|
| Status |
Public on Dec 18, 2014 |
| Title |
HCT116_ASO_lncRNA-1_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
HCT116, 5FU, 12h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
transfection: 100nM ASOs (target one of the candidate lncRNA for depletion)
treatment: 5 FU for 12h
passages: 8-10passeges
|
| Treatment protocol |
Cells were treated with the DNA damage drug 5 FU for 12h.
|
| Growth protocol |
HCT116 cells were transfected with 100nM ASOs for 48h and treated with the DNA damage drug 5FU for 12h. RNA was isolate and performed the arrays.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
|
| Label |
biotin
|
| Label protocol |
The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).
|
| |
|
| Hybridization protocol |
Labeled sense cDNA was hybridized to the Affymetrix Human Transcriptome Array 2.0 (HTA) chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.
|
| Scan protocol |
Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.
|
| Description |
Transfected 100nM ASO
|
| Data processing |
The data were normalized with Affymetrix Power Tools (APT) software using RMA algorithm.
|
| |
|
| Submission date |
Jun 11, 2014 |
| Last update date |
Dec 18, 2014 |
| Contact name |
Maite Huarte |
| E-mail(s) |
maitehuarte@unav.es
|
| Organization name |
CIMA
|
| Street address |
c/ Avd Pio XII, 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17586 |
| Series (2) |
| GSE58409 |
Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (expression) |
| GSE58528 |
Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature |
|
