|
| Status |
Public on Sep 03, 2010 |
| Title |
WT ES+GATA4, biological repeat2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse wild-type (WT) Gata4GR ES +Dex
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Line J1G4.2
genotype: wild type, carrying the Gata4GR transgene
cell type: Primitive endoderm cells differentiated from ES cells
|
| Treatment protocol |
ES cells carrying the Gata4GR transgene were plated at 1 x 10^4 cells in a 10-cm gelatinized dish in medium without dexamethasone (Dex). The next day, the medium was replaced with fresh medium containing 100 nM Dex. The total RNA was prepared from these cells after culturing them for more 4 days.
|
| Growth protocol |
ES cells carrying a transgene encoding Gata4 fused with the ligand-binding domain of human glucocorticoid receptor (Gata4GR) driven by the CAG promoter, which can be activated by the addition of dexamethasone (Dex), were maintained in Glasgow Minimum Essential Medium (GMEM, Sigma) supplemented with 10% fetal bovine serum, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, and 2000 U/ml leukemia inhibitory factor on gelatinized culture dishes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were extracted from the cells using Trizol Reagent (Invitrogen) and cleaned up using an RN-easy column (Qiagen) according to these manufacturers' instructions.
|
| Label |
biotin
|
| Label protocol |
Double-stranded cDNAs synthesized from the RNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix).
|
| |
|
| Hybridization protocol |
Labeled cRNAs were fragmented and hybridized to Affymetrix GeneChip arrays according to the manufacturer’s instructions. The GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).
|
| Description |
Gene expression data from primitive endoderm cells differentiated from mouse WT ES cells
|
| Data processing |
Probe set signal intensities of the CHP files were calculated using MAS5.0.
|
| |
|
| Submission date |
Feb 03, 2010 |
| Last update date |
Sep 03, 2010 |
| Contact name |
Morito Sakaue |
| E-mail(s) |
sakaue@cdb.riken.jp
|
| Phone |
81-78-306-3164
|
| Fax |
81-78-306-3167
|
| Organization name |
RIKEN
|
| Department |
CDB
|
| Lab |
Mammalian Epigenetic Studies
|
| Street address |
2-2-3 Minatojimaminamimachi, Chuoku
|
| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE20177 |
Expression data from mouse wild-type and Dnmt1-/-Dnmt3a-/-Dnmt3b-/- embryonic stem(ES) cells and nuclear transfer-trophoblastic stem(ntTS) cells, and wild-type trophoblastic stem(TS) cells, primitive endoderm cells, and extra-embryonic endoderm(XEN) cells |
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