|
| Status |
Public on Mar 15, 2012 |
| Title |
Mouse Embryonic Fibroblasts KO3 vs WT3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT Mouse Embryonic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
embryo stage: E12.5
|
| Treatment protocol |
Untreated
|
| Growth protocol |
MEFs were grown in DMEM supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Qiagen RNeasy kit according to manufacturer's conditions
|
| Label |
Cy5
|
| Label protocol |
Amount of nucleic acid labeled: 1µg. Amplification: by RNA polymerases. Commercial Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit by following manufacturer instructions. Agilent manual G4140-90050 Ver. 5.7 March 2008.
|
| |
|
| Channel 2 |
| Source name |
SA1-KO Mouse Embryonic Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: SA1-null
embryo stage: E12.5
|
| Treatment protocol |
Untreated
|
| Growth protocol |
MEFs were grown in DMEM supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Qiagen RNeasy kit according to manufacturer's conditions
|
| Label |
Cy3
|
| Label protocol |
Amount of nucleic acid labeled: 1µg. Amplification: by RNA polymerases. Commercial Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit by following manufacturer instructions. Agilent manual G4140-90050 Ver. 5.7 March 2008.
|
| |
|
| |
| Hybridization protocol |
Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 825 ng. Volume: 100 uL. Temperature (C): 65. Duration: 17 hours.
|
| Scan protocol |
Scanned on an G2565C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).
|
| Description |
Biological replicate 3 of 3. Primary Mouse Embryonic Fibroblasts, untreated.
|
| Data processing |
Data were preprocessed using Bioconductor's limma package. Background correction was performed usign normexp. Data were normalized using whithin-array lowess and between array quantile normalization.
|
| |
|
| Submission date |
Sep 20, 2011 |
| Last update date |
Mar 15, 2012 |
| Contact name |
Silvia Remeseiro |
| E-mail(s) |
sremeseiro@cnio.es
|
| Organization name |
Spanish National Cancer Research Centre (CNIO)
|
| Lab |
Ana Losada's lab
|
| Street address |
Calle Melchor Fernandez Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE32234 |
A unique role of Cohesin-SA1 in gene regulation and development [Expression] |
| GSE32320 |
A unique role of Cohesin-SA1 in gene regulation and development |
|
