|
| Status |
Public on Oct 01, 2010 |
| Title |
MEFs_Ing1_deficient_replicate_C4 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse embryonic fibroblasts isolated from Ing1 deficient mice
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryonic fibroblasts
developmental stage: embryos
genome/variation: Ing1 locus inactivated by the insertion of a gene trap cassette
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRI-REAGENT (Sigma) and integrity assayed with an Agilent 2100 Bioanalyzer.
|
| Label |
Biotin
|
| Label protocol |
Labeling was performed using the CodeLink iExpress Expression Assay Reagent kit according manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Hybridization was performed according manufacturer's instructions described in the CodeLink Expression Bioarray System protocol.
|
| Scan protocol |
Slides were scanned in an Axon GenePix Scanner.
|
| Description |
CodeLinkTM Mouse Whole Genome microarrays (Applied Microarrays Inc., Tempe, AZ) were used to analyze gene expression profiles. Total RNA was isolated with TriReagent (Sigma) and its integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeling and hybridization were performed using the CodeLinkTM iExpress assay reagent kit according to manufacturers instructions. After hybridization and washing, slides were scanned in an Axon GenePix Scanner (Arlington, TX) and analyzed using CodeLinkTM Expression Analysis Software. Data were median normalized, log2-transformed and exported to the MeV software (TIGR, Rockville, MD) for additional statistical analysis and graphical visualization. We analyzed three independent preparations of early passage, MEF for each genotype, each derived from an individual embryo. Genes with ratios between Ing1-deficient and wild type higher than 2 or lower than 0.5, with statistical significance (P < 0.05, Students T Test) were selected for further analysis.
|
| Data processing |
Images were analyzed using CodeLink Expression Analysis Software 4.1. Raw data were median-normalized and exported to MeV Software for graphical visualization and statistical analyses.
|
| |
|
| Submission date |
Oct 10, 2009 |
| Last update date |
Oct 14, 2009 |
| Contact name |
Javier Alonso |
| E-mail(s) |
fjalonso@isciii.es
|
| Phone |
34-91-8223217
|
| Organization name |
INSTITUTO DE SALUD CARLOS III - IIER
|
| Department |
AREA DE GENÉTICA HUMANA
|
| Lab |
UNIDAD DE TUMORES SOLIDOS INFANTILES
|
| Street address |
CTRA. MAJADAHONDA-POZUELO KM 2
|
| City |
MAJADAHONDA |
| State/province |
MADRID |
| ZIP/Postal code |
28220 |
| Country |
Spain |
| |
|
| Platform ID |
GPL2897 |
| Series (1) |
| GSE18519 |
Analysis of gene expression profiles in primary embryonic fibroblasts deficient for the Ing1 locus |
|
