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Sample GSM1108733 Query DataSets for GSM1108733
Status Public on Mar 28, 2013
Title NB_E_333
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: 2a
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 252038210101_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 88499.9305198777
2 4.22581444954128
3 4.18158285779817
4 4.14900501529052
5 4.12306862844037
6 4.0981935382263
7 4.07773822477064
8 4.057437
9 4.03511066055046
10 4.01193818195719
11 3.99643654434251
12 66.0791158899083
13 986.876990948012
14 26.7929881896024
15 626.922138929664
16 366.132419984709
17 15684.4713119266
18 575.667766819572
19 8640.24304740061
20 491.688567324159

Total number of rows: 44708

Table truncated, full table size 987 Kbytes.




Supplementary file Size Download File type/resource
GSM1108733_US22502540_252038210101_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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