|
| Status |
Public on Oct 01, 2015 |
| Title |
scramble+doxy+ins 4 poly |
| Sample type |
RNA |
| |
|
| Source name |
AML12 scramble+doxy+ins 4 poly
|
| Organism |
Mus musculus |
| Characteristics |
cells: AML12 hepatocytes
gender: male
treatment: scramble+doxy+ins
|
| Treatment protocol |
AML12 were treated with 100 mM insulin (Life technologies), diluited in DMEM-F12. The cultures were incubated for 1 hour at 37 ºC in a humidified incubator with 5% CO2.
|
| Growth protocol |
AML12 hepatocytes were grown in DMEM-F12 plus 1% glutamine-penycillin-streptomycin (Gibco),10% heat-inactivated FBS, ITS 1X reagent (Life technologies) and dexamethasone 40 ug/ul. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Phenol:Chloroform acid reagent (Sigma), following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| 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 |
For microarray on AML12, polysomal and subpolysomal RNAs were hybridized on the Agilent SurePrint G3 Mouse GE 8x60K Microarray G4852A following the manifacturer’s protocol. The experiment was performed in biological quadruplicate.
|
| Scan protocol |
Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner G2505C at 3μm resolution with the manufacturer’s software (Agilent Scan Control 8.1.3).
|
| Description |
Gene expression after 1 hr insulin 100 nM
|
| Data processing |
The scanned TIFF images were analyzed numerically and the background was corrected using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09. 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/). Low signal Agilent features, distinguished by a repeated “undetected” flag across the majority of the arrays in every condition, were filtered out from the analysis, leaving 18905 features corresponding to 14108 MGI genes. Signal intensities across arrays were normalized with the quantile method.
|
| |
|
| Submission date |
Sep 04, 2014 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Daniela Brina |
| E-mail(s) |
brina@ingm.org
|
| Phone |
+390200660307
|
| Organization name |
INGM
|
| Street address |
Via Sforza 35
|
| City |
Milan |
| ZIP/Postal code |
20122 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE61126 |
Characterization of polysome enriched mRNAs following insulin treatment |
|
