|
| Status |
Public on Dec 31, 2012 |
| Title |
HK1-EBER_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
HK1 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HK1
plasmid: EBERs-positive
|
| Growth protocol |
Mycoplasma-free, stably transfected HK1 cells were maintained in the exponential growth phase in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 10 U of penicillin per ml and 10 μg streptomycin per ml at 37°C in a 5% CO2 humidified atmosphere. Stable transfectants were selected by culturing in fully supplemented medium containing G418. Colonies that emerged were pooled and used for this microarray experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell line with TRIZOL® (Invitrogen) reagent
|
| Label |
biotin
|
| Label protocol |
300ug total RNA was reverse transcribed into cDNA, processed using GeneChip® Whole Transcript (WT) Sense Target Labelling Assay.
|
| |
|
| Hybridization protocol |
Samples were hybridized and analysed on GeneChip ® Human Gene 1.0 ST Array, with three repeats.
|
| Scan protocol |
Microarray scanning and data acquisition were carried out at ORIGEN LABS (Singapore), using an Affymetrix 3000 7G Scanner.
|
| Description |
EBERs plasmid containing 10 tandem repeats of the EBER-1 and EBER-2 subfragment inserted into a pcDNA 3 plasmid was introduced into HK1 cells by the lipofection method.
|
| Data processing |
CEL files were generated from GCOS and analyzed in GeneSpring GX10. RMA16 normalization was performed and signal intensities that showed <20th percentile were excluded. This resulted in 24067 transcripts (see matrix table).
|
| |
|
| Submission date |
May 06, 2011 |
| Last update date |
Dec 31, 2012 |
| Contact name |
Lu Ping Tan |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Medical Research
|
| Department |
Molecular Pathology Unit
|
| Street address |
Jalan Pahang
|
| City |
Kuala Lumpur |
| ZIP/Postal code |
50588 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE29123 |
ABBERANT GENE EXPRESSION BY EBERs IN EBV-NEGATIVE NPC HK1 CELL LINE |
|
