|
| Status |
Public on Jul 07, 2011 |
| Title |
HepG2 infected with Foxa 1 Adenovirus, replicate 4 |
| Sample type |
RNA |
| |
|
| Source name |
HepG2 infected with Foxa1 adenovirus passage 11
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: liver hepatocellular carcinoma cells
transfection: Ad-Foxa1
passage: 11
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol Reagent from Invitrogen and re-purified using the RNeasy Plus Mini Kit from Qiagen. The amount and integrity of purified RNA was estimated by micro-capillary electrophoresis (2100 Bioanalyzer, Agilent Technologies), and purity was assessed by the ratio A260/A280.
|
| Label |
biotin
|
| Label protocol |
Amplified and biotinylated sense-strand DNA was generated from total RNA according to the Affymetrix Whole Transcript Sense Target Labeling Assay.
|
| |
|
| Hybridization protocol |
Labeled ssDNA (5.5 ug) was combined with hybridization and spike controls, and hybridized with a pre-equilibrated Affymetrix chip for 16-18 h. Following hybridization, arrays were washed and stained with a streptavidin phycoerythrin conjugate (SAPE) using an automated GeneChip Fluidics Station 450.
|
| Scan protocol |
Chips were scanned with a GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.
|
| Description |
RJB4
|
| Data processing |
Microarray quality control assessment and data acquisition were performed with the GeneChip Operating Software (Affymetrix).
Normalization among the different microarray data files was performed by using robust multiarray analysis (RMA). We applied a conservative probe filtering step excluding those probes not reaching a log2 expression value of 5 in at least one sample, which resulted in the selection of a total of 14,833 probes out of the original 32,320 set.
|
| |
|
| Submission date |
Jul 06, 2011 |
| Last update date |
Jul 07, 2011 |
| Contact name |
RAMIRO JOVER |
| E-mail(s) |
[email protected]
|
| Organization name |
IIS Hospital La Fe
|
| Department |
Experimental Hepatology Unit
|
| Lab |
Torre A. Lab 6.07
|
| Street address |
Avenida Fernando Abril Martorell, 106.
|
| City |
Valencia |
| ZIP/Postal code |
E-46026 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE30447 |
Foxa1 Reduces Lipid Accumulation in Human Hepatocytes and Is Down-regulated in Nonalcoholic Fatty Liver (HepG2 data) |
| GSE30451 |
Foxa1 Reduces Lipid Accumulation in Human Hepatocytes and Is Down-regulated in Nonalcoholic Fatty Liver |
|
