|
| Status |
Public on Feb 25, 2010 |
| Title |
Daoy_Biologicalreplicate1_2 |
| Sample type |
RNA |
| |
|
| Source name |
Daoy medulloblastoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: WT
cell line: Daoy medulloblastoma cell line
|
| Growth protocol |
MEM Richter’s modification medium (Gibco), supplemented with 10% fetal bovine serum (Atlanta Biologicals Inc., Lawrenceville, GA), 100 units/ml penicillin, and 100microg/ml streptomycin (Herndon, VA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using TRIzol as recommended by Invitrogen and re-purified with the RNeasy kit from Qiagen.
|
| Label |
Cy3
|
| Label protocol |
Samples were labeled with Cy3-9mer primers using Klenow enzyme.
|
| |
|
| Hybridization protocol |
Labeled products were precipitated with isopropanol and resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit.
|
| Scan protocol |
Microarrays were scanned with the Agilent Microarray Scanner G2565AA.
|
| Description |
Biological Replicate 1
|
| Data processing |
Gene expression values were generated using NimbleScan expression RMA (Robust Multi-array Analysis). Report files were further analyzed in the R Project for Statistical Computing using the Bioconductor package limma. First to assess quality control (one microarray was eliminated) and then to achieve the same empirical distribution on the single channel microarray intensities of the two biological replicates. Finally, we averaged gene expression values to obtain the final values.
|
| |
|
| Submission date |
Feb 23, 2010 |
| Last update date |
Feb 25, 2010 |
| Contact name |
raquel abreu |
| Organization name |
CCRI
|
| Street address |
8403 Floyd Curl Drive
|
| City |
san antonio |
| State/province |
TX |
| ZIP/Postal code |
78229-3900 |
| Country |
USA |
| |
|
| Platform ID |
GPL8971 |
| Series (1) |
|
