|
| Status |
Public on Mar 14, 2011 |
| Title |
intestine-EphB2Low-R1 |
| Sample type |
RNA |
| |
|
| Source name |
EphB2 Low Rep1
|
| Organism |
Mus musculus |
| Characteristics |
cell type: intestinal crypt cells
strain: C57BL/6
group: EphB2 Low
hybridization_date: Feb_2009
|
| Treatment protocol |
Intestinal single cell suspensions were sorted in a FACS Aria 2.0 (BD) according to high, medium or low EphB2 levels (anti-EphB2 Mab 2H9 -Genentech, 6g/ml detected by secondary anti-mouse IgG-APC -1/500, Jackson) or Lgr5 levels (High or Low expression of the Lgr5-EGFP knock-in allele
|
| Growth protocol |
Intestinal epithelial single cell suspensions were obtained from mouse intestines after several rounds of shaking in HBSS containing 8mM EDTA followed by enzyme treatment with 0.4mg/mL Dispase / 0.8U/µL DNAse I.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from sorted cells was extracted using Trizol Reagent following manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)
|
| |
|
| Hybridization protocol |
3.75 µg of cDNA was hybridized per Affymetrix GeneChip® Mouse 430 2.0 Array for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions (http://www.affymetrix.com).
|
| Scan protocol |
according to the manufacturer’s instructions (http://www.affymetrix.com)
|
| Description |
Gene expression data from intestinal EphB2 Low sorted cells
|
| Data processing |
Lgr5 samples (samples 1 and 2) and EphB2 samples (samples 3 to 8) were obtained at different dates and pre-processed separately. In both cases quantile normalization and RMA summarization were used. Genespring software was used for samples 1 and 2. Bioconductor software was used for samples 3 to 8. (Bioc version: 2.8.0; Bioc packages: affy, mouse4302cdf)
|
| |
|
| Submission date |
Mar 01, 2011 |
| Last update date |
Mar 14, 2011 |
| Contact name |
Eduard Batlle |
| E-mail(s) |
[email protected]
|
| Phone |
+34 934039008
|
| Organization name |
Institute for Research in Biomedicine
|
| Street address |
Baldiri i Reixach 10
|
| City |
Barcelona |
| ZIP/Postal code |
08032 |
| Country |
Spain |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE27605 |
The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse |
|
