|
| Status |
Public on Sep 03, 2010 |
| Title |
WT TS, biological repeat2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse wild-type (WT) TS
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Line 5
genotype: Wild type, carrying the GFP transgene
cell type: Trophoblastic stem (TS) cells derived from a wild-type blastocyst (BDF1xC57BL/6, TgN(acro/act-EGFP)OsbC3-N01-FJ002)
|
| Treatment protocol |
The TS cells from a 12.5-cm2 flask at 70-80% confluency were plated on a 75-cm2 flask with feeder cells (mouse embryonic fibroblasts), and cultured for three days. The medium was replaced with fresh medium on the second day. To remove feeder cells from the TS cell culture, the trypsinized cell suspension in the medium was plated on a culture dish and incubated at 37˚C, 5% CO2 for 30 minutes. The supernatant of the cell suspension was collected and used for RNA preparation.
|
| Growth protocol |
The TS cells were maintained in RPMI 1640 GlutaMax (Invitrogen) supplemented with 20% fetal bovine serum, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 25 ng/ml FGF4, and 1 micro-g/ml heparin with mouse embryonic fibroblast feeder cells.
|
| 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. 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 trophoblastic stem cells derived from a wild-type blastocyst
|
| 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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