|
| Status |
Public on Jun 24, 2013 |
| Title |
PE from mt ES, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Primitive endoderm cells directly differentiated from Dnmt3a-/-Dnmt3b-/- mouse ES cells by activation of Gata4GR transgene
|
| Organism |
Mus musculus |
| Characteristics |
background strain: 129sv/Jae ES cell line (J1)
genotype: Dnmt3a-/-Dnmt3b-/-, stably expressing Gata4-glucocorticoid receptor ligand-binding domain fusion gene
clone name: 16G4.3
cell type: primitive endoderm cells
gata4gr induction: yes
|
| Treatment protocol |
100 nM dexamethasone (Dex) was added to ES cells stably expressing Gata4GR. Total RNA was prepared 4 days after addition of Dex.
|
| Growth protocol |
ES cells were cultured in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% fetal calf serum (FCS), 0.1 mM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor (LIF) on gelatinized culture dishes without feeder cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by TRIZOL Reagent (Invitrogen) and cleaned up by the RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocols.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared using a two-cycle target-labeling assay according to the Affymetrix protocol from 50 ng total RNA (Small Sample Labeling Protocol Version II).
|
| |
|
| Hybridization protocol |
The 10 micro-g cRNA was hybridized at 45 C for 16 hours on the GeneChip Mouse Genome 430 2.0 array (Affymetrix) according to the Affymetrix Standard Protocol. GeneChips were washed and stained using the EukGE-Ws2v5_450 protocol in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
PE_mutant_1
Primitive endoderm cells directly differentiated from Dnmt3a-/-Dnmt3b-/- ES cells.
|
| Data processing |
Data values were calculated using the Bioconductor implementation (affy module) of the RMA algorithm in conjunction with quantiles normalisation of perfect match values (mismatches ignored). The specific function call used was: expresso(data, bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly, summary.method=median.polish).
|
| |
|
| Submission date |
Mar 26, 2012 |
| Last update date |
Jul 29, 2013 |
| Contact name |
Masaki Okano |
| E-mail(s) |
okano@cdb.riken.jp
|
| Phone |
81-78-306-3164
|
| Fax |
81-78-306-3167
|
| Organization name |
RIKEN
|
| Department |
Center for Developmental Biology
|
| Lab |
Laboratory for Mammalian Epigenetic Studies
|
| Street address |
2-2-3 Minatojima-Minamimachi, Chuo-ku
|
| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE36814 |
Role for DNA methylation in response to Gata4 activation in embryonic stem cell-derived mesoderm |
|
