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Sample GSM2256923 Query DataSets for GSM2256923
Status Public on Jul 02, 2018
Title primary NB tumor_nrc2385
Sample type RNA
 
Source name primary untreated neuroblastoma tumor
Organism Homo sapiens
Characteristics age_at_diagnosis(days): 731
event_overall: yes
event_progression_free: yes
inss: st4
mycn_amplification: no
overall_survival_time(days): 666
profression_free_survival_time(days): 638
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the miRNeasy kit (Qiagen) according to the manufacturer's instructions
Label Biotin
Label protocol Biotinylated cDNA was prepared according to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Rev. 5) from 1000 ng total RNA, including the rRNA reduction step
 
Hybridization protocol Following fragmentation, ~5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip Human Exon 1.0 ST Arrays (Affymetrix Part No. 900 651). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol Arrays were scanned in the Affymetrix GeneChip Scanner 3000 with G7 update
Data processing In order to obtain expression information per gene, exon data was merged by transcript clusters (hg18/core exons). Exon array data was normalized according to the RMA-sketch algorithm using Affymetrix Power Tools (Affymetrix).
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
CEL files were rma-sketch normalized using Affymetrix Power Tools (v1.10.0). The resulting data were batch corrected using zscores and rescaled to the largest batch to re-obtain untransformed values.
 
Submission date Aug 01, 2016
Last update date Jul 02, 2018
Contact name Pieter mestdagh
E-mail(s) [email protected]
Organization name Center for Medical Genetics
Street address De Pintelaan 185
City Gent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL5175
Series (1)
GSE85047 Gene expression data from primary neuroblastoma tumors

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
2318743 7.927777962
2318744 10.37025148
2318746 10.42511098
2318747 9.618385502
2318751 7.651769271
2318754 7.108524457
2318755 6.102238194
2318759 4.478971805
2318761 4.292781749
2318763 5.845490051
2318765 11.51560129
2318767 2.925999419
2318769 4.112700133
2318771 2.137503524
2318773 2.201633861
2318775 6.995484519
2318777 3.053111336
2318779 6.263034406
2318781 5.935459748
2318783 5.008988783

Total number of rows: 13092

Table truncated, full table size 253 Kbytes.




Supplementary file Size Download File type/resource
GSM2256923_nrc2385.CEL.gz 22.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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