|
| Status |
Public on Apr 16, 2010 |
| Title |
Neuroblastoma SH-SY5Y cells_cloneB_stably transfected with RNAi against DJ-1_replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
Neuroblastoma SH-SY5Y cells, stably transfected with RNAi against DJ-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human neuroblastoma cells
cell line: SH-SY5Y
clone: B
transfectant type: stably transfected with RNAi against DJ-1
|
| Growth protocol |
Human neuroblastoma SH-SY5Y cells (ATCC) were maintained in culture as suggested by vendors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIZOL reagent (Invitrogen) following the manufacturer’s instructions, and purified using the RNeasy mini kit (Qiagen). The quality of total RNA was assessed using a bioanalyzer (Agilent 2100; Agilent Technologies) and RNA was quantified using a ND-1000 Nanodrop spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
10 micrograms of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol developed by Affymetrix (Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Labeled cRNA was hybridized on Affymetrix GeneChip Human U133A 2.0 Arrays containing over 14,500 transcripts. Hybridized GeneChips were stained and washed (GeneChip Fluidics Station 450).
|
| Scan protocol |
GeneChips were scanned using a GeneChip Scanner 3000 7G.
|
| Description |
B1.CEL
|
| Data processing |
Cell intensity values and probe detection calls were computed from the raw microarray data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) using packages from the BioConductor software project (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes with a Present call in at least one of the arrays were retained. Data were then imported in the MultiExperiment Viewer (MeV) software, and statistical analysis was performed using SAM (Significance Analysis of Microarrays). Additionally, an expression fold-change cutoff of 2 was applied to detect significantly differentially expressed genes.
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| |
|
| Submission date |
Jul 20, 2009 |
| Last update date |
Apr 16, 2010 |
| Contact name |
Paola Roncaglia |
| Organization name |
SISSA/ISAS (International School for Advanced Studies)
|
| Department |
Neurobiology
|
| Street address |
via Bonomea 265
|
| City |
Trieste |
| State/province |
TS |
| ZIP/Postal code |
34136 |
| Country |
Italy |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE17204 |
Parkinson's disease-associated DJ-1 is required for the expression of GDNF receptor Ret in human neuroblastoma cells |
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