|
| Status |
Public on Feb 15, 2013 |
| Title |
PGK12.1_NSL1 RNAi_D |
| Sample type |
RNA |
| |
|
| Source name |
Mouse female ES cells PGK12.1 after single RNAi treatment of NSL1 siRNAs.
|
| Organism |
Mus musculus |
| Characteristics |
strain: Derived from blastcysts from a 129 female crossed to a (129 X PGK)F1 male.
cell type: PGK12.1 ES cell line
passage: 14-18
treatment: single RNAi treatment of NSL1 siRNA
|
| Treatment protocol |
100pmol of gene-specific siRNAs or negative control siRNAs (Invitrogen Stealth or Silencer control) were transfected into 2x105 ES or MEF cells in six-well plates using a standard reverse transfection protocol with Lipofectamine RNAiMax (Invitrogen). For co-transfection, 100pmol of Mof siRNAs and 50 pmol of Msl1 siRNAs were used. Cells were harvested after 48h of RNAi treatment. For the double RNAi knockdown of MOF, after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest.
|
| Growth protocol |
ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for RNAi experiments and cell collection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared by the Qiagen RNeasy kit with on-column DNaseI digestion
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
|
| |
|
| Hybridization protocol |
Hybridization and washing were performed according to the standard Affymetrix protocol.
|
| Scan protocol |
Array hybridizations were done at the Microarray Facility at CHDD (University of Washington, Seattle WA).
|
| Description |
Single-RNAi experiment 7 in PGK12.1.
|
| Data processing |
Raw data files from paired RNAi experiments were analyzed with Affymetrix® Expression Console™ Software using the RMA gene default.
|
| |
|
| Submission date |
Feb 11, 2013 |
| Last update date |
Feb 15, 2013 |
| Contact name |
Xinxian Deng |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Washington
|
| Department |
Laboratory Medicine and Pathology
|
| Lab |
HSB C526
|
| Street address |
1959 NE Pacific St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE30761 |
Mammalian X upregulation |
| GSE44252 |
Expression data from mouse ES cells after control RNAi (scramble siRNAs) or specific RNAi (siRNAs for specific genes) treatment |
|
