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Status
Public on Jul 09, 2008
Title
Upper respiratory tract infection (Viro3P10-041)
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
50
109
110
34
59
65
51
50
51
50
2
51
115
118
23
64
63
14
51
54
51
3
85
145
148
33
60
60
16
85
88
85
4
55
109
106
26
54
56
15
55
52
55
5
56
113
109
30
57
58
16
56
52
56
6
66
127
127
23
61
62
16
66
66
66
7
66
128
131
30
62
66
22
66
69
66
8
65
122
121
28
57
58
14
65
64
65
9
62
123
130
40
61
63
18
62
69
62
10
58
118
147
114
60
65
21
58
87
58
11
60
117
117
28
57
59
16
60
60
60
12
159
217
216
40
58
61
19
159
158
159
13
205
261
249
54
56
59
15
205
193
205
14
215
273
271
45
58
59
15
215
213
215
15
49
109
109
21
60
61
16
49
49
49
16
50
107
101
30
57
57
15
50
44
50
17
38
108
118
47
70
74
36
38
48
38
18
58
126
128
39
68
69
17
58
60
58
19
65
133
167
161
68
79
75
65
99
65
20
66
129
371
860
63
70
44
66
308
66
21888 820 Kbytes .Supplementary file Size Download File type/resource GSM259929.gpr.gz
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(ftp) (http) GPR
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