|
| Status |
Public on Oct 01, 2010 |
| Title |
Nrarp1 |
| Sample type |
RNA |
| |
|
| Source name |
Embryo of Nrarp knockout mouse
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Presomitic mesoderm (PSM) cells
stage: E10.5
|
| Biomaterial provider |
Nrarp knockout mice were generated by Woong Kim.
|
| Treatment protocol |
PSM cells were dissected from E10.5 embryo and immediately preserved in liquid nitrogen for 1-2 weeks.
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from PSM cells using SV total RNA Isolation Kit (Promega) according to the manufacturer’s instructions. The purity and quantity of the RNA were assessed by the Gene Quant pro (Amersham Biosciences)
|
| Label |
Digoxigenin
|
| Label protocol |
1-2 ug total RNA were introduced into an RT-IVT reaction: the RNA was reverse-transcribed into ds-cDNA and then converted into labelled cRNA by in vitro transcription (Nano-Amp RT-IVT Labeling Kit, Applied Biosystems) using digoxigenin-conjugated UTP nucleotides (Roche).
|
| |
|
| Hybridization protocol |
10 ug of digoxigenin-labeled cRNA samples were fragmented for 30 min at 60℃ and hybridized for 16h to Human Genome Survey Microarrays V2.0 (Applied Biosystems) at a temperature of 55℃. After several washing steps of increasing stringency, an anti-digoxigenin-antibody conjugated to alkaline phosphatase (Roche Diagnostics) was added.
|
| Scan protocol |
Chemiluminescence and fluorescence signals were detected on an AB1700 microarray reader. Reagents from the Chemiluminescence Detection Kit (Applied Biosystems) were used in this procedure. Human Genome Survey Microarrays V2.0 feature numerous control probes and 32878 target gene specific 60 mer probes detecting more than 27000 different genes
|
| Description |
Transcriptome profiles were acquired using Applied Biosystems AB1700 technology. Human Genome Survey Microarrays V2.0 feature numerous control probes and 32878 target gene specific 60 mer probes detecting more than 27000 different genes.
|
| Data processing |
Detectable probes were determined by a signal to noise ratio (S/N) > 3 and quality flag < 5,000 determined by the AB1700 microarray software tool.
|
| |
|
| Submission date |
Oct 06, 2009 |
| Last update date |
Oct 07, 2009 |
| Contact name |
Woong Kim |
| E-mail(s) |
u-kimu@bs.naist.jp
|
| Organization name |
NAIST
|
| Department |
Biosciences
|
| Lab |
Bessho
|
| Street address |
Takayama8916-5
|
| City |
Ikoma |
| State/province |
Nara |
| ZIP/Postal code |
630-0101 |
| Country |
Japan |
| |
|
| Platform ID |
GPL2995 |
| Series (1) |
| GSE18419 |
Number of vertebrae is fine-tuned by Notch signaling via control of period of the somite segmentation clock. |
|
