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Sample GSM454048 Query DataSets for GSM454048
Status Public on Sep 14, 2010
Title 4382-8249-Cy3
Sample type RNA
 
Channel 1
Source name 8076-8077
Organism Homo sapiens
Characteristics reference: Universal Human Reference Total RNA
Extracted molecule total RNA
Extraction protocol 2ug universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000)
Label Cy5
Label protocol Samples were amplified and labeled using TAcKLE Protocol [PMID: 15718295]
 
Channel 2
Source name 4382-8249
Organism Homo sapiens
Characteristics sex: M
sample_type: sample
tumor_entity_subtype: pGBIV
ageatsampling: 54
overall.survival..days.: 994
chemotherapy: yes
radiation.therapy: yes
Extracted molecule total RNA
Extraction protocol RNA were prepared from fresh frozen tumor tissue using ultracentrifugation [PMID: 12937144]
Label Cy3
Label protocol Samples were amplified and labeled using TAcKLE Protocol [PMID: 15718295]
 
 
Hybridization protocol Purified and dye-labeled sample and reference cDNA (Human Reference RNA, Stratagene, LaJolla, USA) was pooled an mixed with 520 µl hybridisation buffer (4x SSC, 50perc formamide, 2perc SDS), agitated for 60 min at 60C, heated for 10 min at 70C on a thermo mixer and subsequently applied to preheated (60C) microarrays mounted in hybridisation chambers. Hybridisations were performed for 23 h at 42C and a rotation speed of 4 rpm in an Agilent DNA Microarray Hybridisation Oven (Agilent, Santa Clara, USA). The arrays were washed at 35C with (i) 0.5x SSC, 0.1perc SDS for 4 min; (ii) 0.05x SSC, 0.1perc SDS for 4 min; (iii) 0.05x SSC for 2 min; (iv) 0.05x SSC, 0.05perc Tween for 30 sec. Immediately thereafter, slides were dried by centrifugation in 50 ml Falcon tubes at 2500 rpm for 5 min.
Scan protocol Hybridized microarrays were scanned at 5 µm resolution in a two-color Agilent Scanner G25505B (Agilent, Santa Clara, USA) with automatically adjusted PMT voltages according to manufacturer’s specification. Array raw data were generated from scanned images using Axon GenePixPro Software (v6.1.0.2)
Description N/A
Data processing Spots not recognized by the image analysis software, or not passing the quality criteria were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002).
 
Submission date Sep 18, 2009
Last update date Sep 21, 2009
Contact name Grischa Toedt
Organization name German Cancer Research Center (DKFZ)
Department Molecular Genetics (B060)
Lab Prof. Peter Lichter
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL9190
Series (1)
GSE18166 Genome-Wide Profiling of Astrocytic Gliomas

Data table header descriptions
ID_REF ID column of the reference platform
VALUE normalized log2 ratio (test/reference)
INV_VALUE normalized log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE INV_VALUE
1 1.02819 -1.0281928268812
2 0.776834 -0.776834210563036
3
4 -1.26145 1.26145038807813
5 -0.428769 0.428769009712139
6 0.374284 -0.374284072563636
7 -1.73289 1.7328919249213
8 -0.461778 0.461777629643098
9 -0.0491698 0.0491698273839987
10 0.508011 -0.508010825493949
11 0.45553 -0.455529641895977
12 -1.00537 1.00536704893671
13 -0.683485 0.683484530334642
14 6.18257 -6.18256815689537
15 2.63534 -2.63533770792286
16 1.95603 -1.95602854775335
17 1.45572 -1.45571838209199
18 1.26488 -1.26488138357594
19 -0.118246 0.118245982657308
20 0.282522 -0.282522249087194

Total number of rows: 37632

Table truncated, full table size 862 Kbytes.




Supplementary file Size Download File type/resource
GSM454048_5087.gpr.gz 3.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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