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Sample GSM2257037 Query DataSets for GSM2257037
Status Public on Jul 02, 2018
Title primary NB tumor_nrc4100
Sample type RNA
 
Source name primary untreated neuroblastoma tumor
Organism Homo sapiens
Characteristics age_at_diagnosis(days): 0
event_overall: no
event_progression_free: no
inss: st1
mycn_amplification: no
overall_survival_time(days): 2167
profression_free_survival_time(days): 2167
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 9.328674927
2318744 11.04637373
2318746 11.07775037
2318747 9.742983042
2318751 7.277054876
2318754 7.860466259
2318755 6.215290306
2318759 4.781359714
2318761 4.738767837
2318763 5.675251386
2318765 11.57638986
2318767 3.053111336
2318769 3.99095486
2318771 2.678071905
2318773 1.925999419
2318775 6.943686952
2318777 3.608809243
2318779 6.110613806
2318781 5.569855608
2318783 4.887525271

Total number of rows: 13092

Table truncated, full table size 253 Kbytes.




Supplementary file Size Download File type/resource
GSM2257037_nrc4100.CEL.gz 20.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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