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Sample GSM81094 Query DataSets for GSM81094
Status Public on Nov 23, 2005
Title Characterization of an Arabidopsis mutant deficient in the non-phosphorylating of GAPN gene.
Sample type RNA
 
Channel 1
Source name GAPN mutant arabidopsis plant
Organism Arabidopsis thaliana
Characteristics The experimental RNA sample was directly labeled with Cy3-dUTP fluorescent dye
Extracted molecule total RNA
Label Cy3-dUTP
 
Channel 2
Source name WT arabidopsis plant
Organism Arabidopsis thaliana
Characteristics The experimental RNA sample was directly labeled with Cy5-dUTP fluorescent dye
Extracted molecule total RNA
Label Cy5-dUTP
 
 
Hybridization protocol Labeled samples were mixed and then hybridized to a microarray for 15 h at 60C. The slides were washed at room temperature in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC for 5 min each with gentle shaking.
Scan protocol The slides were scanned with a GenePix 4000B Scanner
Description The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria: spots flagged as having false intensity caused by dust or background on the array were removed; and spots for which intensity was less than three fold above background were also eliminated. Data from multiple experiments were normalized (Bolstad et al., 2003) and signals from spots from different experiments were analyzed using Significance Analysis of Microarrays using the one class response (SAM, Tusher et al., 2001, http://www-stat.stanford.edu/~tibs/SAM/.), with a false discovery rate <10%.
Data processing Significance Analysis of Microarrays using the one class response
 
Submission date Oct 31, 2005
Last update date Nov 23, 2005
Contact name Paula Casati
E-mail(s) casati@cefobi-conicet.gov.ar
Phone 54-341-4371955
Organization name Universidad Nacional de Rosario
Department Biological Sciences
Lab Casati
Street address Suipacha 531
City Rosario
State/province Santa Fe
ZIP/Postal code 2000
Country Argentina
 
Platform ID GPL1941
Series (1)
GSE3539 Characterization of an Arabidopsis mutant deficient in the non-phosphorylating of GAPN gene.

Data table header descriptions
ID_REF
VALUE log 2 ratio GAPN/WT intensity
ratio (GAPN-Cy3/WT-Cy5) ratio GAPN/WT intensity
CH1I GAPN chanel intensity
CH1B GAPN media background of chanel intensity
CH1AB GAPN median background chanel intensity
CH2I WT chanel intensity
CH2B WT media background of chanel intensity
CH2AB WT median background chanel intensity
SPIX see Scanalyze 2 manual
BGPIX see Scanalyze 2 manual
EDGE see Scanalyze 2 manual
RAT2 see Scanalyze 2 manual
MRAT see Scanalyze 2 manual
REGR see Scanalyze 2 manual
CORR see Scanalyze 2 manual
LFRAT see Scanalyze 2 manual
CH1GTB1 see Scanalyze 2 manual
CH2GTB1 see Scanalyze 2 manual
CH1GTB2 see Scanalyze 2 manual
CH2GTB2 see Scanalyze 2 manual
CH1EDGEA see Scanalyze 2 manual
CH2EDGEA see Scanalyze 2 manual
FLAG see Scanalyze 2 manual
CH1KSD see Scanalyze 2 manual
CH1KSP see Scanalyze 2 manual
CH2KSD see Scanalyze 2 manual
CH2KSP see Scanalyze 2 manual

Data table
ID_REF VALUE ratio (GAPN-Cy3/WT-Cy5) CH1I CH1B CH1AB CH2I CH2B CH2AB SPIX BGPIX EDGE RAT2 MRAT REGR CORR LFRAT CH1GTB1 CH2GTB1 CH1GTB2 CH2GTB2 CH1EDGEA CH2EDGEA FLAG CH1KSD CH1KSP CH2KSD CH2KSP
10101 0.216453394 1.161873815 9370 723 773 8820 747 780 137 1210 0 0.6308 1.689 0.04468 0.1158 0.05235 0.6788 0.6204 0.1752 0.2336 0.1297 0.1275 0 0.2085 3.52E-05 0.144 1.08E-02
10102 0.078667463 1.056042183 8600 727 762 8830 743 768 137 999 0 1.053 1.364 0.194 0.1616 2.653 0.6788 0.5985 0.1387 0.2117 0.1024 0.1518 0 0.2183 1.56E-05 0.1616 3.19E-03
10103 0.202715825 1.150862778 9970 727 752 9460 748 780 137 999 0 0.7333 1.462 0.04403 0.1202 0.05073 0.708 0.6861 0.1606 0.2701 0.1467 0.1343 0 0.2452 7.21E-07 0.2415 1.13E-06
10104 0.114782683 1.082811926 8550 716 732 8600 752 781 137 999 0 0.777 1.34 0.06179 0.05956 1.794 0.6642 0.5766 0.1387 0.1898 0.1121 0.1391 0 0.2496 4.23E-07 0.1077 1.14E-01
10105 -0.128724457 0.914639762 8380 718 738 9850 763 791 137 999 0 1.85 1.875 0.5914 0.3987 2.44 0.6715 0.6131 0.1387 0.2555 0.1085 0.1457 0 0.2071 5.05E-05 0.1864 3.77E-04
10106 0.323634993 1.25147979 10270 730 814 9010 741 777 137 999 0 0.5387 1.05 0.04863 0.1639 0.05318 0.7445 0.6788 0.2117 0.2044 0.1304 0.136 0 0.3301 4.23E-12 0.2124 2.93E-05
10107 0.14860353 1.108495974 9530 755 907 9350 763 817 137 999 0 0.8687 1.237 0.4411 0.7178 0.5183 0.8029 0.6423 0.1679 0.292 0.1189 0.1551 0 0.3317 3.26E-12 0.1797 6.92E-04
10108 0.327411847 1.254760351 10910 762 945 9550 777 899 137 999 0 0.541 1.67 0.5328 0.7843 0.615 0.7007 0.5839 0.1825 0.2774 0.1357 0.1542 0 0.2823 5.75E-09 0.1669 2.07E-03
10109 0.07882628 1.056158442 8590 758 917 8820 776 868 137 1009 0 1.05 1.047 0.7469 0.8874 0.8236 0.6861 0.5255 0.06569 0.1752 0.08664 0.1272 0 0.2348 2.44E-06 0.09034 2.66E-01
10110 0.610025997 1.526286712 11230 763 979 8200 761 870 137 1020 0 0.1639 0.6414 0.5104 0.7161 0.6281 0.781 0.5182 0.1898 0.1606 0.1575 0.1204 0 0.3257 8.13E-12 0.07068 5.67E-01
10111 0.5621174 1.476434546 11550 777 998 8690 775 846 137 1010 0 0.2487 0.7854 0.1328 0.3696 0.149 0.635 0.5912 0.1606 0.1606 0.1395 0.1401 0 0.1724 1.29E-03 0.1259 4.00E-02
10112 0.471070347 1.386137473 11510 794 1044 9150 764 848 137 999 0 0.423 0.9529 0.3464 0.6384 0.4089 0.7153 0.5474 0.219 0.219 0.1556 0.1723 0 0.2469 5.92E-07 0.1284 3.43E-02
10113 0.594765133 1.510226704 11820 806 994 8670 759 814 137 999 0 0.2872 0.7626 0.3428 0.6718 0.3922 0.8759 0.6277 0.365 0.1679 0.1228 0.1188 0 0.4659 1.11E-23 0.1427 1.32E-02
10114 0.833736239 1.782295114 14110 821 1038 8850 762 794 137 999 0 0.2085 0.8058 0.009625 0.0749 0.009786 0.8321 0.5985 0.3285 0.1752 0.1711 0.1183 0 0.4392 4.33E-21 0.1342 2.35E-02
10115 0.393862318 1.31390623 11050 827 1178 9210 770 879 137 999 0 0.5432 1.27 0.5214 0.7891 0.5963 0.6861 0.5182 0.1022 0.1752 0.1346 0.145 0 0.2184 1.55E-05 0.09941 1.75E-01
10116 0.036000757 1.025267776 10390 806 1106 10900 760 889 137 999 0 1.416 1.564 0.5478 0.8427 0.6034 0.708 0.6861 0.1825 0.3577 0.1581 0.1487 0 0.2205 1.23E-05 0.2767 1.25E-08
10117 -0.067382189 0.954368156 8450 786 1003 9460 749 840 137 999 0 3.339 1.928 0.5432 0.8052 0.6171 0.6204 0.6569 0.05839 0.292 0.09287 0.1347 0 0.14 1.59E-02 0.233 3.04E-06
10118 0.050317367 1.035492689 7950 760 935 8280 748 791 137 999 0 2.286 2.246 0.0809 0.2121 0.09384 0.562 0.5474 0.05839 0.1679 0.08215 0.1346 0 0.07226 5.40E-01 0.111 9.57E-02
10119 0.19374264 1.143726927 9270 757 935 8810 736 770 137 999 0 0.8529 1.206 0.04966 0.1053 0.06362 0.6642 0.5693 0.09489 0.1606 0.1273 0.1502 0 0.2013 9.09E-05 0.09858 1.82E-01
10120 -0.031811443 0.978191312 8490 742 908 9320 728 770 137 999 0 1.907 1.471 0.01372 0.04911 0.01488 0.5912 0.6715 0.1168 0.292 0.09984 0.162 0 0.1817 5.81E-04 0.1963 1.49E-04

Total number of rows: 31200

Table truncated, full table size 5437 Kbytes.




Supplementary data files not provided
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