|
| Status |
Public on Oct 01, 2012 |
| Title |
K562_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
K562 cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
|
| Growth protocol |
Cells were grown in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by DNAseI treatment.
|
| Label |
biotin
|
| Label protocol |
Gene expression array analysis was performed using Affymetrix GeneChip Human Gene 1.0ST Array system (Affymetrix, Santa Clara, CA) according to manufacturer’s instructions. Briefly, for each sample, 200ng of total RNA in a volume of 5µl was amplified using the Applause WT Amp ST, RNA Amplification System (NuGen, San Carlos, CA) and labelled with Encore Biotin Module, Post–Amplification System (NuGen).
|
| |
|
| Hybridization protocol |
A total of 2.5µg of labelled cDNA, along with GeneChip Hybridization Control reagents (Affymetrix), was injected into an Affymetrix GeneChip Human Gene 1.0 ST Array. The chips were incubated for 18 hours at 45oC and rotated at 60rpm to allow hybridization. The chips were then washed and stained using GeneChip Hybridization Wash and Stain Kit (Affymetrix) using the Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affimetrix GeneChip Scanner GCS 3000 with the GeneChip Operating software version 1.4.0.036
|
| Description |
Gene expression data from cell lines K562
|
| Data processing |
CEL files were RMA normalized using R/bioconductor
|
| |
|
| Submission date |
Oct 25, 2011 |
| Last update date |
Oct 01, 2012 |
| Contact name |
Touati Benoukraf |
| E-mail(s) |
tbenoukraf@mun.ca
|
| Phone |
+1 (709) 864-6671
|
| Organization name |
Memorial University of Newfoundland
|
| Department |
Faculty of Medicine, Division of BioMedical Sciences
|
| Street address |
Craig L. Dobbin Genetics Research Centre,
|
| City |
St. John's |
| State/province |
NL |
| ZIP/Postal code |
A1B 3V6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE33226 |
Genome wide DNA methylation analysis of leukemia and reprogrammed leukemia cells (gene expression) |
| GSE33231 |
Genome wide DNA methylation analysis of leukemia and reprogrammed leukemia cells |
|
