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Sample GSM1108811 Query DataSets for GSM1108811
Status Public on Mar 29, 2013
Title NB_E_411
Sample type RNA
 
Source name tumor sample
Organism Homo sapiens
Characteristics tissue: Neuroblastoma
Sex: F
mycn (1: not amplified; Amp: amplified; n.a.:not available): 1
Stage: 1
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 252038210126_1_2
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 29, 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]

Data table header descriptions
ID_REF
VALUE quantile normalized intensities

Data table
ID_REF VALUE
1 78480.1114373089
2 5.85865815749235
3 5.91553267431193
4 5.98100854892966
5 6.03793884097859
6 6.07915791743119
7 6.11298324923547
8 6.14686590825688
9 6.17653884250764
10 6.20256045565749
11 6.21572099541284
12 82.8481093562691
13 1054.40885611621
14 59.8618144143731
15 748.13294383792
16 248.687244327217
17 19849.9687798165
18 736.538852553517
19 10005.1586972477
20 563.023125091743

Total number of rows: 44708

Table truncated, full table size 987 Kbytes.




Supplementary file Size Download File type/resource
GSM1108811_US22502540_252038210126_S01_GE1-v5_10_Apr08_1_2.txt.gz 1.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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