
Mari Sekine |
| E-mail(s) |
s1220999@u.tsukuba.ac.jp
|
| Organization name |
The University of Tsukuba
|
| Department |
Graduate School of Life and Environmental Sciences
|
| Street address |
1-1-1 Tennoudai
|
| City |
Tsukuba |
| ZIP/Postal code |
305-8577 |
| Country |
Japan |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE55312 |
Transcription profile of primordium gut organs |
|
