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Sample GSM568672 Query DataSets for GSM568672
Status Public on Nov 01, 2011
Title 14-day Carcass WNV Infected, rep2
Sample type RNA
 
Channel 1
Source name 14-day carcass WNV infected
Organism Culex quinquefasciatus
Characteristics strain: Sebring
tissue: 14-day carcass
treatment: West Nile virus (WNV) infection
Extracted molecule total RNA
Extraction protocol Carcasses and midguts from WNV-infected and uninfected (blood fed only) C. quinquefasciatus (Sebring colony) were collected at 7 and 14 days post-infection (per os, fed on viremic hamster). RNA was isolated using a QIAGEN kit.
Label Cy5
Label protocol The Agilent Technologies Low Input Linear Amplification RNA labeling kit was used to synthesize fluorochrome-labeled cRNA probes from 3 g of RNA according to the manufacturer's instructions. Probes were quantified with the Nanodrop spectrophotomer (ND1000, Thermo Scientific, Wilmington, DE). Technologies Low Input Linear Amplification RNA labeling kit was used to synthesize fluorochrome-labeled cRNA probes from 3 g of RNA according to the manufacturer's instructions. Probes were quantified with the Nanodrop spectrophotomer (ND1000, Thermo Scientific, Wilmington, DE).
 
Channel 2
Source name 14-day carcass
Organism Culex quinquefasciatus
Characteristics strain: Sebring
tissue: 14-day carcass
treatment: uninfected
Extracted molecule total RNA
Extraction protocol Carcasses and midguts from WNV-infected and uninfected (blood fed only) C. quinquefasciatus (Sebring colony) were collected at 7 and 14 days post-infection (per os, fed on viremic hamster). RNA was isolated using a QIAGEN kit.
Label Cy3
Label protocol The Agilent Technologies Low Input Linear Amplification RNA labeling kit was used to synthesize fluorochrome-labeled cRNA probes from 3 g of RNA according to the manufacturer's instructions. Probes were quantified with the Nanodrop spectrophotomer (ND1000, Thermo Scientific, Wilmington, DE). Technologies Low Input Linear Amplification RNA labeling kit was used to synthesize fluorochrome-labeled cRNA probes from 3 g of RNA according to the manufacturer's instructions. Probes were quantified with the Nanodrop spectrophotomer (ND1000, Thermo Scientific, Wilmington, DE).
 
 
Hybridization protocol The Agilent Technologies in situ hybridization kit was used for hybridizations according to the manufacturer's instructions. After washes, the microarrays were instantaneously dried with pressurized air.
Scan protocol Microarrays were scanned with an Axon GenePix 4200AL scanner using a 10 µm pixel size. Laser power was set to 60%, and the PMT was adjusted to maximize effective dynamic range and minimize pixel saturation (Axon Instruments, Union City, CA). Spot parameters were determined with the GenePix software Pro 6.0 algorithms, and potential misidentifications of spot locations and quality were corrected manually.
Data processing TIGR
 
Submission date Jul 20, 2010
Last update date Nov 01, 2011
Contact name George Dimopoulos
E-mail(s) gdimopo1@jhu.edu
Phone 443 28 70128
Organization name Johns Hopkins School of Public Health
Department Molecular Microbiology and Immunology
Street address 615 N. Wolfe Street
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL10712
Series (1)
GSE23045 Analysis of Culex quinquefasciatus responses to WNV infection

Data table header descriptions
ID_REF
F635 Median GENEPIX
F635 Mean GENEPIX
F635 SD GENEPIX
F635 CV GENEPIX
B635 GENEPIX
B635 Median GENEPIX
B635 Mean GENEPIX
B635 SD GENEPIX
B635 CV GENEPIX
% > B635+1SD GENEPIX
% > B635+2SD GENEPIX
F635 % Sat. GENEPIX
F532 Median GENEPIX
F532 Mean GENEPIX
F532 SD GENEPIX
F532 CV GENEPIX
B532 GENEPIX
B532 Median GENEPIX
B532 Mean GENEPIX
B532 SD GENEPIX
B532 CV GENEPIX
% > B532+1SD GENEPIX
% > B532+2SD GENEPIX
F532 % Sat. GENEPIX
Ratio of Medians (532/635)
Ratio of Means (532/635)
Median of Ratios (532/635)
Mean of Ratios (532/635)
Ratios SD (532/635)
Rgn Ratio (532/635)
Rgn R2 (532/635)
F Pixels GENEPIX
B Pixels GENEPIX
Circularity GENEPIX
Sum of Medians (532/635)
Sum of Means (532/635)
VALUE GENEPIX
F635 Median - B635 GENEPIX
F532 Median - B532 GENEPIX
F635 Mean - B635 GENEPIX
F532 Mean - B532 GENEPIX
F635 Total Intensity GENEPIX
F532 Total Intensity GENEPIX
SNR 635 GENEPIX
SNR 532 GENEPIX
Flags GENEPIX

Data table
ID_REF F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (532/635) Ratio of Means (532/635) Median of Ratios (532/635) Mean of Ratios (532/635) Ratios SD (532/635) Rgn Ratio (532/635) Rgn R2 (532/635) F Pixels B Pixels Circularity Sum of Medians (532/635) Sum of Means (532/635) VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags
913 98 101 54 53 47 47 52 24 46 62 50 0 199 165 89 53 25 25 27 6 22 91 85 0 3.412 2.593 2.612 2.643 2.294 2.201 0.639 120 18 100 225 194 1.771 51 174 54 140 12101 19817 2.042 23 0
28215 47 69 76 110 43 43 48 21 43 26 15 0 35 44 33 75 27 27 28 7 25 51 31 0 2 0.654 0.538 0.619 3.6 0.407 0.745 120 16 100 12 43 1 4 8 26 17 8308 5238 1 2.286 -50
3504 55 86 100 116 32 32 38 17 44 57 37 0 50 61 49 80 22 22 23 3 13 87 85 0 1.217 0.722 0.844 0.912 2.651 0.493 0.788 120 29 100 51 93 0.284 23 28 54 39 10337 7318 2.824 12.667 0
41799 491 501 390 77 41 41 43 13 30 87 78 0 710 581 364 62 25 25 26 4 15 96 95 0 1.522 1.209 1.345 1.489 2.14 1.046 0.892 120 11 100 1135 1016 0.606 450 685 460 556 60085 69686 35.231 138.75 0
1390 410 356 214 60 34 34 34 9 26 94 90 0 888 696 393 56 24 24 24 4 16 99 99 0 2.298 2.087 2.142 2.156 1.601 2.057 0.889 120 26 100 1240 994 1.2 376 864 322 672 42774 83547 35.778 168 0
12352 96 115 101 87 47 47 46 21 45 74 55 0 80 83 46 55 26 26 26 4 15 90 84 0 1.102 0.838 0.91 0.926 2.776 0.459 0.982 120 20 100 103 125 0.14 49 54 68 57 13743 9945 3.286 14.25 0
44328 36 37 12 32 32 32 36 16 44 20 1 0 25 26 6 23 23 23 24 4 16 34 15 0 0.5 0.6 0.5 0.498 2.88 0.049 0.011 120 48 100 6 8 -1 4 2 5 3 4482 3111 0.063 0.5 -50
32660 41 45 17 37 61 61 66 36 54 0 0 0 34 36 13 36 43 43 40 15 37 6 2 0 0.45 0.438 0.603 0.544 2.734 0.328 0.184 120 10 100 -29 -23 -1.152 -20 -9 -16 -7 5377 4309 -0.583 -0.267 -50
13685 47 48 19 39 39 39 42 16 38 30 10 0 41 42 17 40 23 23 23 4 17 73 66 0 2.25 2.111 1.226 1.18 3.145 0.817 0.217 120 18 100 26 28 1.17 8 18 9 19 5791 5082 0.375 4.75 0
40120 138 182 190 104 35 35 38 15 39 80 75 0 166 171 120 70 22 22 23 5 21 95 92 0 1.398 1.014 1.14 1.229 1.955 0.732 0.81 120 317 100 247 296 0.483 103 144 147 149 21847 20532 9.6 29.6 0
29391 200 253 201 79 38 38 42 18 42 87 79 0 224 212 142 66 24 24 27 12 44 88 81 0 1.235 0.874 0.872 0.915 1.823 0.57 0.931 120 17 100 362 403 0.304 162 200 215 188 30329 25399 11.722 15.417 0
43404 53 75 86 114 36 36 39 11 28 53 36 0 42 54 40 74 27 27 28 6 21 70 56 0 0.882 0.692 0.687 0.801 3.439 0.451 0.751 120 15 100 32 66 -0.181 17 15 39 27 8945 6516 3.273 4.333 0
44805 43 71 187 263 39 39 42 15 35 29 19 0 36 52 117 225 25 25 28 7 25 58 34 0 2.75 0.844 0.663 0.799 3.145 0.831 0.985 120 45 100 15 59 1.459 4 11 32 27 8461 6288 1.933 3.429 0
33816 42 44 15 34 41 41 45 21 46 7 1 0 30 31 9 29 22 22 22 4 18 63 48 0 8 3 0.692 0.946 3.499 0.169 0.048 120 14 100 9 12 3 1 8 3 9 5254 3753 -0.048 2.25 -50
17398 62 96 113 117 32 32 33 11 33 75 60 0 55 63 59 93 25 25 25 5 20 78 72 0 1 0.594 0.789 0.769 2.229 0.498 0.768 120 13 100 60 102 0 30 30 64 38 11576 7587 5.727 7.6 0
6072 274 1044 3884 372 34 34 35 12 34 93 90 0 223 415 928 223 25 25 26 4 15 92 90 0 0.825 0.386 0.73 0.672 1.975 0.228 0.859 120 20 100 438 1400 -0.278 240 198 1010 390 125315 49833 84.083 97.25 0
10592 7365 5994 3574 59 39 39 38 14 36 99 99 0 7015 5515 3157 57 23 23 25 5 20 100 100 0 0.954 0.922 0.922 0.937 1.368 0.905 0.979 120 25 100 14318 11447 -0.067 7326 6992 5955 5492 719294 661813 425.429 1098 0
42310 103 137 144 105 30 30 31 8 25 79 73 0 112 117 87 74 26 26 26 3 11 85 80 0 1.178 0.85 1.012 1.072 2.505 0.638 0.793 120 12 100 159 198 0.236 73 86 107 91 16393 14067 13.25 30.333 0
36290 45 58 49 84 40 40 42 15 35 29 16 0 35 42 22 52 27 27 28 5 17 60 45 0 1.6 0.833 0.654 0.674 3.14 0.463 0.549 120 21 100 13 33 0.678 5 8 18 15 6946 4995 1.067 2.8 -50
37019 854 856 613 71 34 34 42 27 64 94 85 0 1251 1036 636 61 24 24 26 8 30 99 96 0 1.496 1.231 1.282 1.389 1.771 1.137 0.925 120 16 100 2047 1834 0.581 820 1227 822 1012 102719 124357 30.148 126.25 0

Total number of rows: 43803

Table truncated, full table size 7739 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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