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Sample GSM1108872 Query DataSets for GSM1108872
Status Public on Mar 29, 2013
Title NB_E_472
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): n.a.
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 252038210159_1_3
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 61590.3501070336
2 17.092593911315
3 6.25778516972477
4 6.35892424923547
5 6.45488974006116
6 16.5331879801223
7 6.71871291896024
8 12.8854217614679
9 6.95685236391437
10 7.08074259327217
11 7.16570207798165
12 123.928594036697
13 995.228033700306
14 30.6330278975535
15 729.979772155963
16 144.733464584098
17 16430.1638593272
18 859.456094862385
19 6828.16373761468
20 652.037551834862

Total number of rows: 44708

Table truncated, full table size 987 Kbytes.




Supplementary file Size Download File type/resource
GSM1108872_US22502540_252038210159_S01_GE1-v5_10_Apr08_1_3.txt.gz 1.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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