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Status
Public on Jul 09, 2008
Title
Upper respiratory tract infection (Viro3P10-009)
Sample type
RNA
Source name
RdABC amplified RNA from Nasal Lavage
Organism
Viruses Characteristics
Upper respiratory tract infection
Extracted molecule
total RNA
Extraction protocol
RNeasy followed by DNAse treatment
Label
Cy3
Label protocol
Rd C Cy3 incorporation
Hybridization protocol
standard overnight hybridization
Scan protocol
Axon 4000 scanner
Description
RdABC amplified RNA from Nasal Lavage
Data processing
Median feature intensity minus median background intensity. The data analysis software used is E-Predict, which normalizes the data using a variety of measures: sum, quadratic, unit-vector, or no normalization (please see Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL.E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.Genome Biol. 2005;6(9):R78. Epub 2005 Aug 30). E-Predict is public access. For the purposes of this paper, sum-normalized intensities were used in the analysis.
Submission date
Jan 28, 2008
Last update date
Jul 09, 2008
Contact name
Joe DeRisi
E-mail(s)
joe@derisilab.ucsf.edu Phone
415-476-4132
URL
http://derisilab.ucsf.edu Organization name
University of California, San Francisco
Department
Biochemistry and Biophysics
Lab
Joseph DeRisi Laboratory
Street address
City
San Francisco
State/province
CA
ZIP/Postal code
94107
Country
USA
Platform ID
GPL3429 Series (1)
Data table header descriptions ID_REF VALUE same as UNF_VALUE but with flagged values removed
CH1_MEDIAN Channel 1 intensity median
CH1_MEAN Channel 1 intensity mean
CH1_SD Channel 1 intensity standard deviation
CH1_BGD_MEDIAN Channel 1 background intensity median
CH1_BGD_MEAN Channel 1 background intensity mean
CH1_BGD_SD Channel 1 background intensity standard deviation
CH1_NET_MEDIAN Channel 1 net intensity median
CH1_NET_MEAN Channel 1 net intensity median
FLAG GenePix spot flag
UNF_VALUE Channel 1 net intensity median (same as CH1_NET_MEDIAN)
Data table ID_REF VALUE CH1_MEDIAN CH1_MEAN CH1_SD CH1_BGD_MEDIAN CH1_BGD_MEAN CH1_BGD_SD CH1_NET_MEDIAN CH1_NET_MEAN FLAG UNF_VALUE 1
56
116
118
28
60
63
18
56
58
56
2
54
111
114
27
57
61
18
54
57
54
3
79
136
141
42
57
59
17
79
84
79
4
61
116
112
20
55
55
14
61
57
61
5
68
129
129
29
61
62
15
68
68
68
6
52
109
110
25
57
59
15
52
53
52
7
47
107
108
23
60
62
16
47
48
47
8
67
122
119
33
55
57
15
67
64
67
9
52
119
115
33
67
68
18
52
48
52
10
62
119
118
29
57
58
15
62
61
62
11
67
127
126
32
60
61
17
67
66
67
12
107
168
169
39
61
74
186
107
108
107
13
69
130
124
28
61
62
16
69
63
69
14
58
116
118
34
58
59
15
58
60
58
15
45
107
105
40
62
63
16
45
43
45
16
54
110
112
28
56
57
15
54
56
54
17
55
124
121
29
69
71
18
55
52
55
18
64
131
135
35
67
70
17
64
68
64
19
47
120
124
30
73
73
18
47
51
47
20
42
121
121
36
79
79
19
42
42
42
21888 833 Kbytes .Supplementary file Size Download File type/resource GSM259927.gpr.gz
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(ftp) (http) GPR
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