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Sample GSM2256940 Query DataSets for GSM2256940
Status Public on Jul 02, 2018
Title primary NB tumor_nrc2551
Sample type RNA
 
Source name primary untreated neuroblastoma tumor
Organism Homo sapiens
Characteristics age_at_diagnosis(days): NA
event_overall: NA
event_progression_free: NA
inss: NA
mycn_amplification: no
overall_survival_time(days): NA
profression_free_survival_time(days): NA
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 8.574782721
2318744 10.73420154
2318746 10.55458885
2318747 9.729620744
2318751 7.584210901
2318754 8.032872249
2318755 5.894817763
2318759 3.087462841
2318761 3.277984747
2318763 5.937815169
2318765 11.52669485
2318767 2.847996907
2318769 3.897240426
2318771 2.765534746
2318773 2.655351829
2318775 6.8899602
2318777 2.292781749
2318779 5.697662633
2318781 5.727920455
2318783 5.116863758

Total number of rows: 13092

Table truncated, full table size 253 Kbytes.




Supplementary file Size Download File type/resource
GSM2256940_nrc2551.CEL.gz 22.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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