|
| Status |
Public on Jan 17, 2014 |
| Title |
KO TSCs at d0, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
trophoblast stem cells, Lsd1-deficient, d0
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed C57Bl/6 and 129Sv
genotype: Lsd1-deficient
cell type: trophoblast stem cells (TSCs)
differentiation state: stemness state
time point: before induction of differentiation (d0)
|
| Treatment protocol |
To induce differentiation, TSCs were cultured in TS medium in the absence of FGF4, heparin, and MEF-conditioned medium.
|
| Growth protocol |
TSCs were cultured in the absence of primary mouse embryonic fibroblasts (MEFs) in medium supplemented with FGF4 (RD, 235-F4-025/CF, 30 ng/ml) and heparin (Sigma, H3149, 1.2 µg/ml). The medium contained 30 vol% TS medium (RPMI 1640, BD Biosciences, 354230), which includes 20% ES cell-qualified foetal bovine serum (Invitrogen), 1% penicillin-streptomycin (Lonza, DE17-602E), 1% glutamine (Lonza, BE17-605E), 1% sodium pyruvate (Invitrogen, 11360), 0.1 mM ß-mercaptoethanol and 70 vol% MEF-conditioned medium (collected from mitomycin C-treated (Sigma, M4287) MEFs cultured in TS medium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.
|
| Scan protocol |
Arrays were scanned in a GeneArray Scanner (Agilent).
|
| Description |
F-d0+3_Mouse430_2
|
| Data processing |
The data were RMA normalized using R/Bioconductor. The normalized data were analyzed with Genedata Analyst 7.0 (Box Plot; Principal Component Analysis; Hierarchical Clustering; N-Way ANOVA; T-Test).
|
| |
|
| Submission date |
May 25, 2012 |
| Last update date |
Jan 17, 2014 |
| Contact name |
Thomas Günther |
| E-mail(s) |
[email protected]
|
| URL |
http://www.uniklinik-freiburg.de/molgyn/live/Persons-1/TG_en.html
|
| Organization name |
Freiburg University Medical Center
|
| Department |
Central Clinical Research
|
| Street address |
Breisacherstr. 66
|
| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE38277 |
Lsd1 coordinates trophoblast development by retaining stem cells in their niche and directing cell fate |
|
