|
| Status |
Public on Apr 09, 2009 |
| Title |
NOD EpiSC-like ES #1 P7 |
| Sample type |
RNA |
| |
|
| Source name |
NOD EpiSC-like ES #1 P7
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOD
cell line: EpiSC-like ES
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from MEF depleted mouse ES line by preplating on gelatin or from mechanically separated EpiSC and EpiSC-like cells lines using the RNeasy Mini Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Cy3-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 0.5 µg total RNA.
|
| |
|
| Hybridization protocol |
Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 1.65ug cy3-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% n-laurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetronitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.
|
| Scan protocol |
Arrays were scanned using an Agilent scanner and the data was extracted using Agilent’s Feature Extraction software.
|
| Description |
Gene expression in NOD EpiSC-like ES #1 P7
|
| Data processing |
Microarray data were processed and normalized between arrays using Limma package.
|
| |
|
| Submission date |
Apr 08, 2009 |
| Last update date |
Apr 08, 2009 |
| Contact name |
Albert W Cheng |
| E-mail(s) |
awcheng@mit.edu
|
| Organization name |
Whitehead Institute
|
| Street address |
Room 453, 9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE15603 |
Metastable pluripotent states in NOD mouse derived ES cells |
|
