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Sample GSM42397 Query DataSets for GSM42397
Status Public on May 12, 2005
Title S007
Sample type RNA
 
Channel 1
Source name Mixture of human neuroblastoma cell lines reference RNA
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name S007
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Primary human neuroblastoma
Total RNA was extracted from each frozen tissue according to the AGPC method (Chomczynski and Sacchi, 1987). As a reference, a mixture of equal amounts of RNA from each of four neuroblastoma cell lines (NB69, NBL-S, SK-N-AS, and SH-SY5Y) were used. Ten micrograms each of total RNA were labeled with the CyScribe RNA labeling kit according to the manufacturer's manual (Amersham Pharmacia Biotech), followed by probe purification with the Qiagen MinElute PCR purification kit (Qiagen).
RNAs extracted from primary neuroblastoma tissues and RNAs of the reference mixture were labeled with Cy3- and Cy5- conjugated deoxynucleotides (Amersham), respectively, and were used as probes in 3.4 x SSC / 0.3% SDS together with 40 micrograms yeast tRNA and 100 micrograms polyA for suppression. Prior to hybridization, each microarray was soaked at room temperature for 30 min in Blocking solution containing 3% BSA, 0.2M NaCl, 0.1M Tris/HCl (pH 7.5) and 0.05% Triton X-100, dried at 37 degree celcius for 15 min, and washed with TE twice. After removing the remaining TE by centrifugation at 1000 rpm for 2 min, 20 microlitter of probe was applied onto the microarray and covered with a cover glass. The microarray was transferred to humidiated tightly covered box and incubated in 65 degree celcius chamber for 16 hours. The slides were washed twice for 5 min with 2xSSC, 0.1% SDS and then twice with 0.2xSSC, 0.1% SDS for 5 min at room temperature followed by centrifugation at 1000 rpm for 2 min.
Hybridized microarrays were scanned using the Agilent G2505A confocal laser scanner (Agilent Technologies, Inc.), and fluorescent intensities were quantified using the GenePix Pro microarray analysis software (Axon Instruments, Inc.).
Keywords = Primary human neuroblastoma
 
Submission date Feb 17, 2005
Last update date May 29, 2005
Contact name Akira Nakagawara
E-mail(s) akiranak@chiba-cc.jp
Phone +81-43-264-5431
Fax +81-43-265-4459
Organization name Chiba Cancer Center Research Institute
Lab Division of Biochemistry
Street address 666-2 Nitona, Chuo-ku
City Chiba
ZIP/Postal code 260-8717
Country Japan
 
Platform ID GPL1875
Series (1)
GSE2283 Primary human neuroblastoma

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of medians defined by CH1/ CH2
CH1_Median - CH1_BKD Channel 1 median signal
CH2_Median - CH2_BKD Channel 2 median signal

Data table
ID_REF VALUE CH1_Median - CH1_BKD CH2_Median - CH2_BKD
1 -0.2474 1349 2123
2 -0.5158 563 962
3 -0.0533 965 1827
4 -0.0283 979 1875
5 -0.0060 1311 2431
6 0.0143 1282 2415
7 0.0322 20 108
8 -0.3598 9688 18078
9 -0.2586 8187 15742
10 -0.1704 7885 16086
11 0.0187 5838 12758
12 -0.1012 7031 14672
13 -0.0861 6187 12642
14 -0.1356 24 115
15 0.1176 25 146
16 -0.8528 101 275
17 -0.0784 24 121
18 -1.5014 51 96
19 -0.0465 20 103
20 0.0024 17 90

Total number of rows: 5340

Table truncated, full table size 102 Kbytes.




Supplementary data files not provided

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