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Status
Public on Jul 09, 2008
Title
No respiratory symptoms (Viro3P10-001)
Sample type
RNA
Source name
RdABC amplified RNA from Nasal Lavage
Organism
Viruses Characteristics
No respiratory symptoms
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
30
74
77
22
44
45
13
30
33
30
2
49
93
99
30
44
45
12
49
55
49
3
87
133
131
28
46
48
14
87
85
87
4
37
88
90
23
51
51
14
37
39
37
5
41
86
88
29
45
46
14
41
43
41
6
37
90
94
24
53
55
15
37
41
37
7
32
80
79
23
48
50
16
32
31
32
8
48
96
96
29
48
49
13
48
48
48
9
28
70
73
22
42
44
14
28
31
28
10
71
118
119
25
47
50
15
71
72
71
11
87
135
138
30
48
52
26
87
90
87
12
270
319
307
119
49
53
31
270
258
270
13
24
71
76
26
47
95
659
24
29
24
14
61
110
114
25
49
60
123
61
65
61
15
35
82
82
24
47
49
18
35
35
35
16
30
76
78
24
46
47
13
30
32
30
17
28
75
79
27
47
48
13
28
32
28
18
44
91
90
21
47
48
12
44
43
44
19
50
108
107
25
58
59
16
50
49
50
20
40
88
88
23
48
49
14
40
40
40
21888 800 Kbytes .Supplementary file Size Download File type/resource GSM259920.gpr.gz
1.6 Mb
(ftp) (http) GPR
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