|
| Status |
Public on Apr 25, 2013 |
| Title |
Lgr5ki-0511-GFPbright, ext179 |
| Sample type |
RNA |
| |
|
| Source name |
FACS-sorted epithelial intestinal cells from Lgr5-EGFP-ires-CreERT2 mice
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype: Lgr5-EGFP-ires-CreERT2
cell type: epithelial intestinal cells
lgr5 expression level: high
|
| Treatment protocol |
Cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice were used, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS-sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlow).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
|
| |
|
| Hybridization protocol |
cRNA was hybridized to Affymetrix HT MG-430 PM Array Plates according to manufacturer's protocol (Affymetrix).
|
| Scan protocol |
Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol.
|
| Data processing |
The expression data extracted from the raw CEL files were normalized with RMAalgorithm from Affymetrix Power Tools. Data were analyzed using the R2 web application, which is freely available at (http://r2.amc.nl).
|
| |
|
| Submission date |
Apr 23, 2013 |
| Last update date |
Apr 25, 2013 |
| Contact name |
Richard Volckmann |
| E-mail(s) |
r.volckmann@amsterdamumc.nl
|
| Organization name |
Academic Medical Centre, University of Amsterdam
|
| Department |
Department of Oncogenomics
|
| Street address |
P.O. Box 22700
|
| City |
Amsterdam |
| ZIP/Postal code |
1100DE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11180 |
| Series (1) |
| GSE46303 |
DNA Methylation Dynamics During Lgr5+ Intestinal Stem Cell Differentiation (Affymetrix Arrays) |
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