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Status
Public on Dec 08, 2006
Title
Hyperplastic lymphoid tissue VUMC_L090_b33_s14
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
tonsil
Organism
Homo sapiens Characteristics
hyperplastic lymphoid tissue
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 18, 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
1273.509
650.036
-0.97
0.85
-0.114870485
2
182.968
130.307
-0.49
0.41
-0.324124351
3
1062.055
234.748
-2.178
0.68
0.163036611
4
5109.557
3320.317
-0.622
0.96
0.087215974
5
215.596
380.353
0.819
0.69
0.421754653
6
622.441
2725.225
2.13
0.91
0.457553194
7
239.023
269.359
0.172
0.66
0.524543872
8
5879.686
1741.576
-1.755
0.94
-0.28628669
9
1535.914
730.007
-1.073
0.87
-0.575023276
10
7858.625
2438.308
-1.688
0.94
-0.887343602
11
3544.869
1639.491
-1.112
0.94
-0.536226925
12
4741.924
1943.481
-1.287
0.86
-0.862303849
13
2657.567
714.7
-1.895
0.92
-0.949725284
14
353.459
1242.562
1.814
0.83
0.737426481
15
1726.896
1187.507
-0.54
0.78
-0.035032453
16
1646.537
784.418
-1.07
0.95
-0.865862933
17
884.67
584.637
-0.598
0.75
-0.114870485
18
112.986
119.722
0.084
0.28
-0.324124351
19
771.367
207.895
-1.892
0.7
0.163036611
20
4548.762
2968.577
-0.616
0.95
0.087215974
30000 1326 Kbytes .Supplementary data files not provided
