|
| Status |
Public on Jun 21, 2013 |
| Title |
Rap1 -/- liver, rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Liver, Rap1 knockout mouse -/-, 10 weeks
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL6/129SV (90%: 10%)
genotype/variation: Rap1 -/-
tissue: liver
age: 10 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol. The QIAGEN kit was employed for purification. RNA Integrity Numbers were in the range 6.5 to 8.5 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
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.
|
| |
|
| Hybridization protocol |
Total RNA samples were analyzed on Agilent's Mouse Genome DNA microarray by following manufacturer instructions. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1).
|
| Description |
LIVER_RAP1_KO_2
|
| Data processing |
Microarray background subtraction was carried out using normexp method. Normalization was performed using quantiles. Differentially expressed genes were obtained by applying linear models with R limma package (Smyth, 2005) (Bioconductor project, http://www.bioconductor.org). To account for multiple hypotheses testing, the estimated significance level (p-value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.
|
| |
|
| Submission date |
Dec 27, 2012 |
| Last update date |
Jun 21, 2013 |
| Contact name |
Paula Martinez |
| E-mail(s) |
pmartinez@cnio.es
|
| Organization name |
CNIO
|
| Street address |
Melchor Fernandez Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10787 |
| Series (2) |
| GSE43171 |
RAP1 protects from obesity, diabetes and metabolic syndrome through its extra telomeric role regulating gene expression (young mouse liver) |
| GSE43174 |
RAP1 protects from obesity, diabetes and metabolic syndrome through its extra telomeric role regulating gene expression |
|
