NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM430341 Query DataSets for GSM430341
Status Public on Apr 16, 2010
Title Neuroblastoma SH-SY5Y cells_cloneG_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: G
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 G1.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.
 
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

Data table header descriptions
ID_REF
VALUE Log2 RMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 10.10126545
1053_at 10.64960834
117_at 6.348281281
121_at 9.271971313
1255_g_at 8.053976158
1294_at 6.751829973
1316_at 6.849181643
1320_at 7.76747106
1405_i_at 4.16236684
1431_at 4.844749993
1438_at 7.574799101
1487_at 9.476700177
1494_f_at 7.484708658
1598_g_at 10.74479265
160020_at 7.811765401
1729_at 8.721995963
177_at 5.405719706
1773_at 8.622664421
179_at 10.06841706
1861_at 8.724279831

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM430341.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap