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Sample GSM143225 Query DataSets for GSM143225
Status Public on Nov 03, 2006
Title Gene Transcription Profiles during Development of Mucosal Immunity Slide17 (T22-T1)
Sample type RNA
 
Channel 1
Source name T22
Organism Gallus gallus
Characteristics Ti: RNA derived from chicken trachea tissues at day i (i=1,3,5,8,12,21,22,24) after the initial IBV-Mass inoculation; Ci: Control RNA derived from chicken trachea tissue at day i after inoculation with sterile distilled water.
Note: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization. The pooled control RNA was used for hybridization.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the pooled samples of age-matched control and vaccinated chickens using RNeasy mini tissue kit from QIAGEN Inc. (Valencia, CA). Residue DNA was removed with RNase-free DNase (QIAGEN). The concentration of total RNA was determined using NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). The quality and quantity of selected RNA samples was examined by gel electrophoresis.
Label Cy3
Label protocol Message RNA amplification was carried out with MessageAmp aminoallyl Amplification Kit (Ambion, #1752). Then, amplified RNA was used for cDNA synthesis, which was subsequently labeled with Cy3 and Cy5 Monoreactive dye (Amersham, # PA23001 and # PA25001). Purification of the cDNA was performed with QIAquick PCR Purification Kit (QIAGEN, #28104). All procedures were performed by following the manufacturers’ instructions.
 
Channel 2
Source name T1
Organism Gallus gallus
Characteristics Ti: RNA derived from chicken trachea tissues at day i (i=1,3,5,8,12,21,22,24) after the initial IBV-Mass inoculation; Ci: Control RNA derived from chicken trachea tissue at day i after inoculation with sterile distilled water.
Note: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization. The pooled control RNA was used for hybridization.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the pooled samples of age-matched control and vaccinated chickens using RNeasy mini tissue kit from QIAGEN Inc. (Valencia, CA). Residue DNA was removed with RNase-free DNase (QIAGEN). The concentration of total RNA was determined using NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). The quality and quantity of selected RNA samples was examined by gel electrophoresis.
Label Cy5
Label protocol Message RNA amplification was carried out with MessageAmp aminoallyl Amplification Kit (Ambion, #1752). Then, amplified RNA was used for cDNA synthesis, which was subsequently labeled with Cy3 and Cy5 Monoreactive dye (Amersham, # PA23001 and # PA25001). Purification of the cDNA was performed with QIAquick PCR Purification Kit (QIAGEN, #28104). All procedures were performed by following the manufacturers’ instructions.
 
 
Hybridization protocol Hybridization was performed based on the protocol provided by FHCRC (http://www.fhcrc.org/science/shared_resources/genomics/dna_array/spotted_arrays/chicken_array/HybridizationWashProtocol.pdf) with slight modifications. Briefly, nonfat milk was used in pre-hybridization to block non-specific binding sites. For hybridization, the mixture of 20X SSC (6.0µl), 2% SDS (2.4µl) and labeled cDNA samples (5µg for each) was applied to 13k array slide. The total volume was 60µl. Slide was incubated at 63°C for 4hrs followed by incubating at 55°C for 11hrs.
Scan protocol After washing, slides were dried by quick spin and ready for scanning. Arrays were scanned using a GenePix 4000B Microarray Scanner (Molecular Device Corporation, Sunnyvale, CA) and image analysis was performed by using GenePixPro6.0.
Description The goal of the study was to uncover the molecular mechanism of mucosal immunity development using avian infectious bronchitis virus (IBV) as a model system. To achieve this goal, we monitored the kinetics of local gene transcription profiles in trachea tissues after administration of animals with an attenuated IBV strain (IBV-Mass) using chicken 13K cDNA Microarray. More specifically, immune-related gene transcription profiles in trachea at 1, 3, 5, 8, 12 and 21 days after the primary immunization and at 1 and 2 days after a second immunization were characterized. There are total 9 groups including 8 time points for vaccinated groups and 1 pooled age-matched control group. RNAs from each group were used to compare with RNAs from other four groups as determined by the loop-design. Four different RNA samples at each time point were used for hybridization with the respective four other groups. The use of the loop-design allows the direct comparisons between the 9 groups, which would enhance the statistical power and lower the variation. This design is preferred over other methods when the goal of the study is to uncover the kinetics of gene transcription profiles.
Data processing Data were collected using GenePixPro6.0 with the LOWESS normalization.
 
Submission date Oct 30, 2006
Last update date Nov 02, 2006
Contact name Xiuqing Wang
E-mail(s) xiuqing.wang@sdstate.edu
Phone 605-688-5502
Fax 605-688-5624
URL http://www3.sdstate.edu/Academics/CollegeOfAgricultureAndBiologicalSciences/BiologyandMicrobiology/FacultyStaff/WangXiuqing/Index.cfm
Organization name South Dakota State University
Department Department of Biology and Microbiology
Lab Virology lab
Street address NPB 252, SDSU
City Brookings
State/province SD
ZIP/Postal code 57007
Country USA
 
Platform ID GPL1836
Series (1)
GSE6198 Gene Transcription Profiles during Development of Mucosal Immunity

Data table header descriptions
ID_REF
F635 Median median feature pixel intensity at wavelength #1 (635 nm).
F635 Mean mean feature pixel intensity at wavelength #1 (635 nm).
F635 SD the standard deviation of the feature pixel intensity at wavelength #1 (635 nm).
B635 Median the median feature background intensity at wavelength #1 (635 nm).
B635 Mean the mean feature background intensity at wavelength #1 (635 nm).
B635 SD the standard deviation of the feature background intensity at wavelength #1 (635 nm).
F532 Median median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm).
B532 Median the median feature background intensity at wavelength #2 (532 nm).
B532 Mean the mean feature background intensity at wavelength #2 (532 nm).
B532 SD the standard deviation of the feature background intensity at wavelength #2 (532 nm).
Ratio of Medians (635/532) the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (635/532) the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios (635/532) the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (635/532) the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) the geometric standard deviation of the pixel intensity ratios.
VALUE log (base 2) transform of the ratio of the medians.
SNR 635 the signal-to-noise ratio at wavelength #1, defined by (Mean Foreground 1- Mean Background 1) / (Standard deviation of Background 1)
SNR 532 the signal-to-noise ratio at wavelength #2, defined by (Mean Foreground 2- Mean Background 2) / (Standard deviation of Background 2)

Data table
ID_REF F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) VALUE SNR 635 SNR 532
C0004101_A1 541 517 183 75 79 29 597 591 197 88 91 27 0.917 0.879 0.896 0.896 1.602 -0.125 14.862 18.143
C0004101_A10 2852 2906 1105 83 87 30 990 1018 291 94 99 32 3.089 3.055 3.044 2.929 1.43 1.627 92.467 28.303
C0004101_A11 3879 3520 2630 96 103 39 2713 2619 2017 108 119 46 1.452 1.363 1.426 1.517 1.545 0.538 86.205 54.064
C0004101_A12 4615 4175 1693 94 100 37 8183 7604 2531 101 108 40 0.559 0.544 0.558 0.52 1.369 -0.838 108.378 185.805
C0004101_A13 1958 1998 1004 95 100 41 4140 4341 1904 97 103 42 0.461 0.448 0.434 0.436 1.384 -1.118 45.561 100.163
C0004101_A14 2777 3523 2429 97 99 29 1971 2485 1778 100 102 26 1.432 1.436 1.452 1.493 1.35 0.518 116.172 89.704
C0004101_A15 300 1110 1340 99 135 189 308 952 1127 109 150 220 1.007 1.199 1.172 1.092 2.355 0.01 5.161 3.638
C0004101_A16 23634 24720 9642 95 100 39 25101 26015 11163 107 109 26 0.942 0.95 0.962 0.967 1.247 -0.087 621.205 975.074
C0004101_A17 5421 5305 1879 77 81 26 4935 4810 1699 90 92 24 1.103 1.108 1.148 1.123 1.304 0.141 197.731 191.8
C0004101_A18 921 881 276 85 89 32 1570 1521 396 98 104 34 0.568 0.559 0.559 0.542 1.391 -0.816 24.344 41.143
C0004101_A19 439 2491 2755 100 123 215 334 1942 2144 105 130 221 1.476 1.302 1.317 1.458 2.024 0.562 10.991 8.182
C0004101_A2 232 239 69 81 86 35 210 216 56 93 97 29 1.293 1.289 1.341 1.27 1.89 0.371 4.314 4.033
C0004101_A20 1219 1366 746 94 100 37 1224 1389 657 101 108 37 1.002 0.988 0.974 0.926 1.369 0.003 33.676 34.263
C0004101_A21 2200 2110 800 93 96 32 5825 5745 2033 96 101 42 0.368 0.357 0.35 0.352 1.314 -1.443 61.938 133.395
C0004101_A22 29038 27644 9097 94 98 32 21564 20460 6603 97 100 25 1.348 1.353 1.377 1.369 1.282 0.431 847.063 795.808
C0004101_A23 323 1249 1369 106 135 180 278 995 1073 107 141 193 1.264 1.287 1.295 1.295 2.706 0.338 6.163 4.406
C0004101_A24 1419 1373 706 90 95 36 1215 1217 589 99 100 24 1.191 1.148 1.091 1.129 1.406 0.252 34.944 45.4
C0004101_A3 10270 10083 3118 95 105 50 5694 5512 1656 105 116 57 1.82 1.847 1.874 1.846 1.345 0.864 196.36 94.552
C0004101_A4 1947 1978 1054 93 100 43 1175 1188 535 96 102 37 1.717 1.726 1.733 1.64 1.395 0.78 42.977 29.053
C0004101_A5 168 175 53 96 100 35 266 262 72 97 102 30 0.426 0.479 0.43 0.423 2.372 -1.23 2.114 5.258

Total number of rows: 15769

Table truncated, full table size 1652 Kbytes.




Supplementary file Size Download File type/resource
GSM143225.gpr.gz 1.4 Mb (ftp)(http) GPR
GSM143225.jpg.gz 2.2 Mb (ftp)(http) JPG

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