|
| Status |
Public on Apr 22, 2013 |
| Title |
IMR-90-ING4wt1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
primary human diploid fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR-90
cell type: fibroblasts
genotype/variation: wild-type ING4
|
| Growth protocol |
IMR-90 primary human diploid fibroblasts were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and used at a population doubling level (PDL) lower than 30.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Tri Reagent (Sigma) from asynchronously growing cells. RNA was used for cDNA síntesis using M/MLV reverse transcriptase (Promega, Madison, WI, USA).
|
| Label |
Cy5
|
| Label protocol |
1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
IMR-90-control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
cell type: fibroblasts
genotype/variation: vector-infected cells
|
| Growth protocol |
IMR-90 primary human diploid fibroblasts were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and used at a population doubling level (PDL) lower than 30.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Tri Reagent (Sigma) from asynchronously growing cells. RNA was used for cDNA síntesis using M/MLV reverse transcriptase (Promega, Madison, WI, USA).
|
| Label |
Cy3
|
| Label protocol |
1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.
|
| Scan protocol |
After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer's protocol.
|
| Data processing |
Differentially expressed genes in wild-type ING4 versus vector were identified with GEPAS (Gene Expression Pattern Analysis Suite, http://gepas3.bioinfo.cipf.es) selecting genes with a fold difference of at least two in all of the samples and standard deviation lower than 0,5. This subset was further analyzed in the arrays from ING4N214D-infected cells. Functional enrichment analysis was performed using the FatiGO application (http://babelomics.bioinfo.cipf.es).
|
| |
|
| Submission date |
Nov 20, 2012 |
| Last update date |
Apr 23, 2013 |
| Contact name |
Gema Moreno-Bueno |
| E-mail(s) |
[email protected]
|
| Phone |
+34914978974
|
| Organization name |
IIB
|
| Department |
Biochemistry
|
| Lab |
1.13
|
| Street address |
Arturo Duperier
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL8755 |
| Series (1) |
| GSE42412 |
ING4 regulates a secretory phenotype in primary fibroblasts with dual effects on cell proliferation and tumor growth |
|
