|
| Status |
Public on May 29, 2014 |
| Title |
siSLU7_48H_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
PLC/PRF/5 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hepatocellular carcinoma cell line PLC/PRF/5
genotype/variation: SLU7 knockdown
|
| Treatment protocol |
The siRNAs targeting human SLU7 gene (siSLU7) and the control siRNA (siGL) were from Sigma Chemical and have been previously described. Transfections were performed using Lipofectamine RNAiMAX transfection reagent (Invitrogen) following manufacturer’s instructions.
|
| Growth protocol |
PLC/PRF/5 cells were cultured in DMEM supplemented with 10%FCS.
|
| 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 HuExon-1_0-st 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 |
siSlu72
Affymetrix GeneChip Human Exon 1.0 ST (HuEx-1_0-st-v2_core.cdf from aroma.affymetrix)
|
| Data processing |
The data were normalized with Bioconductor software using RMA algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
|
| |
|
| Submission date |
Jan 15, 2014 |
| Last update date |
May 29, 2014 |
| Contact name |
Victor Segura |
| E-mail(s) |
vsegura@unav.es
|
| Organization name |
FIMA
|
| Department |
Unit of Proteomics, Genomics and Bioinformatics
|
| Street address |
Avda. Pío XII, 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE54090 |
Slu7 is essential for liver differentiation, metabolism and quiescence |
|
