|
| Status |
Public on May 09, 2010 |
| Title |
total RNA, EGF treated, 40 min, biological replicate #2 |
| Sample type |
RNA |
| |
|
| Source name |
Hela cells, EGF treated, 40 min, total RNA, biological replicate #2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Hela cells, CCL-2
agent: EGF
time point: 40 min
population: total RNA
biological replicate: #2
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
HeLa cells were seeded on adherent plates and serum starved for 12h with DMEM, 0.5% FBS, 2mM glutamine. Cells were treated for 40 minutes with recombinant human epidermal growth factor (hEGF) at final concentration of 1 μg/ml.
|
| Growth protocol |
HeLa cells were cultured in Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2mM glutamine, 100 units/ml penicillin, and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIZOL reagent according to the manufacturer's protocol. Briefly, the aqueous phase was used for RNA precipitation with an equal volume of isopropanol. The RNA pellet was washed once with 75% ethanol, then air-dried and re-dissolved in 20 μl of RNase-free water. RNA was quantified using a spectrophotometer and its quality was checked by agarose gel electrophoresis and by Agilent 2100 Bioanalyzer platform, following the manifacturer’s guidelines for sample preparation and analysis of data (Agilent 2100 Bioanalyzer 2100 Expert User's Guide, http://www.agilent.com).
|
| Label |
Cy3-CTP
|
| Label protocol |
G4140-90040_One-Color_GE_5.7 (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf)
|
| |
|
| Hybridization protocol |
Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).
|
| Scan protocol |
Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.
|
| Description |
Total RNA sample extracted from serum starved HeLa cells treated with hEGF (1 μg/ml final concentration) for 40 minutes.
|
| Data processing |
Agilent Feature Extraction Software version 10.7.7.1 (standard protocol GE1_107_Sep09) was used for data extraction, background correction and flagging of non-uniform features. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.
|
| |
|
| Submission date |
Feb 09, 2010 |
| Last update date |
Feb 12, 2010 |
| Contact name |
Toma Tebaldi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Trento
|
| Department |
Centre for Integrative Biology
|
| Street address |
via Sommarive n. 9
|
| City |
Povo |
| State/province |
Trento |
| ZIP/Postal code |
38123 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE20277 |
Translatome and transcriptome profiling of EGF response in HeLa cells |
|
