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Status
Public on Jul 09, 2008
Title
Upper respiratory tract infection (Viro3P10-002)
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
48
88
94
23
40
42
13
48
54
48
2
42
78
76
19
36
38
8
42
40
42
3
41
78
80
29
37
38
9
41
43
41
4
35
71
70
16
36
37
8
35
34
35
5
49
86
87
24
37
39
9
49
50
49
6
45
82
82
20
37
39
9
45
45
45
7
44
80
80
17
36
37
9
44
44
44
8
53
90
88
15
37
37
8
53
51
53
9
46
84
81
18
38
38
10
46
43
46
10
53
90
88
15
37
37
8
53
51
53
11
126
166
176
51
40
41
10
126
136
126
12
131
169
168
42
38
38
9
131
130
131
13
29
66
68
16
37
37
8
29
31
29
14
35
72
73
16
37
38
9
35
36
35
15
52
91
94
24
39
40
10
52
55
52
16
30
70
72
17
40
41
10
30
32
30
17
93
106
49
49
56
24
44
57
-50
44
18
49
92
90
22
43
44
9
49
47
49
19
25
64
65
16
39
40
10
25
26
25
20
33
71
71
16
38
40
10
33
33
33
21888 780 Kbytes .Supplementary file Size Download File type/resource GSM259921.gpr.gz
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(ftp) (http) GPR
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