|
| Status |
Public on Jul 10, 2010 |
| Title |
Rap_1_knock_out_replicate_3 |
| Sample type |
RNA |
| |
|
| Source name |
Rap1 knock-out
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embrionic fibroblasts (MEF)
|
| Treatment protocol |
The Mefs were infected with SV40-LT-antigen and with the cre recombinase.
|
| Growth protocol |
Mouse embrionic fibroblast were grown in DMEM supplemented with 2 micrograms / ml of puromycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA fraction was extracted using TRIzol. RNA Integrity Numbers were in the range 9,3 to 10 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Amount of nucleic acid labeled: 1µg. Amplification: by RNA polymerases. Commercial one-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelinlg) kit by following manufacturer instructions. Agilent manual G4140-90040 Ver. 5.7 March 2008. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).
|
| |
|
| Hybridization protocol |
Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used:1,65ug. Duration: 17 hours.Volume: 100 uL.Temperature (ºC): 65
|
| Scan protocol |
Scanned on an G2565C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1)
|
| Description |
Gene expression in Rap1-deficient mouse
|
| Data processing |
Microarray background subtraction was carried out using normexp method. To normalize the dataset, we performed quantiles between arrays normalization using limma package from Bioconductor.
|
| |
|
| Submission date |
Nov 13, 2009 |
| Last update date |
Jul 09, 2010 |
| Contact name |
Paula Martinez |
| E-mail(s) |
[email protected]
|
| Organization name |
CNIO
|
| Street address |
Melchor Fernandez Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE19011 |
Roles of mammalian Rap1 in TERT recruitment to chromatin, subtelomeric gene silencing and transcriptional regulation |
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