|
| Status |
Public on Dec 31, 2014 |
| Title |
Liver B6 SHIVA mouse 2 |
| Sample type |
RNA |
| |
|
| Source name |
Liver RNA, SHIVA, 24 hours fasting
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype: Sox17 mutation
tissue: liver
gender: female
age: 8-12 weeks
treatment: fasting for 24 hr
|
| Treatment protocol |
Female mice (8-12 weeks old) were fasted for 24 hours prior to harvesting liver.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from liver using Trizol and then further purified with Qiagen purification columns.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA total using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 40µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
SHIVA_2
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Jun 27, 2012 |
| Last update date |
Dec 31, 2014 |
| Contact name |
Thien-Phong Vu Manh |
| Organization name |
CIML
|
| Street address |
163 avenue de Luminy
|
| City |
marseille |
| ZIP/Postal code |
13288 |
| Country |
France |
| |
|
| Platform ID |
GPL13912 |
| Series (1) |
| GSE38968 |
Gene expression profiling in liver from control versus mutant Sox17 SHIVA fasted C57BL/6 mice |
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