|
| Status |
Public on Mar 18, 2009 |
| Title |
ES_HoxB4_off |
| Sample type |
RNA |
| |
|
| Source name |
ES cell
|
| Organism |
Mus musculus |
| Characteristics |
treatment: HoxB4 off
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
|
| Label |
biotin
|
| Label protocol |
In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (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 hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
|
| Scan protocol |
Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
|
| Description |
co-culture with OP9 cells in the absence of HOXB4
|
| Data processing |
Affymetrix GCOS was used with target intensity=100.
|
| |
|
| Submission date |
Mar 02, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Hideo Ema |
| E-mail(s) |
hema@ims.u-tokyo.ac.jp
|
| Organization name |
The University of Tokyo
|
| Department |
The Institute of Medical Science
|
| Street address |
4-6-1 Shirokanedai, Minato-ku
|
| City |
Tokyo |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE15053 |
Stepwise development of hematopoietic stem cells from embryonic stem cells |
|
| Relations |
| Reanalyzed by |
GSE119085 |
