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Sample GSM563187 Query DataSets for GSM563187
Status Public on Jul 07, 2011
Title NBL 9 cell line
Sample type RNA
 
Source name NBL cell line 9
Organism Homo sapiens
Characteristics cell type: neuroblastoma cell line
gender: female
mycn status: MYCN amplified
alk mutation status: amplified
Growth protocol cultured in DMEM or RPMI at 37 C and 5% CO2 in non-hypoxic conditions
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU 133 Plus2.0 arrays. GeneChips were washed and stained according to Affymetrix protocol
Scan protocol GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G
Description Gene expression data of neuroblastoma cell line
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (TGT value 500) as normalization method.
 
Submission date Jul 06, 2010
Last update date Jan 20, 2012
Contact name Floor Duijkers
Organization name Erasmus MC
Department Pediatric Oncology-Hematology
Street address Dr. Molewaterplein 50-60 Ee15-02
City Rotterdam
ZIP/Postal code 3015 GE
Country Netherlands
 
Platform ID GPL570
Series (4)
GSE22771 Anaplastic lymphoma kinase (ALK) inhibitor response in neuroblastoma is highly correlated with ALK mutation status, ALK mRNA and protein levels.
GSE33903 Expression array of peripheral neuro-ectodermal cell lines
GSE35218 Nanomolar treatment with epigenetic drug combination induces genome-wide methylation and expression alterations in neuro-ectodermal cell lines [mRNA]

Data table header descriptions
ID_REF
VALUE MAS5.0
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 684.308 P 0.000662269
AFFX-BioB-M_at 899.211 P 8.14279e-05
AFFX-BioB-3_at 512.925 P 0.000581214
AFFX-BioC-5_at 715.697 P 0.000389797
AFFX-BioC-3_at 783.161 P 7.00668e-05
AFFX-BioDn-5_at 4264.88 P 4.42873e-05
AFFX-BioDn-3_at 12270.9 P 9.4506e-05
AFFX-CreX-5_at 30887.4 P 5.16732e-05
AFFX-CreX-3_at 36903.1 P 4.42873e-05
AFFX-DapX-5_at 606.518 P 7.00668e-05
AFFX-DapX-M_at 1179.79 P 0.00255552
AFFX-DapX-3_at 1173.57 P 0.000169227
AFFX-LysX-5_at 118.267 P 0.0044838
AFFX-LysX-M_at 204.391 A 0.139482
AFFX-LysX-3_at 284.749 P 8.13208e-05
AFFX-PheX-5_at 89.9406 A 0.123572
AFFX-PheX-M_at 172.232 P 0.0113844
AFFX-PheX-3_at 108.047 A 0.0780018
AFFX-ThrX-5_at 155.915 P 0.0239288
AFFX-ThrX-M_at 229.918 P 0.00933744

Total number of rows: 54675

Table truncated, full table size 1623 Kbytes.




Supplementary file Size Download File type/resource
GSM563187.CEL.gz 5.1 Mb (ftp)(http) CEL
GSM563187.CHP.gz 292.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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