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Status
Public on Dec 08, 2006
Title
Diffuse large B cell lymphoma VUMC_L056_b33_s48
Sample type
RNA
Channel 1 Source name
universal human reference RNA
Organism
Homo sapiens Characteristics
comprised of 10 cell lines for human giving broad gene coverage
Biomaterial provider
Stratagene
Treatment protocol
n.a.
Growth protocol
n.a.
Extracted molecule
total RNA
Extraction protocol
see www.stratagene.com
Label
Cy3
Label protocol
labeling protocol available via www.vumc.nl/microarrays
Channel 2 Source name
lymph node
Organism
Homo sapiens Characteristics
diffuse large B cell lymphoma
Biomaterial provider
VUMC, Amsterdam, The Netherlands
Treatment protocol
n.a.
Growth protocol
n.a.
Extracted molecule
total RNA
Extraction protocol
RNA isolation protocol available via www.vumc.nl/microarrays
Label
Cy5
Label protocol
labeling protocol available via www.vumc.nl/microarrays
Hybridization protocol
Hybridization protocol available via www.vumc.nl/microarrays
Scan protocol
Microarray Scanner G2505B (Agilent Technologies), default settings
Description
see also Muris et al. submitted
Data processing
Image analysis and feature extraction was done with BlueFuse for Microarrays (version 2.0 (3276), BlueGnome Limited, Cambridge, United Kingdom). Fused values of in duplicate spotted oligos were taken and intensities were divided by the mean intensity of each channel. Next, data were inter array centered by dividing the ratios for each gene across the sample set by the mean observed value. The resulting ratios were log-transformed (base 2) and processed into Stanford file format (rows, mean values for the in duplicate measured oligos; columns, mRNA samples). The resulting dataset contained expression ratios of 14487 genes.
Submission date
Jan 17, 2006
Last update date
Dec 08, 2006
Contact name
Daoud Sie
E-mail(s)
[email protected] Phone
+31 20 4442428
Organization name
Vrije Universiteit Medical Center
Department
Pathology
Lab
Microarray Core Facility
Street address
De Boelelaan 1117
City
Amsterdam
ZIP/Postal code
1081 HV
Country
Netherlands
Platform ID
GPL3255 Series (1)
GSE3892 Diffuse large B cell lymphomas
Data table header descriptions ID_REF AMPCH1 Total signal in channel 1 (Cy3)
AMPCH2 Total signal in channel 2 (Cy5)
LOG2RATIO CH2/CH1 Log, base 2, of the ratio of total signal in channel 2 divided by total signal in channel 1
CONFIDENCE The Confidence Estimate in the calculated ratio, between 0 and 1, calculated by BlueFuse
VALUE Log, base 2, of the ratio of the fused value, mean normalized by array, mean centered for each gene across the entire sample set
Data table ID_REF AMPCH1 AMPCH2 LOG2RATIO CH2/CH1 CONFIDENCE VALUE 1
1036.185
6696.95
2.692
0.83
1.497461881
2
196.18
990.207
2.336
0.68
0.593404239
3
928.419
1003.566
0.112
0.77
0.37511342
4
5282.938
7891.136
0.579
0.92
-0.296310018
5
114.496
518.104
2.178
0.59
0.323083397
6
300.506
2789.971
3.215
0.85
-0.092553352
7
227.257
736.383
1.696
0.77
0.019581391
8
5256.775
8393.184
0.675
0.98
0.380448822
9
1357.39
3381
1.317
0.96
0.17057086
10
6718.853
14246.269
1.084
0.99
0.465390463
11
2650.889
5740.707
1.115
0.96
0.40219422
12
3858.98
12236.931
1.665
0.95
0.617532758
13
2555.156
3033.578
0.248
0.98
-0.18276034
14
386.255
3971.908
3.362
0.78
0.880761335
15
1796.502
4602.092
1.357
0.79
0.304462021
16
1635.177
6984.615
2.095
0.96
0.66535072
17
904.616
3584.099
1.986
0.98
1.497461881
18
113.572
401.415
1.821
0.48
0.593404239
19
908.713
536.22
-0.761
0.77
0.37511342
20
5199.818
7767.717
0.579
0.97
-0.296310018
30000 1325 Kbytes .Supplementary data files not provided
