|
| Status |
Public on Mar 15, 2012 |
| Title |
U-87MG-PK19 set 1 |
| Sample type |
RNA |
| |
|
| Source name |
U-87MG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U-87MG
treatment: parkin
|
| Growth protocol |
The cells were similarly seeded at a concentration of 500,000 cells in 10ml of culture medium in 10-cm tissue culture plate and incubated at 37oC in a 5.0% CO2 incubator for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the various U-87MG parkin expressing and vector control cells were extracted using the RNeasy Mini Kit (Qiagen, USA). The concentration and quality of the total RNA extracted was assessed by the NanoDrop ND-1000 machine (Thermo Scientific, USA) and the Bioanalyzer (Agilent, USA).
|
| Label |
biotin
|
| Label protocol |
After the quality of the RNA was ascertained, the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix, USA) was used to generate the first and second cycle cDNA synthesis and the cRNA synthesis through in vitro transcription amplification. After the second cycle cDNA synthesis and cRNA hydrolysis step, the GeneChip® WT Terminal Labeling Kit was used for the fragmentation and terminal labeling of the cDNA to generate targets compatible with the GeneChip arrays.
|
| |
|
| Hybridization protocol |
The targets were hybridized to the GeneChip® Human Gene 1.0 ST Array according to the manufacturer hybridization protocol which constituted 28,000 gene-level probe sets.
|
| Scan protocol |
300ng of total RNA were used for the experiments and the arrays were washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner. The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC.
|
| Description |
AFGE1068-3.CEL
Gene expression data from parkin-expressing U-87MG
|
| Data processing |
The data was processed using Bioconductor packages in the R statistical software. RMA normalization was applied and p-values were generated by comparing against the detection above background probes. Probe sets with DABG p-value >0.01 in all samples was removed.
|
| |
|
| Submission date |
May 24, 2011 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Felicia Ng |
| Organization name |
Cambridge Institute for Medical Research
|
| Street address |
Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB3 9BB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE29494 |
Parkin pathway activation mitigates glioma cell proliferation and predicts patient survival |
|
