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Sample GSM1108665 Query DataSets for GSM1108665
Status Public on Mar 28, 2013
Title NB_E_265
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): 1
Stage: 3
age (1: <18 months; 2: >18 months): 1
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 252038210081_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]

Data table header descriptions
ID_REF
VALUE quantile normalized intensities

Data table
ID_REF VALUE
1 93280.4730122324
2 4.68930246636086
3 4.83198077828746
4 4.9244294617737
5 5.01027492813456
6 5.09423289296636
7 5.16710138685015
8 5.22253705045872
9 5.28108798318043
10 5.32361272782875
11 5.35619506880734
12 90.4809968577982
13 1186.09562851682
14 46.6969059067278
15 582.829307981651
16 311.760795840979
17 25544.4553195719
18 758.063029159021
19 9920.81504740061
20 1174.02165877676

Total number of rows: 44708

Table truncated, full table size 987 Kbytes.




Supplementary file Size Download File type/resource
GSM1108665_US22502540_252038210081_S01_GE1-v5_10_Apr08_1_4.txt.gz 1.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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