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Sample GSM430340 Query DataSets for GSM430340
Status Public on Apr 16, 2010
Title Neuroblastoma SH-SY5Y cells_cloneB_stably transfected with RNAi against DJ-1_replicate2
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 B2.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 ( using packages from the BioConductor software project ( 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
VALUE Log2 RMA normalized signal intensity

Data table
1007_s_at 9.843896002
1053_at 10.43971057
117_at 6.602416031
121_at 9.458565104
1255_g_at 7.787813848
1294_at 6.90924488
1316_at 7.112845234
1320_at 7.487432278
1405_i_at 4.434718586
1431_at 4.908749042
1438_at 7.745979749
1487_at 9.458747923
1494_f_at 7.693485508
1598_g_at 10.68767026
160020_at 8.117762166
1729_at 8.795139853
177_at 5.485357574
1773_at 8.627047032
179_at 10.24383865
1861_at 8.566455121

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM430340.CEL.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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