|
| Status |
Public on Jul 02, 2018 |
| Title |
primary NB tumor_nrc2022 |
| Sample type |
RNA |
| |
|
| Source name |
primary untreated neuroblastoma tumor
|
| Organism |
Homo sapiens |
| Characteristics |
age_at_diagnosis(days): 549
event_overall: yes
event_progression_free: yes
inss: st4
mycn_amplification: yes
overall_survival_time(days): 394
profression_free_survival_time(days): 394
|
| 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 |
|
