|
| Status |
Public on Feb 15, 2012 |
| Title |
Endoderm_SK7 |
| Sample type |
RNA |
| |
|
| Source name |
Endoderm derived from SK7
|
| Organism |
Mus musculus |
| Characteristics |
gender: male
strain: ICR
cell type: Endoderm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with an RNeasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned up by using Phase Lock Gels (Eppendorf)-Phenol/Chloroform Extraction (Ambion). In vitro transcription was performed on all of cDNA using the GeneChip IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
|
| |
|
| Hybridization protocol |
10 micrograms of fragmented cRNA were hybridized (45 degree Celsius, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
|
| Scan protocol |
Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
|
| Description |
Endoderm derived from SK7
|
| Data processing |
Chip analysis was performed using the Affymetrix GeneChip Operating Software v1.3.
|
| |
|
| Submission date |
Sep 13, 2011 |
| Last update date |
Feb 15, 2012 |
| Contact name |
Takayuki Isagawa |
| E-mail(s) |
isagawa@genome.rcast.u-tokyo.ac.jp
|
| Organization name |
The University of Tokyo
|
| Department |
RCAST
|
| Lab |
Genome Science
|
| Street address |
4-6-1 Komaba, Meguro-ku
|
| City |
Tokyo |
| ZIP/Postal code |
153-8904 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE32081 |
DNA methylation profiling of embryonic stem cell differentiation into the three germ layers [Expression analysis] |
| GSE32082 |
DNA methylation profiling of embryonic stem cell differentiation into the three germ layers |
|
