|
| Status |
Public on Oct 30, 2009 |
| Title |
Sip1|Nestin2.2 |
| Sample type |
RNA |
| |
|
| Source name |
neocortex and hippocampal tissue E18.5
|
| Organism |
Mus musculus |
| Characteristics |
tissue: neocortex and hippocampal tissue
develomental stage: Embryonic day E18.5
genotype/variation: Sip1 knockout mutant
|
| Biomaterial provider |
K.U.Leuven, Laboratory of Molecular Biology (Celgen)
|
| Treatment protocol |
Neocortex and hippocampal tissue was dissected in ice-cold PBS and frozen immediately at -80°C till use
|
| Growth protocol |
Fresh frozen dissected tissue was kept at -80° till use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from mouse neocortex and hippocampus tissues was isolated using RNeasy kit according to the manufacturer’s protocol (QIAGEN).Total RNA was controlled for integrity and purity using an Agilent Bioanalyzer and a NanoDrop spectrophotometer, respectively
|
| Label |
Biotin Streptavidin Cy5
|
| Label protocol |
Total RNA was controlled for integrity and purity using an Agilent Bioanalyzer and a NanoDrop spectrophotometer, respectively. All samples were of similar RNA quality. Starting with 1ug of total RNA, the RNA amplification was performed by in vitro transcription (IVT) with a biotin labeling reaction during the IVT, according to the recommendations of the manufacturer (Amersham Biosciences). The probes were purified and analyzed again for yield (> 20 ug) and purity (260:280 nm and 260:230 nm >1.8). Ten micrograms of the resulting antisense RNA was fragmented according to the recommendations of the manufacturer (Amersham Biosciences) and resuspended in 260ul of hybridization buffer.
|
| |
|
| Hybridization protocol |
The gene array chips were hybridized in a shaker-incubator at 37°C at 300 rpm for 18 hours and washed and stained with Cy5-Streptavidin according to the recommendations of the manufacturer (Amersham Biosciences).
|
| Scan protocol |
The DNA Microarray scanner of Agilent was used for scanning and image analysis was performed with the Codelink Expression Analysis 4.1 software.
|
| Description |
knockout tissue
|
| Data processing |
Statistical data analysis was performed on the mean foreground and median background intensities, as provided by the Codelink Expression Analysis 4.1 software. All probes that were flagged as manufacturing spot removed (M), irregular (I), and saturated (S) by the Codelink Expression Analysis software, were removed, prior to the normalization. Data were background corrected; in case, this results in a negative value, the background corrected intensity for that spot was set equal to 0.5. All data were normalized with quantile normalization and base 2 log-transformed.
|
| |
|
| Submission date |
Jun 18, 2009 |
| Last update date |
Oct 30, 2009 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL2897 |
| Series (1) |
| GSE16699 |
Sip1 regulates sequential fate decisions through feedback signalling from postmitotic neurons to progenitor cells. |
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