|
| Status |
Public on Mar 28, 2013 |
| Title |
NB_E_111 |
| Sample type |
RNA |
| |
|
| Source name |
tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Neuroblastoma
Sex: M
mycn (1: not amplified; Amp: amplified; n.a.:not available): Amp
Stage: 4
age (1: <18 months; 2: >18 months): 2
|
| Treatment protocol |
All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
30-60mg of snap-frozen neuroblastoma specimen was cryo-sliced and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.
|
| Scan protocol |
After washing and scanning, resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.
|
| Description |
252038210033_1_4
|
| Data processing |
Data normalization using the quantile algorithm, Reference: G. K. Smyth. Limma: linear models for microarray data. In: R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.) Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, 2005. pp. 397-420.
|
| |
|
| Submission date |
Mar 27, 2013 |
| Last update date |
Mar 28, 2013 |
| Contact name |
Thomas Wolf |
| E-mail(s) |
t.wolf@dkfz.de
|
| Organization name |
DKFZ
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
Heidelberg |
| ZIP/Postal code |
D-69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16876 |
| Series (2) |
| GSE45480 |
Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma |
| GSE45547 |
Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma [tumor_genex_44k] |
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