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Status
Public on Jul 09, 2008
Title
No respiratory symptoms (Viro3P10-004)
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
70
76
58
40
42
13
30
36
30
2
38
81
78
20
43
45
12
38
35
38
3
77
116
114
27
39
41
13
77
75
77
4
29
70
75
24
41
42
12
29
34
29
5
34
74
75
23
40
42
12
34
35
34
6
32
75
79
20
43
44
13
32
36
32
7
27
67
69
18
40
43
12
27
29
27
8
53
95
102
34
42
43
12
53
60
53
9
40
80
80
20
40
42
13
40
40
40
10
54
97
99
24
43
44
12
54
56
54
11
47
92
96
25
45
49
15
47
51
47
12
61
107
107
21
46
48
13
61
61
61
13
43
86
87
26
43
45
12
43
44
43
14
40
81
83
23
41
42
11
40
42
40
15
42
91
92
26
49
50
13
42
43
42
16
40
87
85
27
47
48
14
40
38
40
17
48
97
99
30
49
53
37
48
50
48
18
30
77
82
27
47
49
14
30
35
30
19
42
96
96
26
54
56
15
42
42
42
20
47
102
105
28
55
58
16
47
50
47
21888 786 Kbytes .Supplementary file Size Download File type/resource GSM259922.gpr.gz
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(ftp) (http) GPR
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